@article{brungardt_alarcon_shiller_young_monteros_randall_bock_2024, title={Transcriptome profile of pecan scab resistant and susceptible trees from a pecan provenance collection}, volume={25}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-024-10010-0}, abstractNote={Abstract Pecan scab is a devastating disease that causes damage to pecan ( Carya illinoinensis (Wangenh.) K. Koch) fruit and leaves. The disease is caused by the fungus Venturia effusa (G. Winter) and the main management practice for controlling the disease is by application of fungicides at 2-to-3-week intervals throughout the growing season. Besides disease-related yield loss, application of fungicides can result in considerable cost and increases the likelihood of fungicide resistance developing in the pathogen. Resistant cultivars are available for pecan growers; although, in several cases resistance has been overcome as the pathogen adapts to infect resistant hosts. Despite the importance of host resistance in scab management, there is little information regarding the molecular basis of genetic resistance to pecan scab. The purpose of this study was to elucidate mechanisms of natural pecan scab resistance by analyzing transcripts that are differentially expressed in pecan leaf samples from scab resistant and susceptible trees. The leaf samples were collected from trees in a provenance collection orchard that represents the natural range of pecan in the US and Mexico. Trees in the orchard have been exposed to natural scab infections since planting in 1989, and scab ratings were collected over three seasons. Based on this data, ten susceptible trees and ten resistant trees were selected for analysis. RNA-seq data was collected and analyzed for diseased and non-diseased parts of susceptible trees as well as for resistant trees. A total of 313 genes were found to be differentially expressed when comparing resistant and susceptible trees without disease. For susceptible samples showing scab symptoms, 1,454 genes were identified as differentially expressed compared to non-diseased susceptible samples. Many genes involved in pathogen recognition, defense responses, and signal transduction were up-regulated in diseased samples of susceptible trees, whereas differentially expressed genes in pecan scab resistant samples were generally down-regulated compared to non-diseased susceptible samples. Our results provide the first account of candidate genes involved in resistance/susceptibility to pecan scab under natural conditions in a pecan orchard. This information can be used to aid pecan breeding programs and development of biotechnology-based approaches for generating pecan cultivars with more durable scab resistance.}, number={1}, journal={BMC GENOMICS}, author={Brungardt, Jordan and Alarcon, Yanina and Shiller, Jason and Young, Carolyn and Monteros, Maria J. and Randall, Jennifer J. and Bock, Clive H.}, year={2024}, month={Feb} }
 @article{young_2023, title={Fescue Toxicosis: Understanding the Fungal Cause and the Fungal Solution}, volume={101}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skad068.003}, abstractNote={
 Dr. Young has been internationally recognized for research on seed transmitted fungal endophytes and their impact on forage grazing systems, endophyte diversity in native grasses and crop wild relatives, pecan scab and a root rot pathogen of alfalfa. She has discovered genes for the synthesis of bioprotective alkaloids, identified and described new endophyte species, and developed genomic and culture resources. Dr. Young will share research on utilizing genomic techniques to better understand the various endophyte species in forage grazing systems.}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Young, Carolyn A.}, year={2023}, month={May} }
 @article{berry_lee_winter_mace_becker_nagabhyru_treindl_bogantes_young_leuchtmann_et al._2022, title={Cross-species transcriptomics identifies core regulatory changes differentiating the asymptomatic asexual and virulent sexual life cycles of grass-symbiotic Epichloë fungi}, url={https://doi.org/10.1093/g3journal/jkac043}, DOI={10.1093/g3journal/jkac043}, abstractNote={Abstract Fungi from the genus Epichloë form systemic endobiotic infections of cool season grasses, producing a range of host-protective natural products in return for access to nutrients. These infections are asymptomatic during vegetative host growth, with associations between asexual Epichloë spp. and their hosts considered mutualistic. However, the sexual cycle of Epichloë spp. involves virulent growth, characterized by the envelopment and sterilization of a developing host inflorescence by a dense sheath of mycelia known as a stroma. Microscopic analysis of stromata revealed a dramatic increase in hyphal propagation and host degradation compared with asymptomatic tissues. RNAseq was used to identify differentially expressed genes in asymptomatic vs stromatized tissues from 3 diverse Epichloë–host associations. Comparative analysis identified a core set of 135 differentially expressed genes that exhibited conserved transcriptional changes across all 3 associations. The core differentially expressed genes more strongly expressed during virulent growth encode proteins associated with host suppression, digestion, adaptation to the external environment, a biosynthetic gene cluster, and 5 transcription factors that may regulate Epichloë stroma formation. An additional 5 transcription factor encoding differentially expressed genes were suppressed during virulent growth, suggesting they regulate mutualistic processes. Expression of biosynthetic gene clusters for natural products that suppress herbivory was universally suppressed during virulent growth, and additional biosynthetic gene clusters that may encode production of novel host-protective natural products were identified. A comparative analysis of 26 Epichloë genomes found a general decrease in core differentially expressed gene conservation among asexual species, and a specific decrease in conservation for the biosynthetic gene cluster expressed during virulent growth and an unusual uncharacterized gene.}, journal={G3 Genes|Genomes|Genetics}, author={Berry, Daniel and Lee, Kate and Winter, David and Mace, Wade and Becker, Yvonne and Nagabhyru, Padmaja and Treindl, Artemis D and Bogantes, Esteban Valverde and Young, Carolyn A and Leuchtmann, Adrian and et al.}, editor={Dunlap, JEditor}, year={2022}, month={Apr} }
 @article{bock_frusso_zoppolo_ortiz_shiller_charlton_young_randall_2022, title={Population Genetic Characteristics and Mating Type Frequency of Venturia effusa from Pecan in South America}, url={https://doi.org/10.1094/PHYTO-01-22-0031-R}, DOI={10.1094/PHYTO-01-22-0031-R}, abstractNote={Scab, caused by the plant pathogenic fungus Venturia effusa, is a major disease of pecan in South America, resulting in loss of quantity and quality of nut yield. Characteristics of the populations of V. effusa in South America are unknown. We used microsatellites to describe the genetic diversity and population structure of V. effusa in South America, and determined the mating type status of the pathogen. The four hierarchically sampled orchard populations from Argentina (AR), Brazil (BRC and BRS) and Uruguay (UR) had moderate to high genotypic and gene diversity. There was evidence of population differentiation (Fst = 0.196), but the correlation between geographic distance and genetic distance was not statistically significant. Genetic differentiation was minimal between the UR, BRC and BRS populations, and these populations were more clearly differentiated from the AR population. The MAT1-1 and MAT1-2 mating types occurred in all four orchards, their frequencies did not deviate from the 1:1 ratio expected under random mating, but multilocus linkage equilibrium was rejected in three of the four populations. The population genetics of South America populations of V. effusa has many similarities to the population genetics of V. effusa previously described in the U.S.A. Characterizing the populations genetics and reproductive systems of V. effusa are important to establish the evolutionary potential of the pathogen, and thus its adaptability - and can provide a basis for informed approaches to utilizing available host resistance and determining phytosanitary needs.}, journal={Phytopathology®}, author={Bock, Clive H. and Frusso, Enrique and Zoppolo, Roberto and Ortiz, Edson R. and Shiller, Jason and Charlton, Nikki D. and Young, Carolyn A. and Randall, Jennifer J.}, year={2022}, month={Oct} }
 @article{quenu_treindl_lee_takemoto_thünen_ashrafi_winter_ganley_leuchtmann_young_et al._2022, title={Telomere-to-Telomere Genome Sequences across a Single Genus Reveal Highly Variable Chromosome Rearrangement Rates but Absolute Stasis of Chromosome Number}, volume={8}, url={https://doi.org/10.3390/jof8070670}, DOI={10.3390/jof8070670}, abstractNote={Genome rearrangements in filamentous fungi are prevalent but little is known about the modalities of their evolution, in part because few complete genomes are available within a single genus. To address this, we have generated and compared 15 complete telomere-to-telomere genomes across the phylogeny of a single genus of filamentous fungi, Epichloë. We find that the striking distinction between gene-rich and repeat-rich regions previously reported for isolated species is ubiquitous across the Epichloë genus. We built a species phylogeny from single-copy gene orthologs to provide a comparative framing to study chromosome composition and structural change through evolutionary time. All Epichloë genomes have exactly seven nuclear chromosomes, but despite this conserved ploidy, analyses reveal low synteny and substantial rearrangement of gene content across the genus. These rearrangements are highly lineage-dependent, with most occurring over short evolutionary distances, with long periods of structural stasis. Quantification of chromosomal rearrangements shows they are uncorrelated with numbers of substitutions and evolutionary distances, suggesting that different modes of evolution are acting to create nucleotide and chromosome-scale changes.}, number={7}, journal={Journal of Fungi}, publisher={MDPI AG}, author={Quenu, Mathieu and Treindl, Artemis D. and Lee, Kate and Takemoto, Daigo and Thünen, Torsten and Ashrafi, Samad and Winter, David and Ganley, Austen R. D. and Leuchtmann, Adrian and Young, Carolyn A. and et al.}, year={2022}, month={Jun}, pages={670} }
 @article{bock_young_zhang_chen_brannen_adaskaveg_charlton_2021, title={Mating Type Idiomorphs, Heterothallism, and High Genetic Diversity in Venturia carpophila, Cause of Peach Scab}, volume={111}, url={https://doi.org/10.1094/PHYTO-12-19-0485-R}, DOI={10.1094/PHYTO-12-19-0485-R}, abstractNote={Scab (caused by Venturia carpophila) is a major disease affecting peach in the eastern U.S.A. The aims of the study were to characterize the mating type loci in V. carpophila, determine whether they are in equilibrium, and to assess the population genetic diversity and structure of the pathogen. The mating type gene MAT1-1-1 was identified in isolate JP3-5 in an available genome sequence, and the MAT1-2-1 gene was PCR amplified from isolate PS1-1, thus indicating a heterothallic structure. Mating type loci structure were consistent with those of other Venturia species (V. effusa and V. inaequalis): the mating type gene is positioned between APN2 encoding a DNA lyase and a gene encoding a Pleckstrin homology domain. Primers designed to each of the mating type genes and a reference gene TUB2 were used as a multiplex PCR reaction to screen a population (n = 81) of V. carpophila from various locations in the eastern U.S.A. Mating types in five of the nine populations studied were in equilibrium. Among the 81 isolates, there were 69 multilocus genotypes. A population genetic analysis of the populations with >10 individuals (four populations) showed them to be genetically diverse. Linkage disequilibrium was found in five of nine populations with ≥4 isolates. A discriminant analysis of principal components indicated three genetic clusters, although extensive admixture was observed. Mating type identification in V. carpophila provides a basis for understanding reproductive methods of the pathogen and can be a basis for further studies of genetics of the peach scab pathogen.}, number={2}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Bock, Clive H. and Young, Carolyn A. and Zhang, Minling and Chen, Chunxian and Brannen, Phillip M. and Adaskaveg, Jim and Charlton, Nikki D.}, year={2021}, month={Feb}, pages={408–424} }
 @article{mattupalli_shiller_kankanala_krom_marek_mysore_young_2021, title={The First Genomic Resources for Phymatotrichopsis omnivora, a Soilborne Pezizomycete Pathogen with a Broad Host Range}, volume={111}, url={https://doi.org/10.1094/PHYTO-01-21-0014-A}, DOI={10.1094/PHYTO-01-21-0014-A}, abstractNote={Phymatotrichopsis omnivora is a destructive plant pathogen causing root rot disease of alfalfa, cotton, pecan, grape, and many other important dicotyledonous species. A member of the family Rhizinaceae, in the class Pezizomycetes, P. omnivora is a soilborne ascomycete fungus that is difficult to maintain in culture, currently genetically intractable, and for which there are no publicly available genomic resources. We have generated draft genome sequences of four P. omnivora isolates obtained from cotton and alfalfa, growing in Texas and Oklahoma, USA. These genome sequences will provide new insights into the biology of the fungus, including the factors responsible for its broad host range and pathogenicity.}, number={10}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Mattupalli, Chakradhar and Shiller, Jason B. and Kankanala, Prasanna and Krom, Nick and Marek, Stephen M. and Mysore, Kirankumar S. and Young, Carolyn A.}, year={2021}, month={Oct}, pages={1897–1900} }
 @article{winter_charlton_krom_shiller_bock_cox_young_2020, title={Chromosome-Level Reference Genome of Venturia effusa, Causative Agent of Pecan Scab}, volume={33}, url={https://doi.org/10.1094/MPMI-08-19-0236-A}, DOI={10.1094/MPMI-08-19-0236-A}, abstractNote={Pecan scab, caused by Venturia effusa, is a devastating disease of pecan (Carya illinoinensis), which results in economic losses on susceptible cultivars throughout the southeastern U.S. To enhance our understanding of pathogenicity in V. effusa, we have generated a complete telomere-to-telomere reference genome of V. effusa isolate FRT5LL7-Albino. By combining Illumina MiSeq and Oxford Nanopore MinION data, we assembled a 45.2 Mb genome represented by 20 chromosomes and containing 10,820 putative genes, of which 7,619 have at least one functional annotation. The likely causative mutation of the albino phenotype was identified as a single base insertion and a resulting frameshift in the gene encoding the polyketide synthase ALM1. This genome represents the first full chromosome-level assembly of any Venturia species.}, number={2}, journal={Molecular Plant-Microbe Interactions®}, publisher={Scientific Societies}, author={Winter, David J. and Charlton, Nikki D. and Krom, Nick and Shiller, Jason and Bock, Clive H. and Cox, Murray P. and Young, Carolyn A.}, year={2020}, month={Feb}, pages={149–152} }
 @article{krauss_vikuk_young_krischke_mueller_baerenfaller_2020, title={Correction: Krauss, J., et al. <i>Epichloë</i> Endophyte Infection Rates and Alkaloid Content in Commercially Available Grass Seed Mixtures in Europe. <i>Microorganisms</i> 2020, <i>8</i>, 498}, url={https://www.mdpi.com/2076-2607/8/10/1616}, DOI={10.3390/microorganisms8101616}, abstractNote={The authors wish to make the following correction to this paper [...].}, journal={Microorganisms}, author={Krauss, Jochen and Vikuk, Veronika and Young, Carolyn and Krischke, Markus and Mueller, Martin J. and Baerenfaller, Katja}, year={2020}, month={Oct} }
 @article{krauss_vikuk_young_krischke_mueller_baerenfaller_2020, title={Epichloë Endophyte Infection Rates and Alkaloid Content in Commercially Available Grass Seed Mixtures in Europe}, volume={8}, url={https://doi.org/10.3390/microorganisms8040498}, DOI={10.3390/microorganisms8040498}, abstractNote={Fungal endophytes of the genus Epichloë live symbiotically in cool season grass species and can produce alkaloids toxic to insects and vertebrates, yet reports of intoxication of grazing animals have been rare in Europe in contrast to overseas. However, due to the beneficial resistance traits observed in Epichloë infected grasses, the inclusion of Epichloë in seed mixtures might become increasingly advantageous. Despite the toxicity of fungal alkaloids, European seed mixtures are rarely tested for Epichloë infection and their infection status is unknown for consumers. In this study, we tested 24 commercially available seed mixtures for their infection rates with Epichloë endophytes and measured the concentrations of the alkaloids ergovaline, lolitrem B, paxilline, and peramine. We detected Epichloë infections in six seed mixtures, and four contained vertebrate and insect toxic alkaloids typical for Epichloë festucae var. lolii infecting Lolium perenne. As Epichloë infected seed mixtures can harm livestock, when infected grasses become dominant in the seeded grasslands, we recommend seed producers to test and communicate Epichloë infection status or avoiding Epichloë infected seed mixtures.}, number={4}, journal={Microorganisms}, publisher={MDPI AG}, author={Krauss, Jochen and Vikuk, Veronika and Young, Carolyn A. and Krischke, Markus and Mueller, Martin J. and Baerenfaller, Katja}, year={2020}, month={Mar}, pages={498} }
 @article{charlton_yi_bock_zhang_young_2020, title={First description of the sexual stage of Venturia effusa, causal agent of pecan scab}, volume={112}, url={https://doi.org/10.1080/00275514.2020.1759998}, DOI={10.1080/00275514.2020.1759998}, abstractNote={Pecan scab, caused by Venturia effusa, is the most prevalent disease of pecan in the southeastern United States. Recent characterization of the mating type (MAT) distribution of V. effusa revealed that the MAT idiomorphs are in equilibrium at various spatial scales, indicative of regular sexual recombination. However, the occurrence of the sexual stage of V. effusa has never been observed, and the pathogen was previously considered to rely entirely on asexual reproduction. We were able to generate the sexual stage by pairing isolates of opposite mating types on oatmeal culture media. Cultures were incubated at 24 C for 2 mo to allow hyphae from isolates of each mating type to interact. Culture plates were then incubated at 4 C for 4 mo, after which immature pseudothecia were observed. Following exposure to a 12-h photoperiod for 2 wk at 24 C, asci and ascospores readily developed. Pseudothecium and ascospore production was optimal when incubated for 4 mo at 4 C. We utilized progeny from a cross of an albino isolate and wild-type (melanized) isolates to determine that recombination had occurred. Multilocus genotyping using 32 microsatellite markers confirmed that progeny were the result of recombination, which was further supported by segregation of mating types and culture pigmentation. Albino progeny were all confirmed to contain the same mutation in the polyketide synthase (PKS1) melanin biosynthesis gene as the albino parent. The results of this study demonstrate the heterothallic nature of V. effusa. The impact of determining the source of the overwintering ascostroma will aid in management decisions to reduce the primary inoculum in the disease cycle.}, number={4}, journal={Mycologia}, publisher={Informa UK Limited}, author={Charlton, Nikki D. and Yi, Mihwa and Bock, Clive H. and Zhang, Minling and Young, Carolyn A.}, year={2020}, month={Jul}, pages={711–721} }
 @article{winter_charlton_krom_shiller_bock_cox_young_2019, title={Chromosome-level genome reference of Venturia effusa, causative agent of pecan scab}, volume={8}, url={https://doi.org/10.1101/746198}, DOI={10.1101/746198}, abstractNote={Pecan scab, caused by Venturia effusa, is a devastating disease of pecan (Carya illinoinensis), which results in economic losses on susceptible cultivars throughout the southeastern U.S. To enhance our understanding of pathogenicity in V. effusa, we have generated a complete telomere-to-telomere genome reference of V. effusa isolate FRT5LL7-Albino. By combining Illumina MiSeq and Oxford Nanopore MinION data, we assembled a 45.2 Mb genome represented by 20 chromosomes and containing 10,820 genes, of which 7,619 have at least one functional annotation. The likely causative mutation of the albino phenotype was identified as a single base insertion and a resulting frameshift in the gene encoding the polyketide synthase ALM1. This genome represents the first full chromosome level assembly of any Venturia species.}, publisher={Cold Spring Harbor Laboratory}, author={Winter, David J. and Charlton, Nikki D. and Krom, Nick and Shiller, Jason and Bock, Clive H. and Cox, Murray P. and Young, Carolyn A.}, year={2019}, month={Aug} }
 @article{mattupalli_seethepalli_york_young_2019, title={Digital Imaging to Evaluate Root System Architectural Changes Associated with Soil Biotic Factors}, volume={3}, url={https://doi.org/10.1094/PBIOMES-12-18-0062-R}, DOI={10.1094/PBIOMES-12-18-0062-R}, abstractNote={Root system architecture is critical for plant growth, which is influenced by several edaphic, environmental, genetic, and biotic factors including beneficial and pathogenic microbes. Studying root system architecture and the dynamic changes that occur during a plant’s lifespan, especially for perennial crops growing over multiple growing seasons, is still a challenge because of the nature of their growing environment. We describe the utility of an imaging platform called RhizoVision Crown to study root system architecture of alfalfa, a perennial forage crop threatened by Phymatotrichopsis root rot (PRR) disease. Phymatotrichopsis omnivora is the causal agent of PRR disease that reduces alfalfa stand longevity. During the lifetime of the stand, PRR disease rings enlarge and the field can be categorized into three zones based upon plant status: asymptomatic, disease front and survivor. To study root system architectural changes associated with PRR, a 4-year-old 25.6-ha alfalfa stand infested with PRR was selected at the Red River Farm, Burneyville, OK during October 2017. Line transect sampling was conducted from four actively growing PRR disease rings. At each disease ring, six line transects were positioned spanning 15 m on either side of the disease front with one alfalfa root crown sampled at every 3 m interval. Each alfalfa root crown was imaged with the RhizoVision Crown platform using a backlight and a high-resolution monochrome CMOS camera enabling preservation of the natural root system integrity. The platform’s image analysis software, RhizoVision Analyzer, automatically segmented images, skeletonized, and extracted a suite of features. Data indicated that the survivor plants compensated for damage or loss to the taproot through the development of more lateral and crown roots, and that a suite of multivariate features could be used to automatically classify roots as from survivor or asymptomatic zones. Root growth is a dynamic process adapting to ever changing interactions among various phytobiome components. By utilizing the low-cost, efficient, and high-throughput RhizoVision Crown platform, we quantified these changes in a mature perennial forage crop.}, number={2}, journal={Phytobiomes Journal}, publisher={Scientific Societies}, author={Mattupalli, Chakradhar and Seethepalli, Anand and York, Larry M. and Young, Carolyn A.}, year={2019}, month={Jan}, pages={102–111} }
 @article{leuchtmann_young_stewart_simpson_hume_scott_2019, title={Epichloe novae-zelandiae, a new endophyte from the endemic New Zealand grass Poa matthewsii}, volume={8}, url={https://doi.org/10.1080/0028825X.2019.1651344}, DOI={10.1080/0028825X.2019.1651344}, abstractNote={ABSTRACT Epichloe endophytes (Clavicipitaceae) infect pooid grass genera worldwide but predominantly in the Northern Hemisphere, but appear to be rare in native grasses of the Southern Hemisphere. Because of benefits that hosts may receive from the symbiosis, Epichloe endophytes have been extensively studied and are considered important components of sustainable agriculture. There are only a few studies available on the incidence of endophyte infection in grasses of the Southern Hemisphere and most grass species have never been examined. Here we report on a survey of native grasses of New Zealand including 25 endemic or indigenous species. We sampled up to 10 plants per species at different sites from both the North and South Island of New Zealand and examined tissues microscopically for endophyte infection. Overall, only two species were found to be infected, Poa matthewsii (Matthew's bluegrass) and Dichelachne micrantha (short-hair plume grass). Based on analyses of tefA and tubB genes, both endophytes were found to be interspecific hybrids. The endophyte of the new host D. micrantha was previously described as Epichloe australiensis, while the endophyte of P. matthewsii is a new species named here E. novae-zelandiae. The new species is a hybrid derived from E. amarillans, E. bromicola and E. typhina subsp. poae. Alkaloid analyses in planta suggested that E. novae-zelandiae can produce small amounts of peramine, early pathway indole-diterpenes and ergot alkaloids, but no lolines or lolitrems. Target specific primers suggested the presence of genes for ergot alkaloids and peramine, but genes of only early pathway steps for the other alkaloids. Furthermore, genes for both mating type idiomorphs (MTA and MTB) were present, a single copy of MTA and two copies of MTB. Endophytes of native grasses may provide a genetic resource that could be exploited for developing pasture grass cultivars with improved performance.}, journal={New Zealand Journal of Botany}, publisher={Informa UK Limited}, author={Leuchtmann, Adrian and Young, Carolyn A. and Stewart, Alan V. and Simpson, Wayne R. and Hume, David E. and Scott, Barry}, year={2019}, month={Oct}, pages={1–18} }
 @article{charlton_yi_bock_zhang_young_2019, title={First description of the sexual stage of Venturia effusa, causal agent of pecan scab}, volume={9}, url={https://doi.org/10.1101/785790}, DOI={10.1101/785790}, abstractNote={Venturia effusa, cause of pecan scab, is the most prevalent disease of pecan in the southeastern USA; epidemics of the disease regularly result in economic losses to the pecan industry. Recent characterization of the mating type distribution revealed the frequency of the MAT idiomorphs are in equilibrium at various spatial scales, indicative of regular sexual recombination. However, the occurrence of the sexual stage of V. effusa has never been observed, and the pathogen was previously believed to rely entirely on asexual reproduction. To explore the existence of a sexual cycle, we paired opposite mating types on oatmeal culture media. In initial experiments, cultures were incubated at 24 C for 2 mo for hyphal interactions to occur between mating types and then maintained at 4 C for 4 mo. Immature pseudothecia were initially observed but following exposure to a 12 h photoperiod for 2 weeks at 24 C, asci and ascospores developed. Further experiments explored the effect of time on pseudothecial development with 4 mo at 4 C as the optimal requirement. The results of this study demonstrate the heterothallic nature of V. effusa. Following experiments investigated progeny from a sexual cross of an albino and a wild-type isolate. Evaluation of isolate pigmentation, mating type, and multilocus genotyping of single ascospore progeny provided evidence that recombination occurred within the sexual crosses. The impact of determining the source of the overwintering ascostroma will aid in management decisions to reduce the primary inoculum in the disease cycle.}, publisher={Cold Spring Harbor Laboratory}, author={Charlton, Nikki D. and Yi, Mihwa and Bock, Clive H. and Zhang, Minling and Young, Carolyn A.}, year={2019}, month={Sep} }
 @article{vikuk_young_lee_nagabhyru_krischke_mueller_krauss_2019, title={Infection Rates and Alkaloid Patterns of Different Grass Species with Systemic Epichloë Endophytes}, volume={85}, url={https://doi.org/10.1128/AEM.00465-19}, DOI={10.1128/AEM.00465-19}, abstractNote={Severe problems of livestock intoxication from Epichloë-infected forage grasses have been reported from New Zealand, Australia, and the United States, but much less frequently from Europe, and particularly not from Germany. Nevertheless, it is important to monitor infection rates and alkaloids of grasses with Epichloë fungi to estimate possible intoxication risks. Most studies focus on agricultural grass species like Lolium perenne and Festuca arundinacea, but other cool-season grass species can also be infected. We show that in Germany, infection rates and alkaloids differ between grass species and that some of the alkaloids can be toxic to livestock. Changes in grassland management due to changing climate, especially with a shift toward grasslands dominated with Epichloë-infected species such as Lolium perenne, may result in greater numbers of intoxicated livestock in the near future. We therefore suggest regular monitoring of grass species for infections and alkaloids and call for maintaining heterogenous grasslands for livestock. ABSTRACT Symbiotic Epichloë species are fungal endophytes of cool-season grasses that can produce alkaloids with toxicity to vertebrates and/or invertebrates. Monitoring infections and presence of alkaloids in grasses infected with Epichloë species can provide an estimate of possible intoxication risks for livestock. We sampled 3,046 individuals of 13 different grass species in three regions on 150 study sites in Germany. We determined infection rates and used PCR to identify Epichloë species diversity based on the presence of different alkaloid biosynthesis genes, then confirmed the possible chemotypes with high-performance liquid chromatography (HPLC)/ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) measurements. Infections of Epichloë spp. were found in Festuca pratensis Huds. (81%), Festuca ovina L. aggregate (agg.) (73%), Lolium perenne L. (15%), Festuca rubra L. (15%) and Dactylis glomerata L. (8%). The other eight grass species did not appear to be infected. For the majority of Epichloë-infected L. perenne samples (98%), the alkaloids lolitrem B and peramine were present, but ergovaline was not detected, which was consistent with the genetic evaluation, as dmaW, the gene encoding the first step of the ergot alkaloid biosynthesis pathway, was absent. Epichloë uncinata in F. pratensis produced anti-insect loline compounds. The Epichloë spp. observed in the F. ovina agg. samples showed the greatest level of diversity, and different intermediates of the indole-diterpene pathway could be detected. Epichloë infection rates alone are insufficient to estimate intoxication risks for livestock, as other factors, like the ability of the endophyte to produce the alkaloids, also need to be assessed. IMPORTANCE Severe problems of livestock intoxication from Epichloë-infected forage grasses have been reported from New Zealand, Australia, and the United States, but much less frequently from Europe, and particularly not from Germany. Nevertheless, it is important to monitor infection rates and alkaloids of grasses with Epichloë fungi to estimate possible intoxication risks. Most studies focus on agricultural grass species like Lolium perenne and Festuca arundinacea, but other cool-season grass species can also be infected. We show that in Germany, infection rates and alkaloids differ between grass species and that some of the alkaloids can be toxic to livestock. Changes in grassland management due to changing climate, especially with a shift toward grasslands dominated with Epichloë-infected species such as Lolium perenne, may result in greater numbers of intoxicated livestock in the near future. We therefore suggest regular monitoring of grass species for infections and alkaloids and call for maintaining heterogenous grasslands for livestock.}, number={17}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Vikuk, Veronika and Young, Carolyn A. and Lee, Stephen T. and Nagabhyru, Padmaja and Krischke, Markus and Mueller, Martin J. and Krauss, Jochen}, editor={Master, Emma R.Editor}, year={2019}, month={Sep} }
 @article{berry_mace_rehner_grage_dijkwel_young_scott_2019, title={Orthologous peramine and pyrrolopyrazine‐producing biosynthetic gene clusters in Metarhizium rileyi, Metarhizium majus and Cladonia grayi}, url={https://doi.org/10.1111/1462-2920.14483}, DOI={10.1111/1462-2920.14483}, abstractNote={Peramine is a non-ribosomal peptide-derived pyrrolopyrazine (PPZ)-containing molecule with anti-insect properties. Peramine is known to be produced by fungi from genus Epichloë, which form mutualistic endophytic associations with cool-season grass hosts. Peramine biosynthesis has been proposed to require only the two-module non-ribosomal peptide synthetase (NRPS) peramine synthetase (PerA), which is encoded by the 8.3 kb gene perA, though this has not been conclusively proven. Until recently, both peramine and perA were thought to be exclusive to fungi of genus Epichloë; however, a putative perA homologue was recently identified in the genome of the insect-pathogenic fungus Metarhizium rileyi. We use a heterologous expression system and a hydrophilic interaction chromatography-based analysis method to confirm that PerA is the only pathway-specific protein required for peramine biosynthesis. The perA homologue from M. rileyi (MR_perA) is shown to encode a functional peramine synthetase, establishing a precedent for distribution of perA orthologs beyond genus Epichloë. Furthermore, perA is part of a larger seven-gene PPZ cluster in M. rileyi, Metarhizium majus and the stalked-cup lichen fungus Cladonia grayi. These PPZ genes encode proteins predicted to derivatize peramine into more complex PPZ metabolites, with the orphaned perA gene of Epichloë spp. representing an example of reductive evolution.}, journal={Environmental Microbiology}, author={Berry, Daniel and Mace, Wade and Rehner, Stephen A. and Grage, Katrin and Dijkwel, Paul P. and Young, Carolyn A. and Scott, Barry}, year={2019}, month={Mar} }
 @article{bushman_singh_lamp_young_charlton_robins_anderson_2019, title={Variation Among Orchardgrass (Dactylis glomerata) Germplasm for Choke Prevalence Caused by Epichloë typhina}, volume={103}, url={https://doi.org/10.1094/PDIS-05-18-0867-RE}, DOI={10.1094/PDIS-05-18-0867-RE}, abstractNote={Orchardgrass, or cocksfoot (Dactylis glomerata L.), is a cool-season forage grass susceptible to the choke disease caused by Epichloë typhina. Choke has been reported in orchardgrass seed production fields across the temperate regions of the world, but fungicides have not been efficacious in reducing choke incidence or prevalence. To assess the potential for genetic resistance or tolerance of orchardgrass to choke, we evaluated the variation in orchardgrass cultivars and accessions for choke prevalence and characterized infected plants for endophyte secondary metabolite and mating type gene presence. Significant variation was detected across years and locations. Choke prevalence did not always increase with the age of the stand, nor did choke prevalence correlate with flowering time or swathing time of the entries. Both mating types of E. typhina were detected in approximately equal proportions, and no evidence for loline, ergot alkaloid, or indole-diterpene biosynthesis was found. Plants with multiple infected tillers often showed more than one mating type present in the plant, indicating multiple infection events rather than a single infection event that spread to multiple tillers. Both accessions and cultivars with significant choke, and no choke, were detected, which constitute sources of germplasm for further testing and breeding.}, number={2}, journal={Plant Disease}, publisher={Scientific Societies}, author={Bushman, B. Shaun and Singh, Devesh and Lamp, Robin and Young, Carolyn A. and Charlton, Nikki D. and Robins, Joseph G. and Anderson, Nicole}, year={2019}, month={Feb}, pages={324–330} }
 @article{young_kinkel_2018, title={A Year of Phytobiomes}, volume={2}, url={https://doi.org/10.1094/PBIOMES-05-18-0023-E}, DOI={10.1094/PBIOMES-05-18-0023-E}, abstractNote={It is hard to believe that we have just celebrated the one-year anniversary of our first issue of the Phytobiomes journal! As we celebrate our first year, and as the term ‘phytobiome’ becomes more deeply embedded in our science, it is worth pausing to reflect on the impetus and science behind the phytobiome concept, and on the next steps for our journal.}, number={2}, journal={Phytobiomes Journal}, publisher={Scientific Societies}, author={Young, Carolyn A. and Kinkel, Linda L.}, year={2018}, month={Jan}, pages={53–54} }
 @article{mattupalli_seethepalli_york_young_2018, title={Digital imaging to evaluate root system architectural changes associated with soil biotic factors}, url={https://doi.org/10.1101/505321}, DOI={10.1101/505321}, abstractNote={Root system architecture (RSA) is critical for plant growth, which is influenced by several edaphic, environmental, genetic and biotic factors including beneficial and pathogenic microbes. Studying root architecture and the dynamic changes that occur during a plant’s lifespan, especially for perennial crops growing over multiple growing seasons, is still a challenge because of the nature of their growing environment in soil. We describe the utility of an imaging platform called RhizoVision Crown to study RSA of alfalfa, a perennial forage crop affected by Phymatotrichopsis Root Rot (PRR) disease. Phymatotrichopsis omnivora is the causal agent of PRR disease that reduces alfalfa stand longevity. During the lifetime of the stand, PRR disease rings enlarge and the field can be categorized into three zones based upon plant status: asymptomatic, disease front and survivor. To study root architectural changes associated with PRR, a four-year old 25.6-hectare alfalfa stand infested with PRR was selected at the Red River Farm, Burneyville, OK during October 2017. Line transect sampling was conducted from four actively growing PRR disease rings. At each disease ring, six line transects were positioned spanning 15 m on either side of the disease front with one alfalfa root sampled at every 3 m interval. Each alfalfa root was imaged with the RhizoVision Crown platform using a backlight and a high-resolution monochrome CMOS camera enabling preservation of the natural root architectural integrity. The platform’s image analysis software, RhizoVision Analyzer, automatically segmented images, skeletonized, and extracted a suite of features. Data indicated that the survivor plants compensated for damage or loss to the taproot through the development of more lateral and crown roots, and that a suite of multivariate features could be used to automatically classify roots as from survivor or asymptomatic zones. Root growth is a dynamic process adapting to ever changing interactions among various phytobiome components, by utilizing a low-cost, efficient and high-throughput Rhizo-Vision Crown platform we showed quantification of these changes occurring in a mature perennial forage crop.}, author={Mattupalli, Chakradhar and Seethepalli, Anand and York, Larry M and Young, Carolyn A}, year={2018}, month={Dec} }
 @article{young_bock_charlton_mattupalli_krom_bowen_templeton_plummer_wood_2018, title={Evidence for Sexual Reproduction: Identification, Frequency, and Spatial Distribution of Venturia effusa (Pecan Scab) Mating Type Idiomorphs}, volume={108}, url={https://doi.org/10.1094/PHYTO-07-17-0233-R}, DOI={10.1094/PHYTO-07-17-0233-R}, abstractNote={Venturia effusa (syn. Fusicladium effusum), causal agent of pecan scab, is the most prevalent pathogen of pecan (Carya illinoinensis), causing severe yield losses in the southeastern United States. V. effusa is currently known only by its asexual (conidial) stage. However, the degree and distribution of genetic diversity observed within and among populations of V. effusa are typical of a sexually reproducing fungal pathogen, and comparable with other dothideomycetes with a known sexual stage, including the closely related apple scab pathogen, V. inaequalis. Using the mating type (MAT) idiomorphs from V. inaequalis, we identified a single MAT gene, MAT1-1-1, in a draft genome of V. effusa. The MAT1-1-1 locus is flanked by two conserved genes encoding a DNA lyase (APN2) and a hypothetical protein. The MAT locus spanning the flanking genes was amplified and sequenced from a subset of 14 isolates, of which 7 contained MAT1-1-1 and the remaining samples contained MAT1-2-1. A multiplex polymerase chain reaction screen was developed to amplify MAT1-1-1, MAT1-2-1, and a conserved reference gene encoding β-tubulin, and used to screen 784 monoconidial isolates of V. effusa collected from 11 populations of pecan across the southeastern United States. A hierarchical sampling protocol representing region, orchard, and tree allowed for analysis of MAT structure at different spatial scales. Analysis of this collection revealed the frequency of the MAT idiomorphs is in a 1:1 equilibrium of MAT1-1:MAT1-2. The apparent equilibrium of the MAT idiomorphs provides impetus for a renewed effort to search for the sexual stage of V. effusa. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .}, number={7}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Young, Carolyn A. and Bock, Clive H. and Charlton, Nikki D. and Mattupalli, Chakradhar and Krom, Nick and Bowen, Joanna K. and Templeton, Matthew and Plummer, Kim M. and Wood, Bruce W.}, year={2018}, month={Jul}, pages={837–846} }
 @article{bock_young_stevenson_charlton_2018, title={Fine-Scale Population Genetic Structure and Within-Tree Distribution of Mating Types of Venturia effusa, Cause of Pecan Scab in the United States}, volume={108}, url={https://doi.org/10.1094/PHYTO-02-18-0068-R}, DOI={10.1094/PHYTO-02-18-0068-R}, abstractNote={Scab (caused by Venturia effusa) is the major disease of pecan in the southeastern United States. There is no information available on the fine-scale population genetic diversity or the occurrence of clonal types at small spatial scales that provides insight into inoculum sources and dispersal mechanisms, and potential opportunity for sexual reproduction. To investigate fine-scale genetic diversity, four trees of cultivar Wichita (populations) were sampled hierarchically: within each tree canopy, four approximately evenly spaced terminals (subpopulations) were selected and up to six leaflets (sub-subpopulations) were sampled from different compound leaves on each terminal. All lesions (n = 1 to 8) on each leaflet were sampled. The isolates were screened against a panel of 29 informative microsatellite markers and the resulting multilocus genotypes (MLG) subject to analysis. Mating type was also determined for each isolate. Of 335 isolates, there were 165 MLG (clonal fraction 49.3%). Nei's unbiased measure of genetic diversity for the clone-corrected data were moderate to high (0.507). An analysis of molecular variance demonstrated differentiation (P = 0.001) between populations on leaflets within individual terminals and between terminals within trees in the tree canopies, with 93.8% of variance explained among isolates within leaflet populations. Other analyses (minimum-spanning network, Bayesian, and discriminant analysis of principal components) all indicated little affinity of isolate for source population. Of the 335 isolates, most unique MLG were found at the stratum of the individual leaflets (n = 242), with similar total numbers of unique MLG observed at the strata of the terminal (n = 170), tree (n = 166), and orchard (n = 165). Thus, the vast majority of shared clones existed on individual leaflets on a terminal at the scale of 10s of centimeters or less, indicating a notable component of short-distance dispersal. There was significant linkage disequilibrium (P < 0.001), and an analysis of Psex showed that where there were multiple encounters of an MLG, they were most probably the result of asexual reproduction (P < 0.05) but there was no evidence that asexual reproduction was involved in single or first encounters of an MLG (P > 0.05). Overall, the MAT1-1-1 and MAT1-2-1 idiomorphs were at equilibrium (73:92) and in most populations, subpopulations, and sub-subpopulations. Both mating types were frequently observed on the same leaflet. The results provide novel information on the characteristics of populations of V. effusa at fine spatial scales, and provide insights into the dispersal of the organism within and between trees. The proximity of both mating idiomorphs on single leaflets is further evidence of opportunity for development of the sexual stage in the field.}, number={11}, journal={Phytopathology®}, publisher={Scientific Societies}, author={Bock, Clive H. and Young, Carolyn A. and Stevenson, Katherine L. and Charlton, Nikki D.}, year={2018}, month={Nov}, pages={1326–1336} }
 @article{yi_hendricks_kaste_charlton_nagabhyru_panaccione_young_2018, title={Molecular identification and characterization of endophytes from uncultivated barley}, volume={110}, url={https://doi.org/10.1080/00275514.2018.1464818}, DOI={10.1080/00275514.2018.1464818}, abstractNote={ABSTRACT Epichloë species (Clavicipitaceae, Ascomycota) are endophytic symbionts of many cool-season grasses. Many interactions between Epichloë and their host grasses contribute to plant growth promotion, protection from many pathogens and insect pests, and tolerance to drought stress. Resistance to insect herbivores by endophytes associated with Hordeum species has been previously shown to vary depending on the endophyte-grass-insect combination. We explored the genetic and chemotypic diversity of endophytes present in wild Hordeum species. We analyzed seeds of Hordeum bogdanii, H. brevisubulatum, and H. comosum obtained from the US Department of Agriculture’s (USDA) National Plant Germplasm System (NPGS), of which some have been reported as endophyte-infected. Using polymerase chain reaction (PCR) with primers specific to Epichloë species, we were able to identify endophytes in seeds from 17 of the 56 Plant Introduction (PI) lines, of which only 9 lines yielded viable seed. Phylogenetic analyses of housekeeping, alkaloid biosynthesis, and mating type genes suggest that the endophytes of the infected PI lines separate into five taxa: Epichloë bromicola, Epichloë tembladerae, and three unnamed interspecific hybrid species. One PI line contained an endophyte that is considered a new taxonomic group, Epichloë sp. HboTG-3 (H. bogdanii Taxonomic Group 3). Phylogenetic analyses of the interspecific hybrid endophytes from H. bogdanii and H. brevisubulatum indicate that these taxa all have an E. bromicola allele but the second allele varies. We verified in planta alkaloid production from the five genotypes yielding viable seed. Morphological characteristics of the isolates from the viable Hordeum species were analyzed for their features in culture and in planta. In the latter, we observed epiphyllous growth and in some cases sporulation on leaves of infected plants.}, number={3}, journal={Mycologia}, publisher={Informa UK Limited}, author={Yi, Mihwa and Hendricks, Will Q. and Kaste, Joshua and Charlton, Nikki D. and Nagabhyru, Padmaja and Panaccione, Daniel G. and Young, Carolyn A.}, year={2018}, month={May}, pages={453–472} }
 @article{winter_ganley_young_liachko_schardl_dupont_berry_ram_scott_cox_2018, title={Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae}, volume={14}, url={https://doi.org/10.1371/journal.pgen.1007467}, DOI={10.1371/journal.pgen.1007467}, abstractNote={Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C data to examine the three-dimensional organisation of the genome, and RNA-seq data to investigate how Epichloë genome structure contributes to the suite of transcriptional changes needed to maintain symbiotic relationships with the grass host. Our results reveal a genome in which very repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences that are almost repeat-free. In contrast to other species reported to date, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.}, number={10}, journal={PLOS Genetics}, publisher={Public Library of Science (PLoS)}, author={Winter, David J. and Ganley, Austen R. D. and Young, Carolyn A. and Liachko, Ivan and Schardl, Christopher L. and Dupont, Pierre-Yves and Berry, Daniel and Ram, Arvina and Scott, Barry and Cox, Murray P.}, editor={Richardson, Paul M.Editor}, year={2018}, month={Oct}, pages={e1007467} }
 @article{winter_ganley_young_liachko_schardl_dupont_berry_ram_scott_cox_2018, title={Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae}, volume={6}, url={https://doi.org/10.1101/339010}, DOI={10.1101/339010}, abstractNote={Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organization influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. Coupling it with RNAseq and HiC data, we investigate how the structure of the genome contributes to the suite of transcriptional changes that an Epichloë species needs to maintain symbiotic relationships with its grass host. Our results reveal a unique “patchwork” genome, in which repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences. In contrast to other species, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.}, publisher={Cold Spring Harbor Laboratory}, author={Winter, David J and Ganley, Austen RD and Young, Carolyn A and Liachko, Ivan and Schardl, Christopher L and Dupont, Pierre-Yves and Berry, Daniel and Ram, Arvina and Scott, D Barry and Cox, Murray P}, year={2018}, month={Jun} }
 @article{supervised classification of rgb aerial imagery to evaluate the impact of a root rot disease_2018, url={http://www.mdpi.com/2072-4292/10/6/917}, DOI={10.3390/rs10060917}, abstractNote={Aerial imaging provides a landscape view of crop fields that can be utilized to monitor plant diseases. Phymatotrichopsis root rot (PRR) is a serious root rot disease affecting several dicotyledonous hosts, including the perennial forage crop alfalfa. PRR disease causes stand loss by spreading as circular to irregular diseased areas that increase over time, but disease progression in alfalfa fields is poorly understood. The objectives of this study were to develop a workflow to produce PRR disease maps from sets of high-resolution red, green and blue (RGB) images acquired from two different platforms and to assess the feasibility of using these PRR disease maps to monitor disease progression in alfalfa fields. Aerial RGB images, two from unmanned aircraft systems (UAS) and four images from a manned aircraft platform were acquired at different time points during the 2014–2015 growing seasons from a center-pivot irrigated, PRR-infested alfalfa field near Burneyville, OK. Supervised classification of images acquired from both platforms were performed using three spectral signatures: image-specific, UAS-platform-specific and manned-aircraft platform-specific. Our results showed that the UAS-platform-specific spectral signature was most efficient for classifying images acquired with the UAS, with accuracy ranging from 90 to 96%. In contrast, manned-aircraft-acquired images classified using image-specific spectral signatures yielded 95 to 100% accuracy. The effect of hue, saturation and value color space transformations (HSV and Hrot60SV) on classification accuracy was determined, but the accuracy estimates showed no improvement in their efficiency compared to the RGB color space. Finally, the data showed that the classification of the bare ground increased by 74% during the study period, indicating the extent of alfalfa stand loss caused by PRR disease. Thus, this study showed the utility of high-resolution RGB aerial images for monitoring PRR disease spread in alfalfa.}, journal={Remote Sensing}, year={2018}, month={Jun} }
 @article{mitic_berry_brasell_green_young_saikia_rakonjac_scott_2017, title={Disruption of calcineurin catalytic subunit (cnaA) in Epichloë festucae induces symbiotic defects and intrahyphal hyphae formation}, volume={10}, DOI={10.1111/mpp.12624}, abstractNote={Calcineurin is a conserved calcium/calmodulin-dependent protein phosphatase, consisting of a catalytic subunit A and a regulatory subunit B, which is involved in calcium-dependent signalling and regulation of various important cellular processes. In this study, we functionally characterized the catalytic subunit A (CnaA) of the endophytic fungus Epichloë festucae which forms a symbiotic association with the grass host Lolium perenne. We deleted the CnaA-encoding gene cnaA in E. festucae and examined its role in hyphal growth, cell wall integrity and symbiosis. This ΔcnaA strain had a severe growth defect with loss of radial growth and hyper-branched hyphae. Transmission electron microscopy and confocal microscopy analysis of the mutant revealed cell wall defects, aberrant septation and the formation of intrahyphal hyphae, both in culture and in planta. The mutant strain also showed a reduced infection rate in planta. The fluorescence of mutant hyphae stained with WGA-AF488 was reduced, indicating reduced chitin accessibility. Together, these results show that E. festucae CnaA is required for fungal growth, maintaining cell wall integrity and host colonization.}, journal={Molecular Plant Pathology}, publisher={Wiley-Blackwell}, author={Mitic, Milena and Berry, Daniel and Brasell, Emma and Green, Kimberly and Young, Carolyn A. and Saikia, Sanjay and Rakonjac, Jasna and Scott, Barry}, year={2017}, month={Oct} }
 @article{shymanovich_charlton_musso_scheerer_cech_faeth_young_2017, title={Interspecific and intraspecific hybrid Epichloë species symbiotic with the North American native grass Poa alsodes}, volume={109}, url={https://doi.org/10.1080/00275514.2017.1340779}, DOI={10.1080/00275514.2017.1340779}, abstractNote={ABSTRACT The endophyte presence and diversity in natural populations of Poa alsodes were evaluated along a latitudinal transect from the southern distribution range in North Carolina to New York. Two distinct Epichloë hybrid taxa were identified from 23 populations. Each taxon could easily be distinguished by polymerase chain reaction (PCR) genotyping with primers designed to mating type genes and alkaloid biosynthesis genes that encode key pathway steps for ergot alkaloids, indole-diterpenes, lolines, and peramine. The most commonly found Epichloë taxon, Poa alsodes Taxonomic Group-1 (PalTG-1), was detected in 22 populations at high infection frequencies (72–100%), with the exception of one population at high elevation (26% infection). The second taxon, PalTG-2, was observed only in five populations in Pennsylvania constituting 12% of infected samples. Phylogenetic analyses placed PalTG-1 as an interspecific hybrid of E. amarillans and E. typhina subsp. poae ancestors, and it is considered a new hybrid species, which the authors name Epichloë alsodes. PalTG-2 is an intraspecific hybrid of two E. typhina subsp. poae ancestors, similar to E. schardlii from the host Cinna arundinacea, which the authors propose as a new variety, Epichloë schardlii var. pennsylvanica. Epichloë alsodes isolates were all mating type MTA MTB and tested positive for dmaW, easC, perA, and some LOL genes, but only the alkaloid N-acetylnorloline was detected in E. alsodes–infected plant material. Epichloë schardlii var. pennsylvanica isolates were all mating type MTB MTB and tested positive for perA, but peramine was not produced. Both E. alsodes and E. schardlii var. pennsylvanica appeared to have complete perA genes, but point mutations were identified in E. alsodes that would render the encoded perA gene nonfunctional.}, number={3}, journal={Mycologia}, publisher={Informa UK Limited}, author={Shymanovich, Tatsiana and Charlton, Nikki D. and Musso, Ashleigh M. and Scheerer, Jonathan and Cech, Nadja B. and Faeth, Stanley H. and Young, Carolyn A.}, year={2017}, month={May}, pages={459–474} }
 @article{bastias_ueno_assefh_alvarez_young_gundel_2017, title={Metabolism or behavior: explaining the performance of aphids on alkaloid-producing fungal endophytes in annual ryegrass (Lolium multiflorum)}, volume={185}, DOI={10.1007/s00442-017-3940-2}, abstractNote={Plant–herbivore interactions are often mediated by plant microorganisms, and the “defensive mutualism” of epichloid fungal endophytes of grasses is an example. These endophytes synthesize bioactive alkaloids that generally have detrimental effects on the performance of insect herbivores, but the underlying mechanisms are not well understood. Our objective was to determine whether changes in the physiology and/or behavior of aphids explain the changes in performance of insects feeding on endophytic plants. We studied the interaction between the aphid Rhopalosiphum padi and the annual ryegrass Lolium multiflorum symbiotic (E+) or not symbiotic (E−) with the fungus Epichloë occultans that can synthesize loline alkaloids. We hypothesized that aphids feeding on E+ plants have higher energetic demands for detoxification of fungal alkaloids, thereby negatively impacting the individual performance, population growth, and structure. Aphids growing on E+ plants had lower values in morphometric and functional variables of individual performance, displayed lower birth rate, smaller population size, and dramatic structural changes. However, aphids exhibited lower values of standard metabolic rate (SMR) on E+ plants, which suggests no high costs of detoxification. Behavioral variables during the first 8 h of feeding showed that aphids did not change the phloem sap ingestion with the presence of fungal endophytes. We hypothesize that aphids may maintain phloem sap ingestion according to their fungal alkaloid tolerance capacity. In other words, when alkaloid concentrations overcome tolerance threshold, ingestion of phloem should decrease, which may explain the observed lower values of SMR in E+ feeding aphids.}, number={2}, journal={Oecologia}, publisher={Springer Nature}, author={Bastias, Daniel A. and Ueno, Andrea C. and Assefh, Cristina R. Machado and Alvarez, Adriana E. and Young, Carolyn A. and Gundel, Pedro E.}, year={2017}, month={Sep}, pages={245–256} }
 @article{bock_hotchkiss_young_charlton_chakradhar_stevenson_wood_2017, title={Population Genetic Structure of Venturia effusa, Cause of Pecan Scab, in the Southeastern United States}, volume={107}, DOI={10.1094/phyto-10-16-0376-r}, abstractNote={Venturia effusa is the most important pathogen of pecan in the southeastern United States. Little information exists on the population biology and genetic diversity of the pathogen. A hierarchical sampling of 784 isolates from 63 trees in 11 pecan orchards in the southeastern United States were screened against a set of 30 previously characterized microsatellite markers. Populations were collected from Georgia (n = 2), Florida (n = 1), Alabama (n = 2), Mississippi (n = 1), Louisiana (n = 1), Illinois (n = 1), Oklahoma (n = 1), Texas (n = 1), and Kansas (n = 1). Clonality was low in all orchard populations (≤10.1% of isolates), and there were consistently high levels of genotypic diversity (Shannon-Weiner's index = 3.49 to 4.59) and gene diversity (Nei's measure = 0.513 to 0.713). Analysis of molecular variance showed that, although 81% of genetic diversity occurred at the scale of the individual tree, 16% occurred between orchards and only 3% between trees within orchards. All populations could be differentiated from each other (P = 0.01), and various cluster analyses indicated that some populations were more closely related compared with other pairs of populations. This is indicative of some limited population differentiation in V. effusa in the southeastern United States. Bayesian and nearest-neighbor methods suggested eight clusters, with orchards from Georgia and Florida being grouped together. A minimum spanning tree of all 784 isolates also indicated some isolate identification with source population. Linkage disequilibrium was detected in all but one population (Kansas), although 8 of the 11 populations had <20% of loci at disequilibrium. A Mantel test demonstrated a relationship between physical and genetic distance between populations (Z = 11.9, r = 0.559, P = 0.001). None of the populations were at mutation-drift equilibrium. All but 3 of the 11 populations had a deficiency of gene diversity compared with that expected at mutation-drift equilibrium (indicating population expansion); the remaining populations had an excess of gene diversity compared with that expected at mutation-drift equilibrium (indicating a recent bottleneck). These observations are consistent with the known history of pecan and pecan scab, which is that V. effusa became an issue on cultivated pecan in the last approximately 120 years (recent population expansion). Recently reported mating type genes and the sexual stage of this fungus may help explain the observed population characteristics, which bear a strong resemblance to those of other well-characterized sexually reproducing ascomycete pathogens.}, number={5}, journal={Phytopathology}, publisher={Scientific Societies}, author={Bock, Clive H. and Hotchkiss, Michael W. and Young, Carolyn A. and Charlton, Nikki D. and Chakradhar, Mattupalli and Stevenson, Katherine L. and Wood, Bruce W.}, year={2017}, month={May}, pages={607–619} }
 @article{shi_an_yao_young_panaccione_lee_schardl_li_2017, title={Toxin-producing Epichloë bromicola strains symbiotic with the forage grass Elymus dahuricus in China}, volume={1}, url={https://doi.org/10.1080/00275514.2018.1426941}, DOI={10.1080/00275514.2018.1426941}, abstractNote={ABSTRACT Cool-season grasses (Poaceae subfamily Poöideae) are an important forage component for livestock in western China, and many have seed-transmitted symbionts of the genus Epichloë, fungal endophytes that are broadly distributed geographically and in many tribes of the Poöideae. Epichloë strains can produce any of several classes of alkaloids, of which ergot alkaloids and indole-diterpenes can be toxic to mammalian and invertebrate herbivores, whereas lolines and peramine are more selective against invertebrates. The authors characterized genotypes and alkaloid profiles of Epichloë bromicola isolates symbiotic with Elymus dahuricus, an important forage grass in rangelands of China. The endophyte was seed-transmitted and occasionally produced fruiting bodies (stromata), but its sexual state was not observed on this host. The genome sequence of E. bromicola isolate E7626 from El. dahuricus in Xinjiang Province revealed gene sets for peramine, ergot alkaloids, and indole-diterpenes. In multiplex polymerase chain reaction (PCR) screens of El. dahuricus-endophyte isolates from Beijing and two locations in Shanxi Province, most were also positive for these genes. Ergovaline and other ergot alkaloids, terpendoles and other indole-diterpenes, and peramine were confirmed in El. dahuricus plants with E. bromicola. The presence of ergot alkaloids and indole-diterpenes in this grass is a potential concern for managers of grazing livestock.}, journal={Mycologia}, publisher={Informa UK Limited}, author={Shi, Chong and An, Shazhou and Yao, Zhengpei and Young, Carolyn A. and Panaccione, Daniel G. and Lee, Stephen T. and Schardl, Christopher L. and Li, Chunjie}, year={2017}, month={Nov}, pages={1–13} }
 @article{sneck_rudgers_young_miller_2017, title={Variation in the Prevalence and Transmission of Heritable Symbionts Across Host Populations in Heterogeneous Environments}, volume={74}, DOI={10.1007/s00248-017-0964-4}, abstractNote={Heritable microbes are abundant in nature and influential to their hosts and the communities in which they reside. However, drivers of variability in the prevalence of heritable symbionts and their rates of transmission are poorly resolved, particularly across host populations experiencing variable biotic and abiotic environments. To fill these gaps, we surveyed 25 populations of two native grasses (Elymus virginicus and Elymus canadensis) across the southern Great Plains (USA). Both grass species host heritable endophytic fungi (genus Epichloё) and can hybridize where their ranges overlap. From a subset of hosts, we characterized endophyte genotype using genetic loci that link to bioactive alkaloid production. First, we found mean vertical transmission rates and population-level prevalence were positively correlated, specifically for E. virginicus. However, both endophyte prevalence and transmission varied substantially across populations and did not strongly correlate with abiotic variables, with one exception: endophyte prevalence decreased as drought stress decreased for E. virginicus hosts. Second, we evaluated the potential influence of biotic factors and found that, after accounting for climate, endophyte genotype explained significant variation in symbiont inheritance. We also contrasted populations where host species co-occurred in sympatry vs. allopatry. Sympatry could potentially increase interspecific hybridization, but this variable did not associate with patterns of symbiont prevalence or transmission success. Our results reveal substantial variability in symbiont prevalence and transmission across host populations and identify symbiont genotype, and to a lesser extent, the abiotic environment as sources of this variation.}, number={3}, journal={Microbial Ecology}, publisher={Springer Nature}, author={Sneck, Michelle E. and Rudgers, Jennifer A. and Young, Carolyn A. and Miller, Tom E. X.}, year={2017}, month={Mar}, pages={640–653} }
 @article{young_kinkel_2017, title={Welcome to Phytobiomes}, url={https://doi.org/10.1094/PBIOMES-12-16-0018-E}, DOI={10.1094/PBIOMES-12-16-0018-E}, abstractNote={In 2014, members of The American Phytopathological Society (APS) began to consider strategically the ways in which the accelerating flow of diverse types of complex data are fundamentally changing the ways in which we study, think about, and manage plant systems. Advancing technical capacities to generate plant, microbial and other organismal ‘omics’, environmental, and data produced at very fine spatial scales, coupled with expanding capabilities to integrate data across diverse scales of space and time, are providing novel insights into the networks of interaction that mediate plant productivity. In response to these enormous advances in technical capacities, APS created a Phytobiomes Initiative to chart a path forward. In 2015, APS brought together a diverse community of scientists in Washington DC for a strategically timed meeting to spearhead a new paradigm for crop improvement focusing on phytobiome-based approaches. The success of the human microbiome project paved the way, challenging us to push t...}, journal={Phytobiomes Journal}, author={Young, Carolyn A. and Kinkel, Linda}, year={2017}, month={Jan} }
 @article{rudgers_fletcher_olivas_young_charlton_pearson_maron_oecologia_2016, title={Long-term ungulate exclusion reduces fungal symbiont prevalence in native grasslands.}, volume={181}, url={http://europepmc.org/abstract/med/27113054}, DOI={10.1007/s00442-016-3620-7}, abstractNote={When symbionts are inherited by offspring, they can have substantial ecological and evolutionary consequences because they occur in all host life stages. Although natural frequencies of inherited symbionts are commonly <100 %, few studies investigate the ecological drivers of variation in symbiont prevalence. In plants, inherited fungal endophytes can improve resistance to herbivory, growth under drought, and competitive ability. We evaluated whether native ungulate herbivory increased the prevalence of a fungal endophyte in the common, native bunchgrass, Festuca campestris (rough fescue, Poaceae). We used large-scale (1 ha) and long-term (7-10 year) fencing treatments to exclude native ungulates and recorded shifts in endophyte prevalence at the scale of plant populations and for individual plants. We characterized the fungal endophyte in F. campestris, Epichloë species FcaTG-1 (F. campestris taxonomic group 1) for the first time. Under ungulate exclusion, endophyte prevalence was 19 % lower in plant populations, 25 % lower within plant individuals, and 39 % lower in offspring (seeds) than in ungulate-exposed controls. Population-level endophyte frequencies were also negatively correlated with soil moisture across geographic sites. Observations of high within-plant variability in symbiont prevalence are novel for the Epichloë species, and contribute to a small, but growing, literature that documents phenotypic plasticity in plant-endophyte symbiota. Altogether, we show that native ungulates can be an important driver of symbiont prevalence in native plant populations, even in the absence of evidence for direct mechanisms of mammal deterrence. Understanding the ecological controls on symbiont prevalence could help to predict future shifts in grasslands that are dominated by Epichloë host plants.}, number={4}, author={Rudgers, J.A. and Fletcher, R.A. and Olivas, E. and Young, C.A. and Charlton, N.D. and Pearson, D.E. and Maron, J.L. and Oecologia}, year={2016}, month={Aug}, pages={1151–1161,} }
 @article{rogers_walker_young_2016, title={The Effect of Endophytic Fungi on Nematode Populations in Summer-dormant and Summer-active Tall Fescue}, volume={48}, DOI={10.21307/jofnem-2017-013}, abstractNote={Abstract Summer-active (continental) and summer-dormant (Mediterranean) tall fescue morphotypes are each adapted to different environmental conditions. Endophyte presence provides plant parasitic nematode resistance, but not with all endophyte strains and cultivar combinations. This study sought to compare effects of four nematode genera on continental and Mediterranean cultivars infected with common toxic or novel endophyte strains. A 6-mon greenhouse study was conducted with continental cultivars, Kentucky 31 (common toxic) and Texoma MaxQ II (novel endophyte) and the Mediterranean cultivar Flecha MaxQ (novel endophyte). Endophyte-free plants of each cultivar were controls. Each cultivar × endophyte combination was randomly assigned to a control, low or high inoculation rate of a mixed nematode culture containing stunt nematodes (Tylenchorhynchus spp.), ring nematodes (Criconemella spp.), spiral nematodes (Helicotylenchus spp.), and lesion nematodes (Pratylenchus spp.). Endophyte infection had no effect on nematode population densities. The cultivar × endophyte interaction was significant. Population densities of stunt nematode, spiral nematode, and ring nematodes were higher for Flecha MaxQ than other cultivar × endophyte combinations. Novel endophyte infection enhances suitability of Flecha MaxQ as a nematode host.}, number={2}, journal={Journal of Nematology}, publisher={Exeley, Inc.}, author={ROGERS, JAMES K. and WALKER, NATHAN R. and YOUNG, CAROLYN A.}, year={2016}, pages={87–94} }
 @article{kazenel_debban_ranelli_hendricks_chung_pendergast_charlton_young_rudgers_2015, title={A mutualistic endophyte alters the niche dimensions of its host plant}, volume={7}, DOI={10.1093/aobpla/plv005}, abstractNote={Few studies have tested whether mutualisms may affect species distributions by altering the niches of partner species. We show that a fungal endophyte is associated with a shift in the soil moisture niche of its host plant relative to a co-occurring, endophyte-free congener. The endophyte appeared to initially restrict its host's distribution to wetter microsites before positively affecting its growth, suggesting the value of considering symbiont effects at different partner life stages. Our study identifies a symbiotic relationship as a potential mechanism facilitating the coexistence of two species, suggesting that symbiont effects on host niche may have community-level consequences.}, number={0}, journal={AoB PLANTS}, publisher={Oxford University Press (OUP)}, author={Kazenel, M. R. and Debban, C. L. and Ranelli, L. and Hendricks, W. Q. and Chung, Y. A. and Pendergast, T. H. and Charlton, N. D. and Young, C. A. and Rudgers, J. A.}, year={2015}, month={Jan}, pages={plv005–plv005} }
 @article{talukder_azhaguvel_mukherjee_young_tang_krom_saha_2015, title={De Novo Assembly and Characterization of Tall Fescue Transcriptome under Water Stress}, volume={8}, DOI={10.3835/plantgenome2014.09.0050}, abstractNote={Water stress is a fundamental problem for tall fescue [Lolium arundinaceum (Schreb.) Darbysh.] cultivation in the south–central United States. Genetic improvement of tall fescue for water‐stress tolerance is the key strategy for improving its persistence in the region. Genotypes with contrasting characteristics for relative water content and osmotic potential were identified from a tall fescue population. Transcriptome profiling between water‐stress‐tolerant (B400) and water‐stress‐susceptible (W279) genotypes was performed to unravel the genetic regulatory mechanism of water‐stress responses in tall fescue. RNA samples from leaf, shoot, root, and inflorescence were pooled and sequenced through Illumina paired‐end sequencing. A total of 199,399 contigs were assembled with an average length of 585 bp. Between the two genotypes, 2986 reference transcripts (RTs) were significantly differentially expressed and 1048 of them could be annotated and found to associate with metabolic pathways and enzyme coding genes. In total, 175 differentially expressed RTs were reported for various stress‐related functions. Among those, 65 encoded kinase proteins, 40 each encoded transposons, and transporter proteins were previously reported to be involved with abiotic stress responses. A total of 6348 simple sequence repeats and 6658 single‐nucleotide polymorphisms were identified in the contig sequences. Primers were developed from the corresponding sequences, which might be used as candidate gene markers in tall fescue. This study will lead to identification of genes or transcription factors related to water‐stress tolerance and development of a comprehensive molecular marker system to facilitate marker‐assisted breeding in tall fescue.}, number={2}, journal={The Plant Genome}, publisher={Crop Science Society of America}, author={Talukder, S. K. and Azhaguvel, P. and Mukherjee, S. and Young, C. A. and Tang, Y. and Krom, N. and Saha, M. C.}, year={2015}, pages={0} }
 @article{berry_takach_schardl_charlton_scott_young_2015, title={Disparate Independent Genetic Events Disrupt the Secondary Metabolism Gene perA in Certain Symbiotic Epichloë Species}, volume={81}, DOI={10.1128/aem.03721-14}, abstractNote={ABSTRACT Peramine is an insect-feeding deterrent produced by Epichloë species in symbiotic association with C3 grasses. The perA gene responsible for peramine synthesis encodes a two-module nonribosomal peptide synthetase. Alleles of perA are found in most Epichloë species; however, peramine is not produced by many perA-containing Epichloë isolates. The genetic basis of these peramine-negative chemotypes is often unknown. Using PCR and DNA sequencing, we analyzed the perA genes from 72 Epichloë isolates and identified causative mutations of perA null alleles. We found nonfunctional perA-ΔR* alleles, which contain a transposon-associated deletion of the perA region encoding the C-terminal reductase domain, are widespread within the Epichloë genus and represent a prevalent mutation found in nonhybrid species. Disparate phylogenies of adjacent A2 and T2 domains indicated that the deletion of the reductase domain (R*) likely occurred once and early in the evolution of the genus, and subsequently there have been several recombinations between those domains. A number of novel point, deletion, and insertion mutations responsible for abolishing peramine production in full-length perA alleles were also identified. The regions encoding the first and second adenylation domains (A1 and A2, respectively) were common sites for such mutations. Using this information, a method was developed to predict peramine chemotypes by combining PCR product size polymorphism analysis with sequencing of the perA adenylation domains.}, number={8}, journal={Appl. Environ. Microbiol.}, publisher={American Society for Microbiology}, author={Berry, Daniel and Takach, Johanna E. and Schardl, Christopher L. and Charlton, Nikki D. and Scott, Barry and Young, Carolyn A.}, editor={Cullen, D.Editor}, year={2015}, month={Feb}, pages={2797–2807} }
 @article{saikkonen_young_helander_schardl_2015, title={Endophytic Epichloë species and their grass hosts: from evolution to applications}, volume={90}, DOI={10.1007/s11103-015-0399-6}, abstractNote={The closely linked fitness of the Epichloë symbiont and the host grass is presumed to align the coevolution of the species towards specialization and mutually beneficial cooperation. Ecological observations demonstrating that Epichloë-grass symbioses can modulate grassland ecosystems via both above- and belowground ecosystem processes support this. In many cases the detected ecological importance of Epichloë species is directly or indirectly linked to defensive mutualism attributable to alkaloids of fungal-origin. Now, modern genetic and molecular techniques enable the precise studies on evolutionary origin of endophytic Epichloë species, their coevolution with host grasses and identification the genetic variation that explains phenotypic diversity in ecologically relevant characteristics of Epichloë-grass associations. Here we briefly review the most recent findings in these areas of research using the present knowledge of the genetic variation that explains the biosynthetic pathways driving the diversity of alkaloids produced by the endophyte. These findings underscore the importance of genetic interplay between the fungus and the host in shaping their coevolution and ecological role in both natural grass ecosystems, and in the agricultural arena.}, number={6}, journal={Plant Mol Biol}, publisher={Springer Science \mathplus Business Media}, author={Saikkonen, Kari and Young, Carolyn A. and Helander, Marjo and Schardl, Christopher L.}, year={2015}, month={Nov}, pages={665–675} }
 @article{young_schardl_panaccione_florea_takach_charlton_moore_webb_jaromczyk_2015, title={Genetics, Genomics and Evolution of Ergot Alkaloid Diversity}, volume={7}, DOI={10.3390/toxins7041273}, abstractNote={The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine.}, number={4}, journal={Toxins}, publisher={MDPI AG}, author={Young, Carolyn and Schardl, Christopher and Panaccione, Daniel and Florea, Simona and Takach, Johanna and Charlton, Nikki and Moore, Neil and Webb, Jennifer and Jaromczyk, Jolanta}, year={2015}, month={Apr}, pages={1273–1302} }
 @article{chen_li_li_swoboda_young_sugawara_leuchtmann_schardl_2015, title={Two distinct Epichloe species symbiotic with Achnatherum inebrians, drunken horse grass}, volume={107}, DOI={10.3852/15-019}, abstractNote={Achnatherum inebrians, colloquially known as drunken horse grass, is associated with livestock toxicity in northern China. Epichloë gansuensis (Eg) was described from endophyte isolates from A. inebrians in Sunan County, Gansu Province, whereas a morphologically distinct variety, E. gansuensis var. inebrians (Ei), was described based on two isolates from A. inebrians seeds collected in Urumqi County, Xinjiang Province. Genome sequencing and alkaloid analyses also distinguish these taxa; the Ei isolates produce neurotropic lysergic acid amides (ergot alkaloids), and an Eg isolate produces paxilline (an indole-diterpene alkaloid). To better elucidate the taxonomic diversity of Epichloë spp. symbiotic with A. inebrians, we surveyed eight populations in Xinjiang, Gansu and Inner Mongolia provinces of China and analyzed their genotypes by multiplex PCR for alkaloid biosynthesis genes and mating-type genes. Genotypes consistent with Ei were present in all eight populations, of which they dominated seven. The Ei isolates were all mating type A and tested positive for the ergot alkaloid gene, dmaW. In contrast Eg isolates were all mating type B and had the indole-diterpene gene, idtG. The genome was sequenced from an Ei isolate from seeds collected in Xiahe County, Gansu, and compared to that of the varietal ex type isolate from Urumqi. Alkaloid genes and four different housekeeping genes were nearly identical between the two sequenced Ei isolates and were distinct from a sequenced Eg isolate. Phylogenetic analysis placed Ei, Eg and Epichloë sibirica into respective subclades of a clade that emanated from the base of the Epichloë phylogeny. Given its chemotypic, genotypic, morphological and phylogenetic distinctiveness, its widespread occurrence in rangelands of northern China, and its importance in livestock toxicity, we propose raising Ei to species rank as Epichloë inebrians.}, number={4}, journal={Mycologia}, publisher={Mycological Society of America}, author={Chen, L. and Li, X. and Li, C. and Swoboda, G. A. and Young, C. A. and Sugawara, K. and Leuchtmann, A. and Schardl, C. L.}, year={2015}, month={Apr}, pages={863–873} }
 @article{shoji_charlton_yi_young_craven_2015, title={Vegetative Hyphal Fusion and Subsequent Nuclear Behavior in Epichloë Grass Endophytes}, volume={10}, DOI={10.1371/journal.pone.0121875}, abstractNote={Epichloë species (including the former genus Neotyphodium) are fungal symbionts of many agronomically important forage grasses, and provide their grass hosts with protection from a wide range of biotic and abiotic stresses. Epichloë species include many interspecific hybrids with allodiploid-like genomes, which may provide the potential for combined traits or recombination to generate new traits. Though circumstantial evidence suggests that such interspecific hybrids might have arisen from nuclear fusion events following vegetative hyphal fusion between different Epichloë strains, this hypothesis has not been addressed empirically. Here, we investigated vegetative hyphal fusion and subsequent nuclear behavior in Epichloë species. A majority of Epichloë strains, especially those having a sexual stage, underwent self vegetative hyphal fusion. Vegetative fusion also occurred between two hyphae from different Epichloë strains. Though Epichloë spp. are uninucleate fungi, hyphal fusion resulted in two nuclei stably sharing the same cytoplasm, which might ultimately lead to nuclear fusion. In addition, protoplast fusion experiments gave rise to uninucleate putative hybrids, which apparently had two markers, one from each parent within the same nucleus. These results are consistent with the notion that interspecific hybrids arise from vegetative hyphal fusion. However, we also discuss additional factors, such as post-hybridization selection, that may be important to explain the recognized prevalence of hybrids in Epichloë species.}, number={4}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Shoji, Jun-ya and Charlton, Nikki D. and Yi, Mihwa and Young, Carolyn A. and Craven, Kelly D.}, editor={Kothe, ErikaEditor}, year={2015}, month={Apr}, pages={e0121875} }
 @article{takach_young_2014, title={Alkaloid Genotype Diversity of Tall Fescue Endophytes}, volume={54}, DOI={10.2135/cropsci2013.06.0423}, abstractNote={ABSTRACT Tall fescue { Festuca arundinacea Schreb. [syn Lolium arundinaceum (Schreb.) Darbysh.]}, a common forage grass used in temperate regions, forms mutually beneficial symbioses with hybrid epichloid endophytes, including the well‐described species Neotyphodium coenophialum . These endophytes confer many benefits to their plant hosts, including the production of bioactive alkaloids that deter insect and/or mammalian herbivory. Individual seeds from 176 tall fescue accessions were collected worldwide, including representatives of both Continental and Mediterranean morphotypes, and screened via polymerase chain reaction (PCR) for endophyte incidence and potential chemotypic diversity. A total of 89 endophyte‐infected seed lines were identified and screened with markers representing key genes within the four alkaloid biosynthesis loci, EAS (ergot alkaloids), IDT (indole‐diterpenes), LOL (lolines), and PER (peramine). Endophyte alkaloid genotypes based on alkaloid biosynthetic gene‐specific patterns were developed for each infected seed, and the alkaloid potential for each endophyte was predicted. Genotype profiles were compared to those of 11 known tall fescue endophytes to identify genotype variation within species as well as the prevalence of each species. Some Plant Introduction (PI) accessions arising from multiple germplasm sources were determined to contain two to three independent endophyte genotypes across the seeds tested. The results from this study provide insight into the genotype and chemotype diversity of endophytes present in populations of tall fescue worldwide and support evidence that tall fescue endophytes are host specific.}, number={2}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Takach, Johanna E. and Young, Carolyn A.}, year={2014}, pages={667} }
 @article{shymanovich_saari_lovin_jarmusch_jarmusch_musso_charlton_young_cech_faeth_2014, title={Alkaloid Variation Among Epichloid Endophytes of Sleepygrass (Achnatherum robustum) and Consequences for Resistance to Insect Herbivores}, volume={41}, DOI={10.1007/s10886-014-0534-x}, abstractNote={Epichloid endophytes are well known symbionts of many cool-season grasses that may alleviate environmental stresses for their hosts. For example, endophytes produce alkaloid compounds that may be toxic to invertebrate or vertebrate herbivores. Achnatherum robustum, commonly called sleepygrass, was aptly named due to the presence of an endophyte that causes toxic effects to livestock and wildlife. Variation in alkaloid production observed in two A. robustum populations located near Weed and Cloudcroft in the Lincoln National Forest, New Mexico, suggests two different endophyte species are present in these populations. Genetic analyses of endophyte-infected samples revealed major differences in the endophyte alkaloid genetic profiles from the two populations, which were supported with chemical analyses. The endophyte present in the Weed population was shown to produce chanoclavine I, paspaline, and terpendoles, so thus resembles the previously described Epichloë funkii. The endophyte present in the Cloudcroft population produces chanoclavineI, ergonovine, lysergic acid amide, and paspaline, and is an undescribed endophyte species. We observed very low survival rates for aphids feeding on plants infected with the Cloudcroft endophyte, while aphid survival was better on endophyte infected plants in the Weed population. This observation led to the hypothesis that the alkaloid ergonovine is responsible for aphid mortality. Direct testing of aphid survival on oat leaves supplemented with ergonovine provided supporting evidence for this hypothesis. The results of this study suggest that alkaloids produced by the Cloudcroft endophyte, specifically ergonovine, have insecticidal properties.}, number={1}, journal={J Chem Ecol}, publisher={Springer Science \mathplus Business Media}, author={Shymanovich, Tatsiana and Saari, Susanna and Lovin, Mary E. and Jarmusch, Alan K. and Jarmusch, Scott A. and Musso, Ashleigh M. and Charlton, Nikki D. and Young, Carolyn A. and Cech, Nadja B. and Faeth, Stanley H.}, year={2014}, pages={93–104} }
 @article{young_charlton_takach_swoboda_trammell_huhman_hopkins_2014, title={Characterization of Epichloë coenophiala within the US: are all tall fescue endophytes created equal?}, volume={2}, DOI={10.3389/fchem.2014.00095}, abstractNote={Tall fescue (Lolium arundinaceum) is a valuable and broadly adapted forage grass that occupies approximately 14 million hectares across the United States. A native to Europe, tall fescue was likely introduced into the US around the late 1800's. Much of the success of tall fescue can be attributed to Epichloë coenophiala (formerly Neotyphodium coenophialum) a seed borne symbiont that aids in host persistence. Epichloë species are capable of producing a range of alkaloids (ergot alkaloids, indole-diterpenes, lolines, and peramine) that provide protection to the plant host from herbivory. Unfortunately, most tall fescue within the US, commonly referred to as “Kentucky-31” (KY31), harbors the endophyte E. coenophiala that causes toxicity to grazing livestock due to the production of ergot alkaloids. Molecular analyses of tall fescue endophytes have identified four independent associations, representing tall fescue with E. coenophiala, Epichloë sp. FaTG-2, Epichloë sp. FaTG-3, or Epichloë sp. FaTG-4. Each of these Epichloë species can be further distinguished based on genetic variation that equates to differences in the alkaloid gene loci. Tall fescue samples were evaluated using markers to simple sequence repeats (SSRs) and alkaloid biosynthesis genes to determine endophyte strain variation present within continental US. Samples represented seed and tillers from the Suiter farm (Menifee County, KY), which is considered the originating site of KY31, as well as plant samples collected from 14 states, breeder's seed and plant introduction lines (National Plant Germplasm System, NPGS). This study revealed two prominent E. coenophiala genotypes based on presence of alkaloid biosynthesis genes and SSR markers and provides insight into endophyte variation within continental US across historical and current tall fescue samples.}, journal={Front. Chem.}, publisher={Frontiers Media SA}, author={Young, Carolyn A. and Charlton, Nikki D. and Takach, Johanna E. and Swoboda, Ginger A. and Trammell, Michael A. and Huhman, David V. and Hopkins, Andrew A.}, year={2014}, month={Nov} }
 @article{pan_bhardwaj_faulkner_nagabhyru_charlton_higashi_miller_young_grossman_schardl_2014, title={Ether bridge formation in loline alkaloid biosynthesis}, volume={98}, DOI={10.1016/j.phytochem.2013.11.015}, abstractNote={Lolines are potent insecticidal agents produced by endophytic fungi of cool-season grasses. These alkaloids are composed of a pyrrolizidine ring system and an uncommon ether bridge linking carbons 2 and 7. Previous results indicated that 1-aminopyrrolizidine was a pathway intermediate. We used RNA interference to knock down expression of lolO, resulting in the accumulation of an alkaloid identified as exo-1-acetamidopyrrolizidine based on high-resolution MS and NMR. Genomes of endophytes differing in alkaloid profiles were sequenced, revealing that those with mutated lolO accumulated exo-1-acetamidopyrrolizidine but no lolines. Heterologous expression of wild-type lolO complemented a lolO mutant, resulting in the production of N-acetylnorloline. These results indicated that the non-heme iron oxygenase, LolO, is required for ether bridge formation, probably through oxidation of exo-1-acetamidopyrrolizidine.}, journal={Phytochemistry}, publisher={Elsevier BV}, author={Pan, Juan and Bhardwaj, Minakshi and Faulkner, Jerome R. and Nagabhyru, Padmaja and Charlton, Nikki D. and Higashi, Richard M. and Miller, Anne-Frances and Young, Carolyn A. and Grossman, Robert B. and Schardl, Christopher L.}, year={2014}, month={Feb}, pages={60–68} }
 @article{schardl_chen_young_2014, title={Fungal Endophytes of Grasses and Morning Glories, and Their Bioprotective Alkaloids}, DOI={10.1002/9781118794623.ch7}, abstractNote={The fungal family Clavicipitaceae includes parasites and symbionts of invertebrate animals and plants, and is known for production of diverse alkaloids. Vertical transmission is characteristic of many symbioses of the epichloae with cool season grasses, as well as Periglandula species in morning glories. The epichloae are also known for their diverse chemotypes comprising various combinations of four different alkaloid classes namely ergot alkaloids, indole-diterpenes, peramine and loline alkaloids. This chapter first reviews the relationships among plant-associated Clavicipitaceae, and then discusses the bioprotective alkaloids that they produce. Particularly interesting features of plant-Clavicipitaceae symbioses include the manner of fungal colonization of infected plant tissues, the location on the plant where they fruit, and whether they are capable of vertical transmission. Many Clavicipitaceae have been described as “epibiotic,” meaning that they are restricted to growth on plant surfaces or between different host tissues, but never are observed to grow between cells within tissues.}, journal={Natural Products}, publisher={Wiley-Blackwell}, author={Schardl, Christopher L. and Chen, Li and Young, Carolyn A.}, year={2014}, month={Mar}, pages={125–145} }
 @article{arif_dobhal_garrido_orquera_espíndola_young_ochoa-corona_marek_garzón_2014, title={Highly Sensitive End-Point PCR and SYBR Green qPCR Detection of Phymatotrichopsis omnivora , Causal Fungus of Cotton Root Rot}, volume={98}, DOI={10.1094/pdis-05-13-0505-re}, abstractNote={Phymatotrichopsis omnivora, the causal pathogen of cotton root rot, is a devastating ascomycete that affects numerous important dicotyledonous plants grown in the southwestern United States and northern Mexico. P. omnivora is notoriously difficult to isolate from infected plants; therefore methods for accurate and sensitive detection directly from symptomatic and asymptomatic plant samples are needed for disease diagnostics and pathogen identification. Primers were designed for P. omnivora based on consensus sequences of the nuclear ribosomal internal transcribed spacer (ITS) region of geographically representative isolates. Primers were compared against published P. omnivora sequences and validated against DNA from P. omnivora isolates and infected plant samples. The primer combinations amplified products from a range of P. omnivora isolates representative of known ITS haplotypes using standard end-point polymerase chain reaction (PCR) methodology. The assays detected P. omnivora from infected root samples of cotton (Gossypium hirsutum) and alfalfa (Medicago sativa). Healthy plants and other relevant root pathogens did not produce PCR products with the P. omnivora-specific primers. Primer pair PO2F/PO2R was the most sensitive in end-point PCR assays and is recommended for use for pathogen identification from mycelial tissue and infected plant materials when quantitative PCR (qPCR) is not available. Primer pair PO3F/PO2R was highly sensitive (1 fg) when used in SYBR Green qPCR assays and is recommended for screening of plant materials potentially infected by P. omnivora or samples with suboptimal DNA quality. The described PCR-based detection methods will be useful for rapid and sensitive screening of infected plants in diagnostic laboratories, plant health inspections, and plant breeding programs.}, number={9}, journal={Plant Disease}, publisher={Scientific Societies}, author={Arif, M. and Dobhal, S. and Garrido, P. A. and Orquera, G. K. and Espíndola, A. S. and Young, C. A. and Ochoa-Corona, F. M. and Marek, S. M. and Garzón, C. D.}, year={2014}, month={Sep}, pages={1205–1212} }
 @article{charlton_craven_afkhami_hall_ghimire_young_2014, title={Interspecific hybridization and bioactive alkaloid variation increases diversity in endophytic Epichloë species of Bromus laevipes}, volume={90}, DOI={10.1111/1574-6941.12393}, abstractNote={Studying geographic variation of microbial mutualists, especially variation in traits related to benefits they provide their host, is critical for understanding how these associations impact key ecological processes. In this study, we investigate the phylogenetic population structure of Epichloë species within Bromus laevipes, a native cool-season bunchgrass found predominantly in California. Phylogenetic classification supported inference of three distinct Epichloë taxa, of which one was nonhybrid and two were interspecific hybrids. Inheritance of mating-type idiomorphs revealed that at least one of the hybrid species arose from independent hybridization events. We further investigated the geographic variation of endophyte-encoded alkaloid genes, which is often associated with key benefits of natural enemy protection for the host. Marker diversity at the ergot alkaloid, loline, indole-diterpene, and peramine loci revealed four alkaloid genotypes across the three identified Epichloë species. Predicted chemotypes were tested using endophyte-infected plant material that represented each endophyte genotype, and 11 of the 13 predicted alkaloids were confirmed. This multifaceted approach combining phylogenetic, genotypic, and chemotypic analyses allowed us to reconstruct the diverse evolutionary histories of Epichloë species present within B. laevipes and highlight the complex and dynamic processes underlying these grass-endophyte symbioses.}, number={1}, journal={FEMS Microbiol Ecol}, publisher={Oxford University Press (OUP)}, author={Charlton, Nikki D. and Craven, Kelly D. and Afkhami, Michelle E. and Hall, Bradley A. and Ghimire, Sita R. and Young, Carolyn A.}, year={2014}, month={Aug}, pages={276–289} }
 @article{rogers_young_mosali_norton_hopkins_2014, title={Stockpiled Forage Yield and Nutritive Value of Summer-Dormant and Summer-Active Tall Fescue in a Marginal Environment}, volume={12}, DOI={10.2134/fg-2014-0065-rs}, abstractNote={Stockpiled forage for grazing during fall and winter can reduce winter feed costs for livestock producers. Tall fescue is used successfully as stockpiled forage in areas of the Midwest and Southeast. In the Southern Great Plains, drought conditions limit production, resulting in summer-active variety stand failure and summer-dormant variety persistence. This study compared the stockpiled production and nutritive value of summer-dormant type to summer-active type tall fescue [Lolium arundinaceum (Schreb.) Darbysh.]. The yield and nutritive value of stockpiled summerdormant tall fescue were similar to that of summer-active tall fescue. At the end of the study, severe drought occurred in the area, resulting in summer-active failure but summer-dormant persistence. BACKGROUND}, number={1}, journal={Forage and Grazinglands}, publisher={American Society of Agronomy}, author={Rogers, James K. and Young, Carolyn A. and Mosali, Jagadeesh and Norton, Shawn L. and Hopkins, Andrew A.}, year={2014}, pages={0} }
 @article{schardl_young_pan_florea_takach_panaccione_farman_webb_jaromczyk_charlton_et al._2013, title={Currencies of mutualisms: sources of alkaloid genes in vertically transmitted epichloae}, volume={6;5(6):1064-88}, journal={Toxins}, author={Schardl, C.L. and Young, C.A. and Pan, J. and Florea, S. and Takach, J.E. and Panaccione, D.G. and Farman, M.L. and Webb, J.S. and Jaromczyk, J. and Charlton, N.D. and et al.}, year={2013}, month={Jun} }
 @article{scott_young_saikia_mcmillan_monahan_koulman_astin_eaton_bryant_wrenn_et al._2013, title={Deletion and Gene Expression Analyses Define the Paxilline Biosynthetic Gene Cluster in Penicillium paxilli}, volume={5}, DOI={10.3390/toxins5081422}, abstractNote={The indole-diterpene paxilline is an abundant secondary metabolite synthesized by Penicillium paxilli. In total, 21 genes have been identified at the PAX locus of which six have been previously confirmed to have a functional role in paxilline biosynthesis. A combination of bioinformatics, gene expression and targeted gene replacement analyses were used to define the boundaries of the PAX gene cluster. Targeted gene replacement identified seven genes, paxG, paxA, paxM, paxB, paxC, paxP and paxQ that were all required for paxilline production, with one additional gene, paxD, required for regular prenylation of the indole ring post paxilline synthesis. The two putative transcription factors, PP104 and PP105, were not co-regulated with the pax genes and based on targeted gene replacement, including the double knockout, did not have a role in paxilline production. The relationship of indole dimethylallyl transferases involved in prenylation of indole-diterpenes such as paxilline or lolitrem B, can be found as two disparate clades, not supported by prenylation type (e.g., regular or reverse). This paper provides insight into the P. paxilli indole-diterpene locus and reviews the recent advances identified in paxilline biosynthesis.}, number={8}, journal={Toxins}, publisher={MDPI AG}, author={Scott, Barry and Young, Carolyn and Saikia, Sanjay and McMillan, Lisa and Monahan, Brendon and Koulman, Albert and Astin, Jonathan and Eaton, Carla and Bryant, Andrea and Wrenn, Ruth and et al.}, year={2013}, month={Aug}, pages={1422–1446} }
 @article{young_hume_mcculley_2013, title={FORAGES AND PASTURES SYMPOSIUM: Fungal endophytes of tall fescue and perennial ryegrass: Pasture friend or foe?}, volume={91}, DOI={10.2527/jas.2012-5951}, abstractNote={Tall fescue [Lolium arundinaceum (Schreb.) Darbysh. syn. Festuca arundinacea Schreb.] and perennial ryegrass (Lolium perenne L.) are important perennial forage grasses utilized throughout the moderate- to high-rainfall temperate zones of the world. These grasses have coevolved with symbiotic fungal endophytes (Epichloë/Neotyphodium spp.) that can impart bioactive properties and environmental stress tolerance to the grass compared with endophyte-free individuals. These endophytes have proven to be very important in pastoral agriculture in the United States, New Zealand, and Australia, where forage grasses are the principal feed for grazing ruminants. In this review, we describe the biology of these grass-endophyte associations and implications for the livestock industries that are dependent on these forages. Endophyte alkaloid production is put in context with endophyte diversity, and we illustrate how this has facilitated utilization of grasses infected with different endophyte strains that reduce livestock toxicity issues. Utilization of tall fescue and use of perennial ryegrass in the United States, New Zealand, and Australia are compared, and management strategies focused predominantly on the success of endophyte-infected perennial ryegrass in New Zealand and Australia are discussed. In addition, we consider the impact of grass-endophyte associations on the sustainability of pasture ecosystems and their likely response to future changes in climate.}, number={5}, journal={Journal of Animal Science}, publisher={American Society of Animal Science (ASAS)}, author={Young, C. A. and Hume, D. E. and McCulley, R. L.}, year={2013}, month={Jan}, pages={2379–2394} }
 @article{schardl_young_hesse_amyotte_andreeva_calie_fleetwood_haws_moore_oeser_et al._2013, title={Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci}, volume={9}, DOI={10.1371/journal.pgen.1003323}, abstractNote={The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids of four distinct classes, all of which deter insects, and some—including the infamous ergot alkaloids—have potent effects on mammals. The exceptional chemotypic diversity of the epichloae may relate to their broad range of host interactions, whereby some are pathogenic and contagious, others are mutualistic and vertically transmitted (seed-borne), and still others vary in pathogenic or mutualistic behavior. We profiled the alkaloids and sequenced the genomes of 10 epichloae, three ergot fungi (Claviceps species), a morning-glory symbiont (Periglandula ipomoeae), and a bamboo pathogen (Aciculosporium take), and compared the gene clusters for four classes of alkaloids. Results indicated a strong tendency for alkaloid loci to have conserved cores that specify the skeleton structures and peripheral genes that determine chemical variations that are known to affect their pharmacological specificities. Generally, gene locations in cluster peripheries positioned them near to transposon-derived, AT-rich repeat blocks, which were probably involved in gene losses, duplications, and neofunctionalizations. The alkaloid loci in the epichloae had unusual structures riddled with large, complex, and dynamic repeat blocks. This feature was not reflective of overall differences in repeat contents in the genomes, nor was it characteristic of most other specialized metabolism loci. The organization and dynamics of alkaloid loci and abundant repeat blocks in the epichloae suggested that these fungi are under selection for alkaloid diversification. We suggest that such selection is related to the variable life histories of the epichloae, their protective roles as symbionts, and their associations with the highly speciose and ecologically diverse cool-season grasses.}, number={2}, journal={PLoS Genet}, publisher={Public Library of Science (PLoS)}, author={Schardl, Christopher L. and Young, Carolyn A. and Hesse, Uljana and Amyotte, Stefan G. and Andreeva, Kalina and Calie, Patrick J. and Fleetwood, Damien J. and Haws, David C. and Moore, Neil and Oeser, Birgitt and et al.}, editor={Heitman, JosephEditor}, year={2013}, month={Feb}, pages={e1003323} }
 @article{singh_interrante_butler_young_2012, title={Characterization and Effectiveness of Co-inoculation of Strains on Annual Medics}, volume={0}, DOI={10.2135/cropsci2011.08.0459}, abstractNote={Selection and identi! cation of better-adapted annual medics with an appropriate rhizobia inoculum is crucial for improved forage quality and yield. The objectives of this study were to characterize 11 rhizobial strains used for an effectiveness study on annual medics and generate an inoculum blend suitable for annual medic species adapted to the southern Great Plains. Each strain was compared to reference rhizobia strains by polymerase chain reaction (PCR) based on repetitive sequences (rep-PCR) and ribosomal gene sequences and analyzed for plant growth promo ting (PGP) activities. Genetic characterization separated the strains into two groups belonging to Sinorhizobium medicae (seven isolates) and Sinorhizobium meliloti (four isolates). Three of the 11 strains tested positive for the PGP activities of indole acetic acid production and phosphate solubilization. A blend of three strains (NFmix3, consisting of WSM1115, 102F85, and M49), of which two were positive for PGP activities, was used in an effectiveness study for the annual medics Medicago minima (L.) Bartal., Medicago orbicularis (L.) Bartal., Medicago rigidula (L.) All., and Medicago rigiduloides E. Small. The NFmix3 association with three of the four annual medic species resulted in equivalent biomass production as that of the single speci! c strain. The NFmix3 blend would be suitable and more economic for use with a mixture of medic species that may provide expansion of the grazing season.}, number={0}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Singh, Ruchi and Interrante, Sindy M. and Butler, Twain J. and Young, Carolyn A.}, year={2012}, pages={1} }
 @article{schardl_young_faulkner_florea_pan_2012, title={Chemotypic diversity of epichloae, fungal symbionts of grasses}, volume={5}, DOI={10.1016/j.funeco.2011.04.005}, abstractNote={The epichloid fungi – comprising sexual Epichloë species and asexual Neotyphodium species – are symbionts of cool-season grasses (subfamily Poöideae), mostly vertically transmissible (seedborne), and well known for production of anti-herbivore alkaloids. Four classes of alkaloids are known to be produced by epichloae: lolines (saturated aminopyrrolizidines), indole–diterpenes, ergot alkaloids, and peramine. There is a wide range of chemotypic diversity among and even within epichloid species. At the molecular level, this diversity may in part reflect the telomeric association of two of the four alkaloid biosynthesis gene clusters. Ecologically, the chemotypic diversity within species may reflect frequency-dependent selection for the alkaloids, which provide defences against insects and, in some cases, vertebrates, but can be expensive to produce. Interspecific hybridization, common among asexual epichloae, can pyramid the alkaloid biosynthesis genes. Compared to sexual epichloae, many asexual epichloae produce high levels of alkaloids – particularly lolines – suggesting that strict vertical transmission selects for enhanced capability of host protection.}, number={3}, journal={Fungal Ecology}, publisher={Elsevier BV}, author={Schardl, Christopher L. and Young, Carolyn A. and Faulkner, Jerome R. and Florea, Simona and Pan, Juan}, year={2012}, month={Jun}, pages={331–344} }
 @article{schardl_young_faulkner_pan_2012, title={Chemotypic diversity of epichloae, fungal symbionts of grasses}, volume={30;5(3):331-44}, journal={fungal ecology}, author={Schardl, C.L. and Young, C.A. and Faulkner, Florea S., JR and Pan, J.}, year={2012}, month={Jun} }
 @article{parish_parish_best_boland_young_2012, title={Effects of selected endophyte and tall fescue cultivar combinations on steer grazing performance, indicators of fescue toxicosis, feedlot performance, and carcass traits-}, volume={91}, DOI={10.2527/jas.2011-4725}, abstractNote={Five tall fescue [Lolium arundinaceum (Schreb.)] pastures [wild-type 'Kentucky-31' with 78.0% of plants infected with ergot alkaloid-producing endophyte Neotyphodium coenophialum (KY31 E+), 'Jesup' AR542 endophyte-infected contaminated with 30.3% tall fescue containing ergot alkaloid producing-endophyte (Jesup AR542 E+); 'GA-186' AR584 endophyte-infected contaminated with 11.8% tall fescue containing ergot alkaloid producing-endophyte (AGRFA 140); 'PDF' AR584 endophyte-infected contaminated with 5.5% tall fescue containing ergot alkaloid producing-endophyte (AGRFA 144); and 'KYFA 9301' AR584 endophyte-infected contaminated with 10.0% tall fescue containing ergot alkaloid producing-endophyte (AGRFA 150)] were compared for steer growth performance, toxicity, feedlot performance, and carcass traits. Steers (mean initial BW=322 kg) grazed pastures for 84 d in spring and 56 d in autumn for 2 yr. Steers were shipped after grazing in Prairie, MS, to Macedonia, IA, for finishing. Mean herbage mass was not different (P=0.15) among pastures. Posttreatment (d 28+) serum prolactin concentrations were depressed (P=0.013) on KY31 E+. Steers grazing KY31 E+ had greater (P<0.01) posttreatment rectal temperatures during spring. Spring hair coat scores were greatest (P<0.01) on KY31 E+ at d 56 and 84. Steer ADG was least (P<0.01) on KY31 E+ in spring and depressed (P=0.014) on KY31 E+ and Jesup AR542 E+ in autumn. Spring grazing ADG was greater (P=0.049) on AGRFA 150 than Jesup AR542 E+ and AGRFA 140. No BW differences (P=0.09) among pastures were seen at reimplant during feedlot finishing. Pasture had no effect on ADG after reimplant (P=0.68), days on feed (P=0.56), or final BW (P=0.55). Exposure to fescue toxicosis did not affect (P≥0.19) carcass traits. Hair coat price discounts applied for spring-grazed steers on KY-31 E+ affected (P<0.01) initial steer monetary values. There were no pasture differences for finishing costs (P≥0.61) or final carcass value (P=0.59). Elite tall fescue cultivar and novel endophyte combinations improve growth performance of grazing calves over KY31 E+. Producers whose calves graze KY-31 E+ tall fescue should consider retaining ownership of these cattle through feedlot finishing to avoid market discounts and capture value from compensatory BW gains during finishing.}, number={1}, journal={Journal of Animal Science}, publisher={American Society of Animal Science (ASAS)}, author={Parish, J. A. and Parish, J. R. and Best, T. F. and Boland, H. T. and Young, C. A.}, year={2012}, month={Oct}, pages={342–355} }
 @article{iannone_novas_young_battista_schardl_2012, title={Endophytes of native grasses from South America: Biodiversity and ecology}, volume={5}, DOI={10.1016/j.funeco.2011.05.007}, abstractNote={We review and present preliminary results of studies on cool-season grass endophytes native to South America. These fungi have been studied only in Argentina, where they have been detected in 36 native grass species. The hybrid Neotyphodium tembladerae is present in an extremely wide host range found in diverse environmental conditions, but some other endophytes seem to be strictly associated with one host species in a particular environment. In host species that inhabit different environments, the incidence of endophytes is highly variable among populations and in most of the cases is clearly associated with environmental conditions. In these native grasses, Neotyphodium presents a mutualistic behaviour, conferring enhanced growth, promoting the symbiosis with arbuscular mycorrhizal fungi, and inhibiting growth of pathogenic fungi. In native forage grasses, preliminary analyses indicate that some Argentinian endophytes can produce lolines but are unlikely to produce lolitrem B or ergot alkaloids.}, number={3}, journal={Fungal Ecology}, publisher={Elsevier BV}, author={Iannone, Leopoldo J. and Novas, María V. and Young, Carolyn A. and Battista, José P. De and Schardl, Christopher L.}, year={2012}, month={Jun}, pages={357–363} }
 @article{charlton_craven_mittal_hopkins_young_2012, title={Epichloe canadensis, a new interspecific epichloid hybrid symbiotic with Canada wildrye (Elymus canadensis)}, volume={104}, DOI={10.3852/11-403}, abstractNote={Many Epichloë endophytes found in cool-season grasses are interspecific hybrids possessing much or all of the genomes of two or three progenitors. Here we characterize Epichloë canadensis sp. nov., a hybrid species inhabiting the grass species Elymus canadensis native to North America. Three distinct morphotypes were identified that were separated into two groups by molecular phylogenetic analysis. Sequence analysis of the translation elongation factor 1-α (tefA) and β-tubulin (tubB) genes revealed two copies in all isolates examined. Phylogenetic analyses indicated that allele 1 of each gene was derived from Epichloë amarillans and allele 2 from Epichloë elymi. This is the first documentation of an interspecific hybrid endophyte derived from parents of strictly North American origins. Alkaloid gene profiling using primers specific to genes in the peramine, loline, indole-diterpene and ergot alkaloid pathways may indicate chemotypic variation in the ergot alkaloid and loline pathways between the assigned morphotypes. All isolates have the gene enabling the production of peramine but lack genes in the indole-diterpene biosynthesis pathway. Morphology and phylogenetic evidence support the designation of isolates from El. canadensis as a new interspecific hybrid species.}, number={5}, journal={Mycologia}, publisher={Mycological Society of America}, author={Charlton, N. D. and Craven, K. D. and Mittal, S. and Hopkins, A. A. and Young, C. A.}, year={2012}, month={Jun}, pages={1187–1199} }
 @article{takach_mittal_swoboda_bright_trammell_hopkins_young_2012, title={Genotypic and Chemotypic Diversity of Neotyphodium Endophytes in Tall Fescue from Greece}, volume={78}, DOI={10.1128/aem.01084-12}, abstractNote={ABSTRACT Epichloid endophytes provide protection from a variety of biotic and abiotic stresses for cool-season grasses, including tall fescue. A collection of 85 tall fescue lines from 15 locations in Greece, including both Continental and Mediterranean germplasm, was screened for the presence of native endophytes. A total of 37 endophyte-infected lines from 10 locations were identified, and the endophytes were classified into five distinct groups (G1 to G5) based on physical characteristics such as colony morphology, growth rate, and conidial morphology. These classifications were supported by phylogenetic analyses of housekeeping genes tefA and tubB, and the endophytes were further categorized as Neotyphodium coenophialum isolates (G1, G4, and G5) or Neotyphodium sp. FaTG-2 (Festuca arundinacea taxonomic group 2 isolates (G2 and G3). Analyses of the tall fescue matK chloroplast genes indicated a population-wide, host-specific association between N. coenophialum and Continental tall fescue and between FaTG-2 and Mediterranean tall fescue that was also reflected by differences in colonization of host tillers by the native endophytes. Genotypic analyses of alkaloid gene loci combined with chemotypic (chemical phenotype) profiles provided insight into the genetic basis of chemotype diversity. Variation in alkaloid gene content, specifically the presence and absence of genes, and copy number of gene clusters explained the alkaloid diversity observed in the endophyte-infected tall fescue, with one exception. The results from this study provide insight into endophyte germplasm diversity present in living tall fescue populations.}, number={16}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Takach, J. E. and Mittal, S. and Swoboda, G. A. and Bright, S. K. and Trammell, M. A. and Hopkins, A. A. and Young, C. A.}, year={2012}, month={Jun}, pages={5501–5510} }
 @article{dierking_young_kallenbach_2012, title={Mediterranean and Continental Tall Fescue: I. Effects of Endophyte Status on Leaf Extension, Proline, Mono- and Disaccharides, Fructan, and Freezing Survivability}, volume={52}, DOI={10.2135/cropsci2011.03.0159}, abstractNote={ABSTRACT Tall fescue [ Festuca arundinacea Schreb. syn. Lolium arundinaceum (Schreb.) Darbysh.] is widely used for hay and pasture in the Eastern regions of the United States, with new types of Mediterranean tall fescue possessing superior growth under cool growing conditions. However, they do not survive Midwestern winters. To date, little research has examined the role of endophyte infection on the ability of tall fescue to grow under cold conditions or survive freezing conditions. This study's objectives determined the endophyte's role in tall fescue growth and production of metabolites for nonfreezing conditions. Additionally, the role of endophyte infection on the ability of plants to survive freezing temperatures was determined. This experiment used five genotypes of tall fescue. Half of the plants from each genotype were endophyte infected (E+), with the remaining genotypes being endophyte free (E–). We report for the first time the effects of endophyte status on proline, simple sugars, and fructan accumulation when plants were grown under cold, nonfreezing temperatures and the survivability at various freezing temperatures. Endophyte removal only affected fructan concentrations at 4.5°C; however, plant genotype affected leaf extension rate, proline, sugars, and fructan concentration. The freezing test found no effect of the endophyte on tiller survival, while plant genotype was significant. These data indicate that endophyte removal has little influence on the measured traits, and plant genotype is more critical for survival under cold conditions.}, number={1}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Dierking, R. M. and Young, C. A. and Kallenbach, R. L.}, year={2012}, pages={451} }
 @article{fleetwood_khan_johnson_young_mittal_wrenn_hesse_foster_schardl_scott_2011, title={Abundant Degenerate Miniature Inverted-Repeat Transposable Elements in Genomes of Epichloid Fungal Endophytes of Grasses}, volume={3}, DOI={10.1093/gbe/evr098}, abstractNote={Miniature inverted-repeat transposable elements (MITEs) are abundant repeat elements in plant and animal genomes; however, there are few analyses of these elements in fungal genomes. Analysis of the draft genome sequence of the fungal endophyte Epichloë festucae revealed 13 MITE families that make up almost 1% of the E. festucae genome, and relics of putative autonomous parent elements were identified for three families. Sequence and DNA hybridization analyses suggest that at least some of the MITEs identified in the study were active early in the evolution of Epichloë but are not found in closely related genera. Analysis of MITE integration sites showed that these elements have a moderate integration site preference for 5′ genic regions of the E. festucae genome and are particularly enriched near genes for secondary metabolism. Copies of the EFT-3m/Toru element appear to have mediated recombination events that may have abolished synthesis of two fungal alkaloids in different epichloae. This work provides insight into the potential impact of MITEs on epichloae evolution and provides a foundation for analysis in other fungal genomes.}, number={0}, journal={Genome Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Fleetwood, D. J. and Khan, A. K. and Johnson, R. D. and Young, C. A. and Mittal, S. and Wrenn, R. E. and Hesse, U. and Foster, S. J. and Schardl, C. L. and Scott, B.}, year={2011}, month={Sep}, pages={1253–1264} }
 @article{interrante_singh_islam_stein_young_butler_2011, title={Effectiveness of Inoculants on Annual Medics}, volume={51}, DOI={10.2135/cropsci2011.02.0076}, abstractNote={Annual medics (Medicago spp.) have potential to be important forage legumes in the south- ern Great Plains of the United States. Currently there are no commercial medic species-spe- cifi c rhizobia strains identifi ed for their inocu- lation. However, commercially available alfalfa (Medicago sativa L.) inoculants may be effec- tive at successfully nodulating annual medics. The objective of this study was to determine the relevant symbiotic rhizobial partner in associa- tion with seven annual medics. A greenhouse experiment arranged in three replications of a randomized complete block design quantifi ed rhizobium effectiveness index and shoot and root dry matter (DM) of Medicago arabica (L.) Huds., Medicago lupulina L., Medicago minima (L.) Bartal., Medicago orbicularis (L.) Bartal., Medicago polymorpha L., Medicago rigidula (L.) All., and Medicago rigiduloides E. Small when inoculated with fi ve Sinorhizobium spp. strains (M2, M49, Nitragin A, Nitragin N (a blend of three isolates), and WSM1115) and an untreated control (UTC). Strain M49 was the only strain that effectively nodulated M. rigiduloides, while Nitragin A commercial alfalfa strain was only effective on M. rigidula. Inoculants M2, Nitragin N, and WSM1115 were able to effectively nodu- late M. polymorpha, M. arabica, M. minima, and M. orbicularis. To a lesser extent, M. lupulina, M. minima, and M. orbicularis were also effectively nodulated by Nitragin A alfalfa strain. These data indicate that there are differences in rhi- zobia specifi city of annual medic species, and further research is warranted to improve nodu- lation of these legumes in the fi eld.}, number={5}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Interrante, Sindy M. and Singh, Ruchi and Islam, M. Anowarul and Stein, Jimmy D. and Young, Carolyn A. and Butler, Twain J.}, year={2011}, pages={2249} }
 @article{hopkins_young_butler_bouton_2011, title={Registration of ‘Texoma’ MaxQ II Tall Fescue}, volume={5}, DOI={10.3198/jpr2010.02.0082crc}, abstractNote={‘Texoma’ MaxQ II (Reg. No. CV‐99; PI 659316) tall fescue [ Lolium arundinaceum (Schreb.) S.J. Darbysh. = Festuca arundinacea Schreb.], also tested under the designations PDF 584, PDF AR584, and AGRFA 144, was developed by the Samuel Roberts Noble Foundation in cooperation with AgResearch Ltd. and was released in 2009. The Continental, summer active, tall fescue ecotype PDF E+ was collected near Ardmore in south‐central Oklahoma and inoculated with the novel endophyte [ Neotyphodium coenophialum (Morgan‐Jones & Gams.) Glenn, Bacon, & Hanlin comb. nov.] AR584. Forage yields of Texoma MaxQ II in Oklahoma have been as much as 20% greater than those of ‘Jesup’ MaxQ. Likewise, persistence in the south‐central USA and seed yield in Oregon have been equal or superior to those of Jesup MaxQ. Transmission of viable endophyte in breeder and foundation seed of Texoma MaxQ II has been consistently greater than 90%. The average daily gain of lambs grazing Texoma MaxQ II has been twice that of animals grazing ‘Kentucky 31’ infected with a toxic endophyte (139 vs. 68 g d −1 , respectively). Texoma MaxQ II was released because of its broad adaptation to the south‐central USA, improved persistence, and forage yield.}, number={1}, journal={Journal of Plant Registrations}, publisher={American Society of Agronomy}, author={Hopkins, A. A. and Young, C. A. and Butler, T. J. and Bouton, J. H.}, year={2011}, pages={14} }
 @article{hopkins_young_panaccione_simpson_mittal_bouton_2010, title={Agronomic Performance and Lamb Health among Several Tall Fescue Novel Endophyte Combinations in the South-Central USA}, volume={50}, DOI={10.2135/cropsci2009.08.0473}, abstractNote={Deployment of novel endophytes [Neotyphodium coenophialum (Morgan-Jones & Gams) Glenn, Bacon & Hanlin] may expand the use of tall fescue [Lolium arundinaceum (Schreb.) S.J. Darbyshire] in the south-central United States. Our objectives were to compare agronomic performance of, and health of lambs (Ovis aries) grazing, several tall fescue-novel endophyte combinations in the south-central United States. Two tall fescue populations (97TF1 and PDF) were inoculated with four novel endophytes (AR514, AR524, AR542, and AR584). At most locations, persistence of the eight combinations under grazing by beef cattle (Bos taurus) was similar to Jesup MaxQ. However, the combination PDF AR584 had greater persistence than Jesup MaxQ at Booneville, AR (24 vs. 14% stands, respectively) and Burneyville, OK (31 vs. 8% stands, respectively). Forage yields of the eight combinations were comparable to Jesup MaxQ, with PDF AR584 having greater yields on occasion. Lambs grazing PDF AR584, 97TF1 AR584, PDF AR542, PDF AR524, and Jesup MaxQ gained an average of >139 g d -1 , more than twice the 68 g d -1 gained by animals grazing endophyte-infected Kentucky-31. Prolactin and urinary alkaloid data indicated no detrimental health effects for animals grazing the novel endophyte combinations. Several tall fescue-novel endophyte combinations, and in particular PDF AR584, appear to be suited for the south-central United States, based on competitive agronomic performance and health of grazing lambs.}, number={4}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Hopkins, A. A. and Young, C. A. and Panaccione, D. G. and Simpson, W. R. and Mittal, S. and Bouton, J. H.}, year={2010}, pages={1552} }
 @article{uppalapati_young_marek_mysore_2010, title={Phymatotrichum (cotton) root rot caused by Phymatotrichopsis omnivora : retrospects and prospects}, volume={11}, DOI={10.1111/j.1364-3703.2010.00616.x}, abstractNote={UNLABELLED
Phymatotrichum (cotton or Texas) root rot is caused by the soil-borne fungus Phymatotrichopsis omnivora (Duggar) Hennebert. The broad host range of the fungus includes numerous crop plants, such as alfalfa and cotton. Together with an overview of existing knowledge, this review is aimed at discussing the recent molecular and genomic approaches that have been undertaken to better understand the disease development at the molecular level with the ultimate goal of developing resistant germplasm.


TAXONOMY
Phymatotrichopsis omnivora (Duggar) Hennebert [synonym Phymatotrichum omnivorum (Shear) Duggar] is an asexual fungus with no known sexual stage. Mitosporic botryoblastospores occasionally form on epigeous spore mats in nature, but perform no known function and do not contribute to the disease cycle. The fungus has been affiliated erroneously with the polypore basidiomycete Sistotrema brinkmannii (Bres.) J. Erikss. Recent phylogenetic studies have placed this fungus in the ascomycete order Pezizales. HOST RANGE AND DISEASE SYMPTOMS: The fungus infects most dicotyledonous field crops, causing significant losses to cotton, alfalfa, grape, fruit and nut trees and ornamental shrubs in the south-western USA, northern Mexico and possibly parts of central Asia. However, this fungus does not cause disease in monocotyledonous plants. Symptoms include an expanding tissue collapse (rot) of infected taproots. In above-ground tissues, the root rot results in vascular discoloration of the stem and rapid wilting of the leaves without abscission, and eventually the death of the plant. Characteristic mycelial strands of the pathogen are typically present on the root's surface, aiding diagnosis.


PATHOGENICITY
Confocal imaging of P. omnivora interactions with Medicago truncatula roots revealed that infecting hyphae do not form any specialized structures for penetration and mainly colonize cortical cells and eventually form a mycelial mantle covering the root's surfaces. Cell wall-degrading enzymes have been implicated in penetration and symptom development. Global gene expression profiling of infected M. truncatula revealed roles for jasmonic acid, ethylene and the flavonoid pathway during disease development. Phymatotrichopsis omnivora apparently evades induced host defences and may suppress the host's phytochemical defences at later stages of infection to favour pathogenesis.


DISEASE CONTROL
No consistently effective control measures are known. The long-lived sclerotia and facultative saprotrophism of P. omnivora make crop rotation ineffective. Chemical fumigation methods are not cost-effective for most crops. Interestingly, no genetic resistance has been reported in any of the susceptible crop species.}, number={3}, journal={Molecular Plant Pathology}, publisher={Wiley-Blackwell}, author={UPPALAPATI, SRINIVASA RAO and YOUNG, CAROLYN A. and MAREK, STEPHEN M. and MYSORE, KIRANKUMAR S.}, year={2010}, month={May}, pages={325–334} }
 @article{ghimire_rudgers_charlton_young_craven_2010, title={Prevalence of an intraspecific Neotyphodium hybrid in natural populations of stout wood reed (Cinna arundinacea L.) from eastern North America}, volume={103}, DOI={10.3852/10-154}, abstractNote={Members of genus Neotyphodium are asexual derivatives of sexual Epichloë species and maintain endophytic relationships with many cool-season grasses. Most Neotyphodium species analyzed so far are interspecific hybrids with combined or partial genomes of two or three ancestral species. In this study we characterized Neotyphodium isolates from Cinna arundinacea, a perennial cool-season grass from eastern North America. A total of 23 isolates grouping into two distinct morphotypes were obtained from five local populations of C. arundinacea. PCR amplification and cloning of translation-elongation factor 1-α (tefA) and β-tubulin (tubB) genes of 10 isolates comprising both morphotypes (two isolates per location) revealed that all 10 contain two copies of tefA and tubB genes. Surprisingly phylogenetic analysis of mainly non-coding sequence from these genes revealed that both copies in each isolate were inherited from Epichloë typhina ancestors, indicating that the C. arundinacea endophytes arose through intraspecific hybridization between two E. typhina progenitors with extant relatives infecting hosts Poa nemoralis and Poa pratensis. Furthermore the tefA sequences were identical between isolates, as were tubB sequences, despite obvious morphological differences. Profiling of alkaloid biosynthetic genes from these isolates indicated the presence of the peramine biosynthetic gene (perA) and the absence of genes required for biosynthesis of lolines, indole-diterpenes and ergot alkaloids. Thus this endophyte is potentially capable of producing peramine in planta and providing protection to its host from insect pests. The absence of genes for indole-diterpenes and ergot alkaloid biosynthesis makes this endophyte a candidate for agricultural applications. Based on our phylogenetic analysis, alkaloid profiling and description of morphological characteristics, we propose the name Neotyphodium schardlii for these isolates from C. arundinacea, a new member of genus Neotyphodium and the first described to have arisen through intraspecific hybridization.}, number={1}, journal={Mycologia}, publisher={Mycological Society of America}, author={Ghimire, S. R. and Rudgers, J. A. and Charlton, N. D. and Young, C. and Craven, K. D.}, year={2010}, month={Aug}, pages={75–84} }
 @article{saha_young_hopkins_2009, title={Genetic Variation within and among Wildrye ( and ) Populations from the Southern Great Plains}, volume={49}, DOI={10.2135/cropsci2008.04.0239}, abstractNote={There is interest in Canada wildrye (CWR, Ely- mus canadensis L.) and Virginia wildrye (VWR, E. virginicus L.) for conservation and forage uses. Our objectives were to identify a set of molecular markers to assess genetic structure within and diversity among populations of CWR and VWR from the Southern Great Plains and to determine if these populations had an associated fungal endophyte. Nine CWR and five VWR populations and two barley (Hor- deum vulgare L.) cultivars were genotyped using simple sequence repeat (SSR) markers isolated from tall fescue [Lolium arundinaceum (Schreb.) Darbysh.] expressed sequence tags (TF ESTs). Scorable fragments were produced by 31% of TF EST-SSRs tested, thus identifying a set of SSR markers for wildrye. Populations grouped into three clusters consisting of (i) three wild populations, one plant introduction, and two commercial sources of CWR; (ii) all VWR populations and three CWR plant introductions; and (iii) barley cultivars. Clustering indicated possible gene flow between CWR and VWR. Genetic variation within populations was minimal and comparable to that of the barley cultivars. Thus, unlike many ancestral cultivars and landraces of self-pollinated crops, CWR and VWR populations consisted of essentially pure lines and can be handled as such in a breeding program. Potentially sexual and asexual epichloe endophytes were found in several populations, indicating the need to account for endophytes in breeding and germplasm conservation efforts of wildrye.}, number={3}, journal={Crop Science}, publisher={Crop Science Society of America}, author={Saha, Malay C. and Young, Carolyn A. and Hopkins, Andrew A.}, year={2009}, pages={913} }
 @article{haas_kamoun_zody_jiang_handsaker_cano_grabherr_kodira_raffaele_torto-alalibo_et al._2009, title={Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans}, volume={461}, ISSN={["1476-4687"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-70349281388&partnerID=MN8TOARS}, DOI={10.1038/nature08358}, abstractNote={The genome of Phytophthora infestans, the pathogen that triggered the Irish potato famine in the nineteenth century, has been sequenced. It remains a devastating pathogen, with late blight destroying crops worth billions of dollars each year. Blight is difficult to control, in part because it adapts so quickly to genetically resistant potato strains. Comparison with two other Phytophthora genomes shows rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes induced during infection that have activities thought to alter host physiology. These fast evolving effector genes are found in highly dynamic and expanded regions of the genome, a factor that may contribute to its rapid adaptability to host plants. The P. infestans genome is the biggest so far sequenced, at about 240 megabases, with an extremely high repeat content of close to 75%. It is a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes related to organisms such as brown algae and diatoms. Phytophthora infestans is a fungus-like eukaryote and the most destructive pathogen of potato, with current annual worldwide potato crop losses due to late blight estimated at $6.7 billion. Here, the sequence of the P. infestans genome is reported. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of certain secreted disease effector proteins, probably explaining the rapid adaptability of the pathogen to host plants. Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement1. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world’s population1. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion2. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars3,4. Here we report the sequence of the P. infestans genome, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for ∼74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.}, number={7262}, journal={NATURE}, publisher={Nature Publishing Group}, author={Haas, Brian J. and Kamoun, Sophien and Zody, Michael C. and Jiang, Rays H. Y. and Handsaker, Robert E. and Cano, Liliana M. and Grabherr, Manfred and Kodira, Chinnappa D. and Raffaele, Sylvain and Torto-Alalibo, Trudy and et al.}, year={2009}, month={Sep}, pages={393–398} }
 @article{oh_young_lee_oliva_bozkurt_cano_win_bos_liu_damme_et al._2009, title={In Planta Expression Screens of Phytophthora infestans RXLR Effectors Reveal Diverse Phenotypes, Including Activation of the Solanum bulbocastanum Disease Resistance Protein Rpi-blb2}, volume={21}, DOI={10.1105/tpc.109.068247}, abstractNote={The Irish potato famine pathogen Phytophthora infestans is predicted to secrete hundreds of effector proteins. To address the challenge of assigning biological functions to computationally predicted effector genes, we combined allele mining with high-throughput in planta expression. We developed a library of 62 infection-ready P. infestans RXLR effector clones, obtained using primer pairs corresponding to 32 genes and assigned activities to several of these genes. This approach revealed that 16 of the 62 examined effectors cause phenotypes when expressed inside plant cells. Besides the well-studied AVR3a effector, two additional effectors, PexRD8 and PexRD3645-1, suppressed the hypersensitive cell death triggered by the elicitin INF1, another secreted protein of P. infestans. One effector, PexRD2, promoted cell death in Nicotiana benthamiana and other solanaceous plants. Finally, two families of effectors induced hypersensitive cell death specifically in the presence of the Solanum bulbocastanum late blight resistance genes Rpi-blb1 and Rpi-blb2, thereby exhibiting the activities expected for Avrblb1 and Avrblb2. The AVRblb2 family was then studied in more detail and found to be highly variable and under diversifying selection in P. infestans. Structure-function experiments indicated that a 34–amino acid region in the C-terminal half of AVRblb2 is sufficient for triggering Rpi-blb2 hypersensitivity and that a single positively selected AVRblb2 residue is critical for recognition by Rpi-blb2.}, number={9}, journal={THE PLANT CELL ONLINE}, publisher={American Society of Plant Biologists (ASPB)}, author={Oh, S.-K. and Young, C. and Lee, M. and Oliva, R. and Bozkurt, T. O. and Cano, L. M. and Win, J. and Bos, J. I.B. and Liu, H.-Y. and Damme, M. and et al.}, year={2009}, month={Sep}, pages={2928–2947} }
 @article{young_tapper_may_moon_schardl_scott_2009, title={Indole-Diterpene Biosynthetic Capability of Epichloe Endophytes as Predicted by ltm Gene Analysis}, volume={75}, DOI={10.1128/aem.00953-08}, abstractNote={ABSTRACT Bioprotective alkaloids produced by Epichloë and closely related asexual Neotyphodium fungal endophytes protect their grass hosts from insect and mammalian herbivory. One class of these compounds, known for antimammalian toxicity, is the indole-diterpenes. The LTM locus of Neotyphodium lolii (Lp19) and Epichloë festuce (Fl1), required for the biosynthesis of the indole-diterpene lolitrem, consists of 10 ltm genes. We have used PCR and Southern analysis to screen a broad taxonomic range of 44 endophyte isolates to determine why indole-diterpenes are present in so few endophyte-grass associations in comparison to that of the other bioprotective alkaloids, which are more widespread among the endophtyes. All 10 ltm genes were present in only three epichloë endophytes. A predominance of the asexual Neotyphodium spp. examined contained 8 of the 10 ltm genes, with only one N. lolii containing the entire LTM locus and the ability to produce lolitrems. Liquid chromatography-tandem mass spectrometry profiles of indole-diterpenes from a subset of endophyte-infected perennial ryegrass showed that endophytes that contained functional genes present in ltm clusters 1 and 2 were capable of producing simple indole-diterpenes such as paspaline, 13-desoxypaxilline, and terpendoles, compounds predicted to be precursors of lolitrem B. Analysis of toxin biosynthesis genes by PCR now enables a diagnostic method to screen endophytes for both beneficial and detrimental alkaloids and can be used as a resource for screening isolates required for forage improvement.}, number={7}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Young, C. A. and Tapper, B. A. and May, K. and Moon, C. D. and Schardl, C. L. and Scott, B.}, year={2009}, month={Jan}, pages={2200–2211} }
 @article{scott_wrenn_may_takemoto_young_tanaka_fleetwood_johnson_2009, title={Regulation and Functional Analysis of Bioprotective Metabolite Genes from the Grass Symbiont Epichloe festucae}, DOI={10.1007/978-1-4020-8804-9_15}, journal={Recent Developments in Management of Plant Diseases}, publisher={Springer Science \mathplus Business Media}, author={Scott, Barry and Wrenn, Ruth E. and May, Kimberley J. and Takemoto, Daigo and Young, Carolyn A. and Tanaka, Aiko and Fleetwood, Damien J. and Johnson, Richard D.}, year={2009}, month={Aug}, pages={199–213} }
 @article{vleeshouwers_rietman_krenek_champouret_young_oh_wang_bouwmeester_vosman_visser_et al._2008, title={Effector Genomics Accelerates Discovery and Functional Profiling of Potato Disease Resistance and Phytophthora Infestans Avirulence Genes}, volume={3}, DOI={10.1371/journal.pone.0002875}, abstractNote={Potato is the world's fourth largest food crop yet it continues to endure late blight, a devastating disease caused by the Irish famine pathogen Phytophthora infestans. Breeding broad-spectrum disease resistance (R) genes into potato (Solanum tuberosum) is the best strategy for genetically managing late blight but current approaches are slow and inefficient. We used a repertoire of effector genes predicted computationally from the P. infestans genome to accelerate the identification, functional characterization, and cloning of potentially broad-spectrum R genes. An initial set of 54 effectors containing a signal peptide and a RXLR motif was profiled for activation of innate immunity (avirulence or Avr activity) on wild Solanum species and tentative Avr candidates were identified. The RXLR effector family IpiO induced hypersensitive responses (HR) in S. stoloniferum, S. papita and the more distantly related S. bulbocastanum, the source of the R gene Rpi-blb1. Genetic studies with S. stoloniferum showed cosegregation of resistance to P. infestans and response to IpiO. Transient co-expression of IpiO with Rpi-blb1 in a heterologous Nicotiana benthamiana system identified IpiO as Avr-blb1. A candidate gene approach led to the rapid cloning of S. stoloniferum Rpi-sto1 and S. papita Rpi-pta1, which are functionally equivalent to Rpi-blb1. Our findings indicate that effector genomics enables discovery and functional profiling of late blight R genes and Avr genes at an unprecedented rate and promises to accelerate the engineering of late blight resistant potato varieties.}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Vleeshouwers, Vivianne G. A. A. and Rietman, Hendrik and Krenek, Pavel and Champouret, Nicolas and Young, Carolyn and Oh, Sang-Keun and Wang, Miqia and Bouwmeester, Klaas and Vosman, Ben and Visser, Richard G. F. and et al.}, editor={El-Shemy, Hany A.Editor}, year={2008}, month={Aug}, pages={e2875} }
 @article{hahn_mcmanus_warnstorff_monahan_young_davies_tapper_scott_2008, title={Neotyphodium fungal endophytes confer physiological protection to perennial ryegrass (Lolium perenne L.) subjected to a water deficit}, volume={63}, DOI={10.1016/j.envexpbot.2007.10.021}, abstractNote={While it is generally accepted that Neotyphodium lolii and related epichloë endophytes are mutualists that provide important benefits to their perennial ryegrass (Lolium perenne) host plants under conditions of biotic stress, relatively little is known about the effect of endophyte on the host under conditions of abiotic stress. Using genetically identical endophyte infected (E+) and uninfected (E−) clones of perennial ryegrass from a natural and a synthetic association grown under conditions of water stress in a controlled environment, we show that N. lolii had minor effects on morphological responses (leaf elongation rate and ground biomass production) but had more pronounced effects on physiological responses (water use efficiency, relative water content and osmotic potential) by the host. The effects were most marked in the natural association. While levels of proline increased in response to water stress, the presence of endophyte had no effect on those levels. The effect of water stress on endophyte bioprotective metabolites was also examined. Ergovaline levels in pseudostem tissue increased in response to increasing water stress for both N. lolii/L. perenne associations but lolitrem B levels only increased in the natural association. No differences in steady state levels of transcripts from genes known to be required for the synthesis of these alkaloids were observed in response to water stress. This study demonstrated that N. lolii can confer protection to perennial ryegrass from water stress and that levels of the bioprotective metabolites, lolitrem B and ergovaline were altered in response to this abiotic stress in a manner that was specific for each symbiotic association.}, number={1-3}, journal={Environmental and Experimental Botany}, publisher={Elsevier BV}, author={Hahn, Heike and McManus, Michael T. and Warnstorff, Kristina and Monahan, Brendon J. and Young, Carolyn A. and Davies, Elizabeth and Tapper, Brian A. and Scott, Barry}, year={2008}, month={May}, pages={183–199} }
 @article{saikia_nicholson_young_parker_scott_2008, title={The genetic basis for indole-diterpene chemical diversity in filamentous fungi}, volume={112}, DOI={10.1016/j.mycres.2007.06.015}, abstractNote={Indole-diterpenes are a structurally diverse group of secondary metabolites with a common cyclic diterpene backbone derived from geranylgeranyl diphosphate and an indole group derived from indole-3-glycerol phosphate. Different types and patterns of ring substitutions and ring stereochemistry generate this structural diversity. This group of compounds is best known for their neurotoxic effects in mammals, causing syndromes such as 'ryegrass staggers' in sheep and cattle. Because many of the fungi that synthesise these compounds form symbiotic relationships with plants, insects, and other fungi, the synthesis of these compounds may confer an ecological advantage to these associations. Considerable recent progress has been made on understanding indole-diterpene biosynthesis in filamentous fungi, principally through the cloning and characterisation of the genes and gene products for paxilline biosynthesis in Penicillium paxilli. Important insights into how the indole-diterpene backbone is synthesised and decorated have been obtained using P. paxilli mutants in this pathway. This review provides an overview of these recent developments.}, number={2}, journal={Mycological Research}, publisher={Elsevier BV}, author={Saikia, Sanjay and Nicholson, Matthew J. and Young, Carolyn and Parker, Emily J. and Scott, Barry}, year={2008}, month={Feb}, pages={184–199} }
 @article{bradshaw_jin_morgan_schwelm_teddy_young_zhang_2006, title={A Polyketide Synthase Gene Required for Biosynthesis of the Aflatoxin-like Toxin, Dothistromin}, volume={161}, DOI={10.1007/s11046-006-0240-5}, abstractNote={Dothistromin is a polyketide toxin, produced by a fungal forest pathogen, with structural similarity to the aflatoxin precursor versicolorin B. Biochemical and genetic studies suggested that there are common steps in the biosynthetic pathways for these metabolites and showed similarities between some of the genes. A polyketide synthase gene (pksA) was isolated from dothistromin-producing Dothistroma septosporum by hybridization with an aflatoxin ortholog from Aspergillus parasiticus. Inactivation of this gene in D. septosporum resulted in mutants that could not produce dothistromin but that could convert exogenous aflatoxin precursors, including norsolorinic acid, into dothistromin. The mutants also had reduced asexual sporulation compared to the wild type. So far four other genes are known to be clustered immediately alongside pksA. Three of these (cypA, moxA, avfA) are predicted to be orthologs of aflatoxin biosynthetic genes. The other gene (epoA), located between avfA and moxA, is predicted to encode an epoxide hydrolase, for which there is no homolog in either the aflatoxin or sterigmatocystin gene clusters. The pksA gene is located on a small chromosome of approximately 1.3 Mb in size, along with the dothistromin ketoreductase (dotA) gene.}, number={5}, journal={Mycopathologia}, publisher={Springer Science \mathplus Business Media}, author={Bradshaw, Rosie E. and Jin, Hongping and Morgan, Branwen S. and Schwelm, Arne and Teddy, Olivia R. and Young, Carolyn A. and Zhang, Shuguang}, year={2006}, month={May}, pages={283–294} }
 @article{young_felitti_shields_spangenberg_johnson_bryan_saikia_scott_2006, title={A complex gene cluster for indole-diterpene biosynthesis in the grass endophyte Neotyphodium lolii}, volume={43}, DOI={10.1016/j.fgb.2006.04.004}, abstractNote={Lolitrems are a structurally diverse group of indole-diterpene mycotoxins synthesized by Epichloë/Neotyphodium endophytes in association with Pooid grasses. Using suppression subtractive hybridization combined with chromosome walking, two clusters of genes for lolitrem biosynthesis were isolated from Neotyphodium lolii, a mutualistic endophyte of perennial ryegrass. The first cluster contains five genes, ltmP, ltmQ, ltmF, ltmC, and ltmB, four of which appear to be orthologues of functionally characterized genes from Penicillium paxilli. The second cluster contains two genes, ltmE and ltmJ, that appear to be unique to lolitrem biosynthesis. The two clusters are separated by a 16 kb AT-rich sequence that includes two imperfect direct repeats. A previously isolated ltm cluster composed of ltmG, ltmM, and ltmK, is linked to these two new clusters by 35 kb of AT-rich retrotransposon relic sequence. All 10 genes at this complex LTM locus were highly expressed in planta but expression was very low or undetectable in mycelia. ltmM and ltmC were shown to be functional orthologues of P. paxilli paxM and paxC, respectively. This work provides a genetic foundation for elucidating the metabolic grid responsible for the diversity of indole-diterpenes synthesized by N. lolii.}, number={10}, journal={Fungal Genetics and Biology}, publisher={Elsevier BV}, author={Young, Carolyn A. and Felitti, Silvina and Shields, Katherine and Spangenberg, German and Johnson, Richard D. and Bryan, Gregory T. and Saikia, Sanjay and Scott, Barry}, year={2006}, month={Oct}, pages={679–693} }
 @article{bos_kanneganti_young_cakir_huitema_win_armstrong_birch_kamoun_2006, title={The C-terminal half of Phytophthora infestans RXLR effector AVR3a is sufficient to trigger R3a-mediated hypersensitivity and suppress INF1-induced cell death in Nicotiana benthamiana}, volume={48}, DOI={10.1111/j.1365-313x.2006.02866.x}, abstractNote={The RXLR cytoplasmic effector AVR3a of Phytophthora infestans confers avirulence on potato plants carrying the R3a gene. Two alleles of Avr3a encode secreted proteins that differ in only three amino acid residues, two of which are in the mature protein. Avirulent isolates carry the Avr3a allele, which encodes AVR3aKI (containing amino acids C19, K80 and I103), whereas virulent isolates express only the virulence allele avr3a, encoding AVR3aEM (S19, E80 and M103). Only the AVR3aKI protein is recognized inside the plant cytoplasm where it triggers R3a-mediated hypersensitivity. Similar to other oomycete avirulence proteins, AVR3aKI carries a signal peptide followed by a conserved motif centered on the consensus RXLR sequence that is functionally similar to a host cell-targeting signal of malaria parasites. The interaction between Avr3a and R3a can be reconstructed by their transient co-expression in Nicotiana benthamiana. We exploited the N. benthamiana experimental system to further characterize the Avr3a-R3a interaction. R3a activation by AVR3aKI is dependent on the ubiquitin ligase-associated protein SGT1 and heat-shock protein HSP90. The AVR3aKI and AVR3aEM proteins are equally stable in planta, suggesting that the difference in R3a-mediated death cannot be attributed to AVR3aEM protein instability. AVR3aKI is able to suppress cell death induced by the elicitin INF1 of P. infestans, suggesting a possible virulence function for this protein. Structure-function experiments indicated that the 75-amino acid C-terminal half of AVR3aKI, which excludes the RXLR region, is sufficient for avirulence and suppression functions, consistent with the view that the N-terminal region of AVR3aKI and other RXLR effectors is involved in secretion and targeting but is not required for effector activity. We also found that both polymorphic amino acids, K80 and I103, of mature AVR3a contribute to the effector functions.}, number={2}, journal={The Plant Journal}, publisher={Wiley-Blackwell}, author={Bos, Jorunn I. B. and Kanneganti, Thirumala-Devi and Young, Carolyn and Cakir, Cahid and Huitema, Edgar and Win, Joe and Armstrong, Miles R. and Birch, Paul R. J. and Kamoun, Sophien}, year={2006}, month={Oct}, pages={165–176} }
 @article{bhattacharjee_hiller_liolios_win_kanneganti_young_kamoun_haldar_2006, title={The Malarial Host-Targeting Signal Is Conserved in the Irish Potato Famine Pathogen}, volume={2}, DOI={10.1371/journal.ppat.0020050}, abstractNote={Animal and plant eukaryotic pathogens, such as the human malaria parasite Plasmodium falciparum and the potato late blight agent Phytophthora infestans, are widely divergent eukaryotic microbes. Yet they both produce secretory virulence and pathogenic proteins that alter host cell functions. In P. falciparum, export of parasite proteins to the host erythrocyte is mediated by leader sequences shown to contain a host-targeting (HT) motif centered on an RxLx (E, D, or Q) core: this motif appears to signify a major pathogenic export pathway with hundreds of putative effectors. Here we show that a secretory protein of P. infestans, which is perceived by plant disease resistance proteins and induces hypersensitive plant cell death, contains a leader sequence that is equivalent to the Plasmodium HT-leader in its ability to export fusion of green fluorescent protein (GFP) from the P. falciparum parasite to the host erythrocyte. This export is dependent on an RxLR sequence conserved in P. infestans leaders, as well as in leaders of all ten secretory oomycete proteins shown to function inside plant cells. The RxLR motif is also detected in hundreds of secretory proteins of P. infestans, Phytophthora sojae, and Phytophthora ramorum and has high value in predicting host-targeted leaders. A consensus motif further reveals E/D residues enriched within ~25 amino acids downstream of the RxLR, which are also needed for export. Together the data suggest that in these plant pathogenic oomycetes, a consensus HT motif may reside in an extended sequence of ~25–30 amino acids, rather than in a short linear sequence. Evidence is presented that although the consensus is much shorter in P. falciparum, information sufficient for vacuolar export is contained in a region of ~30 amino acids, which includes sequences flanking the HT core. Finally, positional conservation between Phytophthora RxLR and P. falciparum RxLx (E, D, Q) is consistent with the idea that the context of their presentation is constrained. These studies provide the first evidence to our knowledge that eukaryotic microbes share equivalent pathogenic HT signals and thus conserved mechanisms to access host cells across plant and animal kingdoms that may present unique targets for prophylaxis across divergent pathogens.}, number={5}, journal={PLoS Pathog}, publisher={Public Library of Science (PLoS)}, author={Bhattacharjee, Souvik and Hiller, N. Luisa and Liolios, Konstantinos and Win, Joe and Kanneganti, Thirumala-Devi and Young, Carolyn and Kamoun, Sophien and Haldar, Kasturi}, year={2006}, pages={e50} }
 @article{young_bryant_christensen_tapper_bryan_scott_2005, title={Molecular cloning and genetic analysis of a symbiosis-expressed gene cluster for lolitrem biosynthesis from a mutualistic endophyte of perennial ryegrass}, volume={274}, DOI={10.1007/s00438-005-1130-0}, abstractNote={Lolitrems are potent tremorgenic mycotoxins that are synthesised by clavicipitaceous fungal endophytes of the Epichloë/Neotyphodium group in association with grasses. These indole-diterpenes confer major ecological benefits on the grass-endophyte symbiotum. A molecular signature for diterpene biosynthesis is the presence of two geranylgeranyl diphosphate (GGPP) synthases. Using degenerate primers for conserved domains of fungal GGPP synthases, we cloned two such genes, ltmG and ggsA, from Neotyphodium lolii. Adjacent to ltmG are two genes, ltmM and ltmK, that are predicted to encode an FAD-dependent monooxygenase and a cytochrome P450 monooxygenase, respectively. The cluster of ltm genes is flanked by AT-rich retrotransposon DNA that appears to have undergone extensive repeat induced point (RIP) mutation. Epichloë festucae, the sexual ancestor of N. lolii, contains an identical ltm gene cluster, but lacks the retrotransposon "platform'' on the right flank. Associations established between perennial ryegrass and an E. festucae mutant deleted for ltmM lack detectable levels of lolitrems. A wild-type copy of ltmM complemented this phenotype, as did paxM from Penicillium paxilli. Northern hybridization and RT-PCR analysis showed that all three genes are weakly expressed in culture but strongly induced in planta. The relative endophyte biomass in these associations was estimated by real-time PCR to be between 0.3 and 1.9%. Taking this difference into account, the steady-state levels of the ltm transcripts are about 100-fold greater than the levels of the endogenous ryegrass beta-tubulin (beta -Tub1) and actin (Act1) RNAs. Based on these results we propose that ltmG, ltmM and ltmK are members of a set of genes required for lolitrem biosynthesis in E. festucae and N. lolii.}, number={1}, journal={Mol Genet Genomics}, publisher={Springer Science \mathplus Business Media}, author={Young, C. A. and Bryant, M. K. and Christensen, M. J. and Tapper, B. A. and Bryan, G. T. and Scott, B.}, year={2005}, month={Jul}, pages={13–29} }
 @article{damrongkool_damrongkool_sedlock_damrongkool_sedlock_young_johnson_damrongkool_sedlock_young_et al._2005, title={Structural analysis of a peptide synthetase gene required for ergopeptine production in the endophytic fungus Neotyphodium lolii}, volume={16}, DOI={10.1080/10425170500273005}, abstractNote={Lysergyl peptide synthetase 1 catalyzes the assembly of toxic ergopeptines from activated D-lysergic acid and three amino acids. The gene encoding this enzyme in the endophytic fungus Neotyphodium lolii was analyzed and compared to a homologous gene from the ergot fungus Claviceps purpurea. Each gene contained two introns, which were found in the same relative position within two modules of the gene. The 5′ ends of the two genes were unusually divergent. Signature sequences determining substrate specificity were similar in adenylation domains that recognized identical amino acids but differed within the adenylation domain for the amino acid that varies between the major ergopeptines of the two fungi. Homologues were detected in several related endophytic fungi; the tall fescue endophyte Neotyphodium coenophialum contained a divergent, second copy of the gene. Our results provide new information on the structure and distribution of this important peptide synthetase involved in ergot alkaloid biosynthesis.}, number={5}, journal={DNA Sequence}, publisher={Informa UK Limited}, author={Damrongkool, Prapassorn and Damrongkool, Prapassorn and Sedlock, Andrea B. and Damrongkool, Prapassorn and Sedlock, Andrea B. and Young, Carolyn A. and Johnson, Richard D. and Damrongkool, Prapassorn and Sedlock, Andrea B. and Young, Carolyn A. and et al.}, year={2005}, month={Jan}, pages={379–385} }
 @article{scott_young_2003, title={Genetic Manipulation of Clavicipitalean Endophytes}, DOI={10.1201/9780203912706.ch14}, journal={Clavicipitalean Fungi}, publisher={Informa UK Limited}, author={Scott, Barry and Young, Carolyn}, year={2003}, month={Jul} }
 @article{mcmillan_carr_young_astin_lowe_parker_jameson_finch_miles_mcmanus_et al._2003, title={Molecular analysis of two cytochrome P450 monooxygenase genes required for paxilline biosynthesis in Penicillium paxilli , and effects of paxilline intermediates on mammalian maxi-K ion channels}, volume={270}, DOI={10.1007/s00438-003-0887-2}, abstractNote={The gene cluster required for paxilline biosynthesis in Penicillium paxilli contains two cytochrome P450 monooxygenase genes, paxP and paxQ. The primary sequences of both proteins are very similar to those of proposed cytochrome P450 monooxygenases from other filamentous fungi, and contain several conserved motifs, including that for a haem-binding site. Alignment of these sequences with mammalian and bacterial P450 enzymes of known 3-D structure predicts that there is also considerable conservation at the level of secondary structure. Deletion of paxP and paxQ results in mutant strains that accumulate paspaline and 13-desoxypaxilline, respectively. These results confirm that paxP and paxQ are essential for paxilline biosynthesis and that paspaline and 13-desoxypaxilline are the most likely substrates for the corresponding enzymes. Chemical complementation of paxilline biosynthesis in paxG (geranygeranyl diphosphate synthase) and paxP, but not paxQ, mutants by the external addition of 13-desoxypaxilline confirms that PaxG and PaxP precede PaxQ, and are functionally part of the same biosynthetic pathway. A pathway for the biosynthesis of paxilline is proposed on the basis of these and earlier results. Electrophysiological experiments demonstrated that 13-desoxypaxilline is a weak inhibitor of mammalian maxi-K channels (Ki=730 nM) compared to paxilline (Ki=30 nM), indicating that the C-13 OH group of paxilline is crucial for the biological activity of this tremorgenic mycotoxin. Paspaline is essentially inactive as a channel blocker, causing only slight inhibition at concentrations up to 1 microM.}, number={1}, journal={Molecular Genetics and Genomics}, publisher={Springer Nature}, author={McMillan, L. K. and Carr, R. L. and Young, C. A. and Astin, J. W. and Lowe, R. G. T. and Parker, E. J. and Jameson, G. B. and Finch, S. C. and Miles, C. O. and McManus, O. B. and et al.}, year={2003}, month={Sep}, pages={9–23} }
 @article{panaccione_johnson_wang_young_damrongkool_scott_schardl_2001, title={Elimination of ergovaline from a grass-Neotyphodium endophyte symbiosis by genetic modification of the endophyte}, volume={98}, DOI={10.1073/pnas.221198698}, abstractNote={The fungal endophytes Neotyphodium lolii and Neotyphodium sp. Lp1 from perennial ryegrass (Lolium perenne), and related endophytes in other grasses, produce the ergopeptine toxin ergovaline, among other alkaloids, while also increasing plant fitness and resistance to biotic and abiotic stress. In the related fungus, Claviceps purpurea, the biosynthesis of ergopeptines requires the activities of two peptide synthetases, LPS1 and LPS2. A peptide synthetase gene hypothesized to be important for ergopeptine biosynthesis was identified in C. purpurea by its clustering with another ergot alkaloid biosynthetic gene, dmaW. Sequence analysis conducted independently of the research presented here indicates that this gene encodes LPS1 [Tudzynski, P., Holter, K., Correia, T., Arntz, C., Grammel, N. & Keller, U. (1999) Mol. Gen. Genet. 261, 133–141]. We have cloned a similar peptide synthetase gene from Neotyphodium lolii and inactivated it by gene knockout in Neotyphodium sp. Lp1. The resulting strain retained full compatibility with its perennial ryegrass host plant as assessed by immunoblotting of tillers and quantitative PCR. However, grass–endophyte associations containing the knockout strain did not produce detectable quantities of ergovaline as analyzed by HPLC with fluorescence detection. Disruption of this gene provides a means to manipulate the accumulation of ergovaline in endophyte-infected grasses for the purpose of determining the roles of ergovaline in endophyte-associated traits and, potentially, for ameliorating toxicoses in livestock.}, number={22}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Panaccione, D. G. and Johnson, R. D. and Wang, J. and Young, C. A. and Damrongkool, P. and Scott, B. and Schardl, C. L.}, year={2001}, month={Oct}, pages={12820–12825} }
 @article{young_mcmillan_telfer_scott_2001, title={Molecular cloning and genetic analysis of an indole-diterpene gene cluster from Penicillium paxilli}, volume={39}, DOI={10.1046/j.1365-2958.2001.02265.x}, abstractNote={The indole‐diterpene paxilline is a potent tremorgenic mammalian mycotoxin and a known inhibitor of maxi‐K ion channels. The gene cluster responsible for paxilline biosynthesis in Penicillium paxilli was identified by mapping four large plasmid‐induced chromosome deletions. The cluster is predicted to lie within a 50 kb region of chromosome Va and to contain 17 genes, including a geranylgeranyl pyrophosphate (GGPP) synthase (paxG), two FAD‐dependent monooxygenases (paxM and N), two cytochrome P450 monooxygenases (paxP and Q), a dimethylallyltryptophan (DMAT) synthase (paxD) and two possible transcription factors (paxR and paxS), which contain a Zn(II)2Cys6 DNA‐binding motif. Targeted replacement of paxG confirmed that it is essential for paxilline biosynthesis but dispensable for growth. The GGPP for primary metabolism is predicted to be provided by a second GGPP synthase (ggs1) that was cloned, sequenced and mapped to chromosome IV. Semi‐quantitative reverse transcriptase–polymerase chain reaction analysis demonstrated that the expression of paxG, paxM and paxP in submerged liquid cultures of P. paxilli increased dramatically with the onset of paxilline biosynthesis. In contrast, the expression of β‐tubulin (tub2) and ggs1 was not induced. This is the first description of the molecular cloning and genetic analysis of an indole‐diterpene gene cluster.}, number={3}, journal={Mol Microbiol}, publisher={Wiley-Blackwell}, author={Young, Carolyn and McMillan, Lisa and Telfer, Emily and Scott, Barry}, year={2001}, month={Feb}, pages={754–764} }
 @article{young_itoh_johnson_garthwaite_miles_munday-finch_scott_1998, title={Paxilline-negative mutants of Penicillium paxilli generated by heterologous and homologous plasmid integration}, volume={33}, DOI={10.1007/s002940050349}, abstractNote={Using a monoclonal antibody based ELISA, 600 pAN7-1 plasmid-tagged mutants of Penicillium paxilli were screened for paxilline accumulation and one paxilline-negative mutant, YI-20, was identified. A molecular analysis of this mutant showed that pAN7-1 was inserted at a single site but was present as 4-6 copies arranged in a head-to-tail tandem array. Rescue of flanking sequences and analysis of the corresponding genomic region revealed that YI-20 has an extensive deletion at the site of pAN7-1 integration. Probing of a CHEF gel with the same sequences showed that associated with the deletion is a rearrangement of chromosome Va. Targeted gene disruption of wild-type sequences adjacent to the site where pAN7-1 inserted, resulted in the generation of two additional paxilline-negative mutants; both were single crossovers with deletions extending outside the region mapped. Neither of these new mutants had a rearrangement of chromosome Va, suggesting that deletion of genes on this chromosome is responsible for the paxilline-negative phenotype. Telomeric fingerprinting of genomic digests of P. paxilli, combined with pulsed-field gel electrophoresis of chromosomal DNA, established that there are a minimum of eight chromosomes in this fungus.}, number={5}, journal={Current Genetics}, publisher={Springer Science \mathplus Business Media}, author={Young, Carolyn and Itoh, Yasuo and Johnson, R. and Garthwaite, I. and Miles, Christopher O. and Munday-Finch, Sarah C. and Scott, B.}, year={1998}, month={Jun}, pages={368–377} }
 @article{scott_1996, title={Novel and Complex Chromosomal Arrangement ofRhizobium/otiNodulation Genes}, volume={9}, DOI={10.1094/mpmi-9-0187}, abstractNote={A mutational and structural analysis of Rhizobium loti nodulation genes in strains NZP2037 and NZP2213 was carried out. Unlike the case with other Rhizobium strains examined to date, nodB was found on an operon separate from nodACIJ. Sequence analysis of the nodACIJ and nodB operon regions confirm that R. loti common nod genes have a gene organization different from that of other Rhizobium spp. At least 4 copies of nodD-like sequences were identified in R. loti. The complete nucleotide sequence of one of these, nodD3, was determined. A new host-specific nod gene, nolL, was identified adjacent to nodD3. NolL shares homology with NodX and other O-acetyl transferases. Mutational analysis of the nod regions of strains NZP2037 and NZP2213 showed that nodD3, nodI, nodJ, and nolL were all essential for R. loti strains to effectively nodulate the extended host Lotus pedunculatus, but were not necessary for effective nodulation of the less restrictive host, Lotus corniculatus. Both nodD3 and nolL were essential for R. loti strains to nodulate Leucaena leucocephala.}, number={3}, journal={MPMI}, publisher={Scientific Societies}, author={Scott, D. Barry}, year={1996}, pages={187} }
 @article{stange_jeffares_young_scott_eason_jameson_1996, title={PCR amplification of the fas-1 gene for the detection of virulent strains of Rhodococcus fascians}, volume={45}, DOI={10.1046/j.1365-3059.1996.d01-154.x}, abstractNote={Thirty-six isolates of the fasciation-inducing bacterium Rhodococcus fascians were evaluated for the presence and location of the fas-1 gene, which codes for an isopentenyl transferase, the committed step in cytokinin biosynthesis. The presence of fas-1 was determined by PCR using a set of primers to the most conserved regions of the gene and by Southern hybridization to genomic digests using the PCR fragment as a probe. Both methods revealed the presence of the gene in 18 virulent isolates and the absence of the gene in 18 avirulent isolates. Thus, there is a strong relationship between the presence of the gene and virulence of the organism. The location of fas-1 was determined by probing blots of linear and circular DNA. For most of the virulent isolates, the gene was localized to a 200 ± 10 kb linear plasmid. Three virulent isolates lacked a plasmid of this size, but contained fas-1 either on a linear plasmid of 130 kb or on a large circular plasmid.}, number={3}, journal={Plant Pathology}, publisher={Wiley-Blackwell}, author={STANGE, R. R. and JEFFARES, D. and YOUNG, C. and SCOTT, D. B. and EASON, J. R. and JAMESON, P. E.}, year={1996}, month={Jun}, pages={407–417} }
 @article{hancock_rockman_young_pearce_maddox_scott_1991, title={Expression and nucleotide sequence of the Clostridium acetobutylicum beta-galactosidase gene cloned in Escherichia coli.}, volume={173}, DOI={10.1128/jb.173.10.3084-3095.1991}, abstractNote={A gene library for Clostridium acetobutylicum NCIB 2951 was constructed in the broad-host-range cosmid pLAFR1, and cosmids containing the beta-galactosidase gene were isolated by direct selection for enzyme activity on X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactoside) plates after conjugal transfer of the library to a lac deletion derivative of Escherichia coli. Analysis of various pSUP202 subclones of the lac cosmids on X-Gal plates localized the beta-galactosidase gene to a 5.1-kb EcoRI fragment. Expression of the Clostridium beta-galactosidase gene in E. coli was not subject to glucose repression. By using transposon Tn5 mutagenesis, two gene loci, cbgA (locus I) and cbgR (locus II), were identified as necessary for beta-galactosidase expression in E. coli. DNA sequence analysis of the entire 5.1-kb fragment identified open reading frames of 2,691 and 303 bp, corresponding to locus I and locus II, respectively, and in addition a third truncated open reading frame of 825 bp. The predicted gene product of locus I, CbgA (molecular size, 105 kDa), showed extensive amino acid sequence homology with E. coli LacZ, E. coli EbgA, and Klebsiella pneumoniae LacZ and was in agreement with the size of a polypeptide synthesized in maxicells containing the cloned 5.1-kb fragment. The predicted gene product of locus II, CbgR (molecular size, 11 kDa) shares no significant homology with any other sequence in the current DNA and protein sequence data bases, but Tn5 insertions in this gene prevent the synthesis of CbgA. Complementation experiments indicate that the gene product of cbgR is required in cis with cbgA for expression of beta-galactosidase in E. coli.}, number={10}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Hancock, K R and Rockman, E and Young, C A and Pearce, L and Maddox, I S and Scott, D B}, year={1991}, month={May}, pages={3084–3095} }
 @article{young_collins-emerson_terzaghi_scott_1990, title={Nucleotide sequence of Rhizobium loti nod I}, volume={18}, DOI={10.1093/nar/18.22.6691}, abstractNote={Journal Article Nucleotide sequence of Rhizobium loti nodI Get access C. Young, C. Young Molecular Genetics Unit, Department of Microbiology and Genetics, Massey UniversityPalmerston North, New Zealand Search for other works by this author on: Oxford Academic PubMed Google Scholar J.M. Collins-Emerson, J.M. Collins-Emerson Molecular Genetics Unit, Department of Microbiology and Genetics, Massey UniversityPalmerston North, New Zealand Search for other works by this author on: Oxford Academic PubMed Google Scholar E.A. Terzaghi, E.A. Terzaghi Molecular Genetics Unit, Department of Microbiology and Genetics, Massey UniversityPalmerston North, New Zealand Search for other works by this author on: Oxford Academic PubMed Google Scholar D.B. Scott D.B. Scott * Molecular Genetics Unit, Department of Microbiology and Genetics, Massey UniversityPalmerston North, New Zealand * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 22, 25 November 1990, Page 6691, https://doi.org/10.1093/nar/18.22.6691 Published: 25 November 1990 Article history Received: 16 October 1990 Published: 25 November 1990}, number={22}, journal={Nucl Acids Res}, publisher={Oxford University Press (OUP)}, author={Young, C. and Collins-Emerson, J.M. and Terzaghi, E.A. and Scott, D.B.}, year={1990}, pages={6691–6691} }
 @article{young_wilkinson, title={Epichloë Endophytes: Models of an Ecological Strategy}, DOI={10.1128/9781555816636.ch41}, abstractNote={This chapter considers our current understanding of the epichloae, for which the recently sequenced Epichloe festucae is considered a model. The epichloae are in the family Clavicipitaceae within the order Hypocreales. While it was not the first recognition of an epichloe endophyte, the discovery of an introduced tall fescue population by University of Kentucky agronomists in the early 1930s led to the development of the (in)famously popular cultivar Kentucky-31. A flourish of studies comparing endophyte-infected (E+) and endophyte-free (E-) conspecific grasses in the 1980s and 1990s established a list of host fitness enhancements attributable to the endophyte: herbivore resistance, disease resistance, competitive ability, drought tolerance, heat tolerance, and tolerance to nutrient deficits. Researchers conducted a study to determine and compare the impacts of E+ and E- tall fescue on a natural grass community. The implications of this study reveal the concern that when introduced symbiota with pronounced fitness enhancements become established in nature, they run the risk of dominating communities and driving out some native plant species. While much of the understanding of ergot alkaloid biosynthesis has come from the characterization of the genes in the Claviceps spp., disruption and characterization of key pathway genes such as dmaW, lpsA, and lpsB have also been performed for epichloe endophytes. Most of the Epichloe and Neotyphodium endophytes screened to date are able to synthesize the alkaloid peramine.}, journal={Cellular and Molecular Biology of Filamentous Fungi}, publisher={American Society for Microbiology}, author={Young, Carolyn and Wilkinson, Heather H.}, pages={660–675} }
 @article{scott_young_tanaka_christenseq_tapper_bryan, title={Molecular and Genetic Analysis of Lolitrem and Peramine Biosynthetic Pathways in Epkhloë Festucae}, DOI={10.1002/9780470384916.ch3}, abstractNote={This chapter contains section titled: Endophyte Synthesis of Bioprotective Metabolites Epichloe Festucae as a Model Experimental System for Genetica Nalysis of Endophytes Genetics and Molecular Cloning of a Peramine Biosynthesis Gene Cluster Molecular Cloning and Genetic Analysis of a Gene Cluster for Paxilline Biosynthesis Molecular Cloning and Genetic Analysis of a Gene Cluster for Lolitrem Biosynthesis Acknowledgments References}, journal={Neotyphodium in Cool-Season Grasses}, publisher={Wiley-Blackwell}, author={Scott, Barry and Young, Carolyn and Tanaka, Aiko and Christenseq, Michael and Tapper, Brian and Bryan, Gregory}, pages={93–101} }
 @article{scott_young_tanaka_parker, title={Molecular and genetic analysis of symbiosis expressed secondary metabolite genes from the mutualistic fungal endophytes Neotyphodium lolii and Epichloë festucae}, DOI={10.1017/cbo9780511902451.006}, abstractNote={Epichloë endophytes (Epichloë/Neotyphodium species) are an important group of clavicipitaceous fungi that form symbiotic associations (symbiota) with temperate grasses of the Pooideae subfamily (Scott, 2001a; Schardl, Leuchtmann & Spiering, 2004). These biotrophic fungi systemically colonize the intercellular spaces of leaf primordia, leaf sheaths and culms of vegetative tissue and the inflorescence of reproductive tissues. The asexual Neotyphodium species have no external growth stage and consequently form symptomless associations with their grass host where they are vertically transmitted through the seed following colonization of the developing ovule. Most of the sexual Epichloë species are also transmitted vertically but because of their ability to form external stromata on inflorescence tissue, can also be transmitted horizontally (Leuchtmann & Schardl, 1998; Schardl & Leuchtmann, 1999). The mating system is heterothallic (outcrossing) and in nature is mediated by anthomyiid flies (Botanophila spp.), which transfer spermatia between stromata (Bultman et al., 1995; Bultman et al., 1998). Formation of perithecia and release of ascospores into the environment provides a source of vegetative hyphae that give rise to conidia that subsequently infect new hosts, probably by way of colonization of the stigma and style of the host inflorescence (Chung & Schardl, 1997).}, journal={Exploitation of Fungi}, publisher={Cambridge University Press (CUP)}, author={Scott, B. and Young, C. A. and Tanaka, A. and Parker, E. J.}, editor={Robson, G. D. and West, Pieter and Gadd, GeoffreyEditors}, pages={59–77} }