@article{duin_montalban_joglekar_d՚amico-willman_ritchie_fagen_huerta_2024, title={First Report of Bacterial Leaf Spot Disease on Sesame (<i>Sesamum indicum</i>) Caused by <i>Pseudomonas syringae</i> pv. <i>sesami</i> in North Carolina}, volume={108}, ISSN={0191-2917 1943-7692}, url={http://dx.doi.org/10.1094/PDIS-02-24-0292-PDN}, DOI={10.1094/PDIS-02-24-0292-PDN}, abstractNote={In July 2022, dark brown to black, angular, water-soaked lesions were observed on sesame leaves (Sesamum indicum L.) in a research plot established to assess yield potential for eight varieties at the North Carolina (NC) Sandhills Research Station (Chavez 2023). Symptoms were indicative of a bacterial leaf spot (BLS). At early flowering stage, leaf spots were present on scattered plants; varieties ES108, SS3301, and ES201 exhibited up to 75% disease prevalence, with lower frequency in ES103, S39, S4302, S3251, and S3276. Symptomatic leaves from 3-4 plants were collected on four different dates from July through September. A section of symptomatic tissue was excised and macerated in sterile deionized water (SDW). A 10 µL aliquot was streaked onto SPA medium (15 g sucrose, 5.0 g proteose peptone, 0.50 g MgSO4 7H2O, 0.25 g K2HPO4, 15 g agar per liter of SDW) and incubated at 28ºC. After 72 h, numerous, smooth, white-cream colored, convex-shaped, colonies were individually isolated. Five randomly selected isolates from the different collection dates, designated as AHP108-AHP111 and AHP116, were genotyped. The 16S rRNA, gyrB, rpoD, and gapA genes were sequenced (Heuer et al. 1997; Hwang et al. 2005) and deposited to NCBI (GenBank Accessions: P213467- PP213470; OQ628040-OQ628042; PP214983-PP214994; and PP255798). These five isolates shared 100% sequence identity for gyrB and rpoD. AHP108-AHP111 shared 100% sequence identity for 16S rRNA and gapA, with 99.7% and 90.8% identity, respectively, for AHP116. A phylogenetic tree was inferred from a maximum-likelihood analysis of concatenated gyrB, rpoD, and gapA sequences of the five isolates and the top 11 hts from a blastn search of the NCBI nucleotide database. Those hits included closely related sequences from Pseudomonas syringae pv. sesami type strains ICMP 763T and ICMP 7459T. Based on this phylogenetic analysis AHP108-AHP111 and AHP116 are P. syringae pv. sesami. Recent genomic analysis suggests this pathovar is part of P. amygdali (Gomila et al. 2017), but an official name change has not been proposed. Each of the five isolates were infiltrated into leaves of sesame varieties ES108, ES103, and S327, consistently resulting in similar symptoms. Thus, strain AHP116, as a representative, was used to fulfill Koch's postulates using five, 30-day-old potted sesame plants (var. S3301). Plants were spray-inoculated with a bacterial suspension of ~108 CFU/ml until runoff; plants were incubated in moist chambers 24 h pre and post inoculation at 28ºC with 80% relative humidity and a 12 h photoperiod. At 13 days post inoculation, symptoms resembling those on plants at the Sandhills Research Stations in 2022 were evident. Reisolated bacteria were confirmed to be AHP116 through 16S rRNA and gyrB amplification and sequencing. No symptoms were observed on the five water-inoculated plants. BLS of sesame has been reported in Asia and is thought to be seedborne (Firdous et al. 2009; Prathuangwong and Yowabutra 1997). To our knowledge, this is the first report of P. syringae pv. sesami causing BLS on sesame in North Carolina. Sesame cultivation in the state increased from approximately 2,000 acres in 2022 to 13,000 acres in 2023 and there is interest in cultivating sesame as a rotational and alternative crop because it requires minimal input costs. Potential outbreaks of BLS in this warm, humid region could negatively affect sesame production, where little is known about the economic impact of the disease.}, number={6}, journal={Plant Disease}, publisher={Scientific Societies}, author={Duin, Izabela Moura and Montalban, Kimberly M. and Joglekar, Prasanna and D՚Amico-Willman, Katherine and Ritchie, David F. and Fagen, Jennie R. and Huerta, Alejandra I.}, year={2024}, month={Jun}, pages={1880} }
 @article{d'amico-willman_joglekar_ritchie_smith_heiberger_huerta_2024, title={Genetically similar <i>Xanthomonas arboricola</i> pv. <i>pruni</i> strains and associated phage display phenotypic and genotypic variation across 35 years}, volume={7}, ISSN={2471-2906}, url={http://dx.doi.org/10.1094/pbiomes-03-24-0033-fi}, DOI={10.1094/pbiomes-03-24-0033-fi}, abstractNote={Bacteriophages (phages), viruses that infect bacteria, have key ecological and evolutionary functions in the phytobiome. Despite the importance of phages as primary drivers for bacterial evolution, phage-bacteria interactions across spatiotemporal scales in natural, agricultural settings are underexplored. With increased interest in phage-based therapies to manage bacterial pathogens, an enhanced understanding of phage genetic and functional diversity at the population level, and how this, in turn, impacts bacterial evolution and virulence, is necessary. This study presents data on the genetic similarity among Xanthomonas arboricola pv. pruni (Xap) strains isolated from different geographic locations that display different lytic phenotypes when challenged with a panel of six phage isolates collected in the same region over four decades. The minor yet significant genetic variation among this small population of Xap strains is structured by both geographic location and response to phage infection. Phage genomes are also highly similar, with conserved and diverse genomic loci that correspond to isolation year. The six phages characterized here cluster into the Kantovirinae subfamily and possibly form a new genus. Only future studies will elucidate the role of Xap and Xapφ phage genes identified here in the virulence and lysis of Xap and how these, in turn, impact bacterial spot disease outcomes. The research and tripartite pathosystem presented here provides a unique opportunity to investigate the coevolution of phage-phytobacterial pathogen-plant host in depth in an agricultural setting with the potential to monitor the rate at which phage populations contribute to bacterial genetic diversity across geographic and temporal scales.}, journal={Phytobiomes Journal}, publisher={Scientific Societies}, author={D'Amico-Willman, Katherine M. and Joglekar, Prasanna and Ritchie, David F. and Smith, Amber M. and Heiberger, Helena and Huerta, Alejandra I.}, year={2024}, month={Jul} }
 @article{d’amico-willman_niederhuth_sovic_anderson_gradziel_fresnedo-ramírez_2024, title={Hypermethylation and small RNA expression are associated with increased age in almond (Prunus dulcis [Mill.] D.A. Webb) accessions}, volume={338}, ISSN={0168-9452}, url={http://dx.doi.org/10.1016/j.plantsci.2023.111918}, DOI={10.1016/j.plantsci.2023.111918}, abstractNote={The focus of this study is to profile changes in DNA methylation and small RNA expression occurring with increased age in almond breeding germplasm to identify possible biomarkers of age that can be used to assess the potential of individuals to develop aging-related disorders. To profile DNA methylation in almond germplasm, 70 methylomes were generated from almond individuals representing three age cohorts (11, 7, and 2 years old) using an enzymatic methyl-seq approach followed by analysis to call differentially methylated regions (DMRs) within these cohorts. Small RNA (sRNA) expression was profiled in three breeding selections, each from two age cohorts (1 and 6 years old), using sRNA-Seq followed by differential expression analysis. Weighted chromosome-level methylation analysis reveals hypermethylation in 11-year-old almond breeding selections when compared to 2-year-old selections in the CG and CHH contexts. Seventeen consensus DMRs were identified in all age contrasts. sRNA expression differed significantly between the two age cohorts tested, with significantly decreased expression in sRNAs in the 6-year-old selections compared to the 1-year-old. Almond shows a pattern of hypermethylation and decreased sRNA expression with increased age. Identified DMRs and differentially expressed sRNAs could function as putative biomarkers of age following validation in additional age groups.}, journal={Plant Science}, publisher={Elsevier BV}, author={D’Amico-Willman, Katherine M. and Niederhuth, Chad E. and Sovic, Michael G. and Anderson, Elizabeth S. and Gradziel, Thomas M. and Fresnedo-Ramírez, Jonathan}, year={2024}, month={Jan}, pages={111918} }
 @article{d'amico-willman_montalban_joglekar_duin_ritchie_fagen_huerta_2024, title={Whole-Genome Sequence Resources for <i>Pseudomonas amygdali</i> pv. <i>sesami</i> and <i>Xanthomonas arboricola</i> Isolated from Sesame (<i>Sesamum indicum</i>) in North Carolina in 2022}, volume={7}, ISSN={2690-5442}, url={http://dx.doi.org/10.1094/PHYTOFR-11-23-0148-A}, DOI={10.1094/PHYTOFR-11-23-0148-A}, abstractNote={Sesame ( Sesamum indicum) is a specialty crop with increasing interest as an alternative, rotational crop for U.S. agricultural systems. This crop is susceptible to several pathogens, including Pseudomonas and Xanthomonas species. Two bacterial isolates were recently cultured from sesame in North Carolina symptomatic of bacterial spot and identified as Pseudomonas amygdali pv. sesami (Pas) and Xanthomonas sp. These isolates were used for hybrid whole-genome sequencing and assembly using Illumina and PacBio to develop robust genomic resources for these disease-causing strains. The results provide the most complete Pas genome available and placed the Xanthomonas sp. isolate into the X. arboricola species designation. Improved genomic resources for pathogens of sesame are needed to accurately detect, characterize, and employ timely management of the disease. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .}, journal={PhytoFrontiers™}, publisher={Scientific Societies}, author={D'Amico-Willman, Katherine M. and Montalban, Kimberly M. and Joglekar, Prasanna and Duin, Izabela Moura and Ritchie, David F. and Fagen, Jennie and Huerta, Alejandra I.}, year={2024}, month={Jul} }
 @article{fresnedo‐ramírez_anderson_d'amico‐willman_gradziel_2023, title={A review of plant epigenetics through the lens of almond}, volume={16}, ISSN={1940-3372 1940-3372}, url={http://dx.doi.org/10.1002/tpg2.20367}, DOI={10.1002/tpg2.20367}, abstractNote={AbstractWhile genomes were originally seen as static entities that stably held and organized genetic information, recent advances in sequencing have uncovered the dynamic nature of the genome. New conceptualizations of the genome include complex relationships between the environment and gene expression that must be maintained, regulated, and sometimes even transmitted over generations. The discovery of epigenetic mechanisms has allowed researchers to understand how traits like phenology, plasticity, and fitness can be altered without changing the underlying deoxyribonucleic acid sequence. While many discoveries were first made in animal systems, plants provide a particularly complex set of epigenetic mechanisms due to unique aspects of their biology and interactions with human selective breeding and cultivation. In the plant kingdom, annual plants have received the most attention; however, perennial plants endure and respond to their environment and human management in distinct ways. Perennials include crops such as almond, for which epigenetic effects have long been linked to phenomena and even considered relevant for breeding. Recent discoveries have elucidated epigenetic phenomena that influence traits such as dormancy and self‐compatibility, as well as disorders like noninfectious bud failure, which are known to be triggered by the environment and influenced by inherent aspects of the plant. Thus, epigenetics represents fertile ground to further understand almond biology and production and optimize its breeding. Here, we provide our current understanding of epigenetic regulation in plants and use almond as an example of how advances in epigenetics research can be used to understand biological fitness and agricultural performance in crop plants.}, number={4}, journal={The Plant Genome}, publisher={Wiley}, author={Fresnedo‐Ramírez, Jonathan and Anderson, Elizabeth S. and D'Amico‐Willman, Katherine and Gradziel, Thomas M.}, year={2023}, month={Jul} }
 @article{d’amico-willman_ritchie_huerta_2023, title={Bacteriophage, Xanthomonas, and peach (Prunus persica): A model for tripartite host-microbe interactions on disease outcomes}, volume={113}, number={11S}, journal={Phytopathology}, author={D’Amico-Willman, K. and Ritchie, D.F. and Huerta, A.I.}, year={2023}, pages={126} }
 @inbook{fresnedo ramírez_d’amico-willman_gradziel_2023, title={Epigenetic Regulation in Almond}, ISBN={9783030303013 9783030303020}, ISSN={2199-4781 2199-479X}, url={http://dx.doi.org/10.1007/978-3-030-30302-0_5}, DOI={10.1007/978-3-030-30302-0_5}, abstractNote={Rapid advances in sequencing technologies have enabled researchers to reconceptualize genomes as dynamic entities with functions beyond storage and organization of genetic information. Evidence of this dynamic nature includes the discovery of epigenetic mechanisms driving feedback loops between environmental stimuli and gene expression. These mechanisms are particularly complex in plant genomes where research has demonstrated epigenetic memory and maintenance, regulation, and even inheritance of genome modifications. These modifications do not alter the coded information stored in DNA but influence traits like phenology, plasticity, and fitness. In this chapter, we provide an overview of the framework of epigenetic regulation in plants and outline advances in our understanding of epigenetic mechanisms influencing biological fitness and agricultural performance in almond.}, booktitle={Compendium of Plant Genomes}, publisher={Springer International Publishing}, author={Fresnedo Ramírez, Jonathan and D’Amico-Willman, Katherine and Gradziel, Thomas M.}, year={2023}, pages={59–75} }
 @inproceedings{heiberger_huerta_d’amico-willman_ritchie_2023, place={Raleigh, NC}, title={Exploring How Bacteriophages Infect the Peach Pathogen, Xanthomonas arboricola pv. pruni}, url={https://undergradresearch.dasa.ncsu.edu/wp-content/uploads/sites/43/2023/07/2023-Summer-Symposium-Abstract-Book.pdf.}, booktitle={22nd Annual Summer Undergraduate Research & Creativity Symposium Abstract Book}, publisher={NC State University}, author={Heiberger, H. and Huerta, A.I. and D’Amico-Willman, K. and Ritchie, D.F.}, year={2023}, month={Jul} }
 @article{busato_chatterjee_d’amico-willman_gnangnon_steck_2023, title={Postdoc leaders share tips for efficient internal management of postdoctoral associations}, volume={21}, number={2}, journal={POSTDOCket}, publisher={National Postdoc Association}, author={Busato, S. and Chatterjee, N. and D’Amico-Willman, K. and Gnangnon, B. and Steck, V.}, year={2023} }
 @article{d’amico-willman_ritchie_huerta_2022, title={Building an ecological model of bacteria-bacteriophage interactions using the Xanthomonas arboricola pv. pruni-peach pathosystem}, volume={112}, number={11S}, journal={Phytopathology}, author={D’Amico-Willman, K. and Ritchie, D.F. and Huerta, A.I.}, year={2022}, pages={S3.189} }
 @article{d’amico-willman_joglekar_luna_ritchie_fagen_huerta_2022, title={Complete Genome Sequence of Xanthomonas arboricola pv.
            <i>pruni
            Strain Xcp1 Isolated in 1984 from a Bacterial Spot Spring Canker on Prunus persica var.
            <i>nucipersica
            cv. “Redgold”}, volume={11}, ISSN={2576-098X}, url={http://dx.doi.org/10.1128/mra.00209-22}, DOI={10.1128/mra.00209-22}, abstractNote={
            Xanthomonas arboricola
            pv.
            pruni
            is an important plant pathogen and the causal agent of bacterial spot of stone fruits (
            Prunus
            spp). Here, we report a complete genome of
            X. arboricola
            pv.
            pruni
            strain Xcp1 generated from hybrid PacBio Sequel and Illumina NextSeq2000 sequencing.
          }, number={12}, journal={Microbiology Resource Announcements}, publisher={American Society for Microbiology}, author={D’Amico-Willman, Katherine M. and Joglekar, Prasanna and Luna, Emily K. and Ritchie, David F. and Fagen, Jennie and Huerta, Alejandra I.}, editor={Dunning Hotopp, Julie C.Editor}, year={2022}, month={Dec} }
 @article{d’amico-willman_sideli_allen_anderson_gradziel_fresnedo-ramírez_2022, title={Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) D.A. Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond × Peach Hybrid Population}, volume={13}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2022.804145}, DOI={10.3389/fpls.2022.804145}, abstractNote={Almond [Prunus dulcis(Mill.) D.A. Webb] is an economically important nut crop susceptible to the genetic disorder, Non-infectious Bud Failure (NBF). Despite the severity of exhibition in several prominent almond cultivars, no causal mechanism has been identified underlying NBF development. The disorder is hypothesized to be associated with differential DNA methylation patterns based on patterns of inheritance (i.e., via sexual reproduction and clonal propagation) and previous work profiling methylation in affected trees. Peach (Prunus persicaL. Batsch) is a closely related species that readily hybridizes with almond; however, peach is not known to exhibit NBF. A cross between an NBF-exhibiting ‘Carmel’ cultivar and early flowering peach (‘40A17’) produced an F1where ∼50% of progeny showed signs of NBF, including canopy die-back, erratic branching patterns (known as “crazy-top”), and rough bark. In this study, whole-genome DNA methylation profiles were generated for three F1progenies exhibiting NBF and three progenies considered NBF-free. Subsequent alignment to both the almond and peach reference genomes showed an increase in genome-wide methylation levels in NBF hybrids in CG and CHG contexts compared to no-NBF hybrids when aligned to the almond genome but no difference in methylation levels when aligned to the peach genome. Significantly differentially methylated regions (DMRs) were identified by comparing methylation levels across the genome between NBF- and no-NBF hybrids in each methylation context. In total, 115,635 DMRs were identified based on alignment to the almond reference genome, and 126,800 DMRs were identified based on alignment to the peach reference genome. Nearby genes were identified as associated with the 39 most significant DMRs occurring either in the almond or peach alignments alone or occurring in both the almond and peach alignments. These DMR-associated genes include several uncharacterized proteins and transposable elements. Quantitative PCR was also performed to analyze the gene expression patterns of these identified gene targets to determine patterns of differential expression associated with differential DNA methylation. These DMR-associated genes, particularly those showing corresponding patterns of differential gene expression, represent key targets for almond breeding for future cultivars and mitigating the effects of NBF-exhibition in currently affected cultivars.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={D’Amico-Willman, Katherine M. and Sideli, Gina M. and Allen, Brian J. and Anderson, Elizabeth S. and Gradziel, Thomas M. and Fresnedo-Ramírez, Jonathan}, year={2022}, month={Feb} }
 @article{d’amico-willman_ouma_meulia_sideli_gradziel_fresnedo-ramírez_2022, title={Whole-genome sequence and methylome profiling of the almond [<i>Prunus dulcis</i> (Mill.) D.A. Webb] cultivar ‘Nonpareil’}, volume={12}, ISSN={2160-1836}, url={http://dx.doi.org/10.1093/g3journal/jkac065}, DOI={10.1093/g3journal/jkac065}, abstractNote={Abstract Almond [Prunus dulcis (Mill.) D.A. Webb] is an economically important, specialty nut crop grown almost exclusively in the United States. Breeding and improvement efforts worldwide have led to the development of key, productive cultivars, including ‘Nonpareil,’ which is the most widely grown almond cultivar. Thus far, genomic resources for this species have been limited, and a whole-genome assembly for ‘Nonpareil’ is not currently available despite its economic importance and use in almond breeding worldwide. We generated a 571X coverage genome sequence using Illumina, PacBio, and optical mapping technologies. Gene prediction revealed 49,321 putative genes using MinION Oxford nanopore and Illumina RNA sequencing, and genome annotation found that 68% of predicted models are associated with at least one biological function. Furthermore, epigenetic signatures of almond, namely DNA cytosine methylation, have been implicated in a variety of phenotypes including self-compatibility, bud dormancy, and development of noninfectious bud failure. In addition to the genome sequence and annotation, this report also provides the complete methylome of several almond tissues, including leaf, flower, endocarp, mesocarp, exocarp, and seed coat. Comparisons between methylation profiles in these tissues revealed differences in genome-wide weighted % methylation and chromosome-level methylation enrichment.}, number={5}, journal={G3 Genes|Genomes|Genetics}, publisher={Oxford University Press (OUP)}, author={D’Amico-Willman, Katherine M and Ouma, Wilberforce Z and Meulia, Tea and Sideli, Gina M and Gradziel, Thomas M and Fresnedo-Ramírez, Jonathan}, editor={Ingvarsson, PEditor}, year={2022}, month={Mar} }
 @misc{d’amico-willman_niederhuth_willman_gradziel_ouma_meulia_fresnedo-ramírez_2021, title={Integrated analysis of the methylome and transcriptome of twin almonds (<i>Prunus dulcis</i>[Mill.] D.A.Webb) reveals genomic features associated with non-infectious bud failure}, url={http://dx.doi.org/10.1101/2021.02.08.430330}, DOI={10.1101/2021.02.08.430330}, abstractNote={I. Summary Almond ( Prunus dulcis [Mill.] D.A.Webb) exhibits an age-related disorder called non-infectious bud-failure (BF) affecting vegetative bud development and nut yield. The underlying cause of BF remains unknown but is hypothesized to be associated with heritable epigenetic mechanisms. To address this disorder and its epigenetic components, we utilized a monozygotic twin study model profiling genome-wide DNA methylation and gene expression in two sets of twin almonds discordant for BF-exhibition. Analysis of DNA methylation patterns show that BF-exhibition and methylation, namely hypomethylation, are not independent phenomena. Transcriptomic data generated from the twin pairs also shows genome-wide differential gene expression associated with BF-exhibition. After identifying differentially methylated regions (DMRs) in each twin pair, a comparison revealed 170 shared DMRs between the two twin pairs. These DMRs and the associated genetic components may play a role in BF-exhibition. A subset of 52 shared DMRs are in close proximity to genes involved in meristem maintenance, cell cycle regulation, and response to heat stress. Annotation of specific genes included involvement in processes like cell wall development, calcium ion signaling, and DNA methylation. Results of this work support the hypothesis that BF-exhibition is associated with hypomethylation in almond, and identified DMRs and differentially expressed genes can serve as potential biomarkers to assess BF-potential in almond germplasm. Our results contribute to an understanding of the contribution of epigenetic disorders in agricultural performance and biological fitness of perennials. II. Significance This study examines epigenetic components underlying noninfectious bud failure, an aging-related disorder affecting almond. Results from this work contribute to our understanding of the implications of DNA methylation on agricultural production, namely perennial fruit and nut production, due to effects on growth, development, and reproduction. Describing the methylome of discordant, monozygotic twin almonds enables the study of genomic features underlying noninfectious bud failure in this economically important crop.}, publisher={Cold Spring Harbor Laboratory}, author={D’Amico-Willman, Katherine M. and Niederhuth, Chad E. and Willman, Matthew R. and Gradziel, Thomas M. and Ouma, Wilburforce Z. and Meulia, Tea and Fresnedo-Ramírez, Jonathan}, year={2021}, month={Feb} }
 @article{d'amico-willman_anderson_gradziel_fresnedo-ramírez_2021, title={Relative Telomere Length and Telomerase Reverse Transcriptase (TERT) Expression Are Associated with Age in Almond (Prunus dulcis [Mill.] D.A.Webb)}, volume={10}, ISSN={2223-7747}, url={http://dx.doi.org/10.3390/plants10020189}, DOI={10.3390/plants10020189}, abstractNote={While all organisms age, our understanding of how aging occurs varies among species. The aging process in perennial plants is not well-defined, yet can have implications on production and yield of valuable fruit and nut crops. Almond exhibits an age-related disorder known as non-infectious bud failure (BF) that affects vegetative bud development, indirectly affecting kernel yield. This species and disorder present an opportunity to address aging in a commercially relevant and vegetatively propagated perennial crop. The hypothesis tested in this study was that relative telomere length and/or telomerase reverse transcriptase (TERT) expression can serve as biomarkers of aging in almond. Relative telomere lengths and expression of TERT, a subunit of the enzyme telomerase, were measured via qPCR methods using bud and leaf samples collected from distinct age cohorts over a two-year period. Results from this work show a marginal but significant association between both relative telomere length and TERT expression, and age, suggesting that as almonds age, telomeres shorten and TERT expression decreases. This work provides information on potential biomarkers of perennial plant aging, contributing to our knowledge of this process. In addition, these results provide opportunities to address BF in almond breeding and nursery propagation.}, number={2}, journal={Plants}, publisher={MDPI AG}, author={D'Amico-Willman, Katherine M. and Anderson, Elizabeth S. and Gradziel, Thomas M. and Fresnedo-Ramírez, Jonathan}, year={2021}, month={Jan}, pages={189} }
 @inproceedings{conrad_d’amico_bonello_mcpherson_wood_lopez-nicora_2020, title={Incidence and distribution of resistance in a coast live oak/sudden oak death pathosystem}, booktitle={Proceedings of the seventh sudden oak death science and management symposium: Healthy plants in a world with Phytophthora}, publisher={U.S. Department of Agriculture Forest Service}, author={Conrad, A.O. and D’Amico, K.M. and Bonello, P. and McPherson, B.A. and Wood, D.L. and Lopez-Nicora, H.D.}, editor={Frankel, S.J. and Alexander, J.M.Editors}, year={2020}, pages={13} }
 @article{conrad_mcpherson_lopez-nicora_d'amico_wood_bonello_2019, title={Disease incidence and spatial distribution of host resistance in a coast live oak/sudden oak death pathosystem}, volume={433}, ISSN={0378-1127}, url={http://dx.doi.org/10.1016/j.foreco.2018.11.035}, DOI={10.1016/j.foreco.2018.11.035}, abstractNote={Sudden oak death (SOD) results in extensive mortality of native populations of red oak (Quercus spp.) and tanoak (Notholithocarpus densiflorus) in coastal California and Oregon. The pathogen, Phytophthora ramorum, causes a syndrome in Q. agrifolia (coast live oak, CLO) characterized by bleeding stem cankers, attacks by bark and ambrosia beetles, and development of the endophytic fungus, Annulohypoxylon thouarsianum. The study examined disease incidence and resistance in CLO within Northern California stands that had no apparent prior exposure to the pathogen. Seven years after artificial inoculation of mature trees distributed between two separate stands in a California wildland, 27% of CLO expressed resistance to P. ramorum, while 61% died (N = 149). The remaining trees were alive but symptomatic. External and subcortical canker lengths, measured approximately one year post-inoculation, were significant predictors of CLO resistance and survival seven years post-inoculation. Spatial analysis also revealed that variation in CLO susceptibility to P. ramorum is aggregated on the landscape, suggesting that more resistant and susceptible trees tend to co-occur and that resistance is a heritable trait. From 2011 to 2017 the incidence of natural infections in a second cohort of non-inoculated trees increased from 2.0% (N = 447) to 13.2% (N = 423). Altogether, these findings suggest that estimating the frequency and determining the spatial distribution of resistant trees on the landscape can be used to identify sites that should be targeted for germplasm collection and habitat conservation.}, journal={Forest Ecology and Management}, publisher={Elsevier BV}, author={Conrad, Anna O. and McPherson, Brice A. and Lopez-Nicora, Horacio D. and D'Amico, Katherine M. and Wood, David L. and Bonello, Pierluigi}, year={2019}, month={Feb}, pages={618–624} }
 @article{d'amico_filiatrault_2017, title={The conserved hypothetical protein PSPTO_3957 is essential for virulence in the plant pathogen Pseudomonas syringae pv. tomato DC3000}, volume={364}, ISSN={1574-6968}, url={http://dx.doi.org/10.1093/femsle/fnx004}, DOI={10.1093/femsle/fnx004}, abstractNote={The plant pathogen Pseudomonas syringae accounts for substantial crop losses and is considered an important agricultural issue. To better manage disease in the field, it is important to have an understanding of the underlying genetic mechanisms that mediate virulence. There are a substantial number of genes in sequenced bacterial genomes, including P. syringae, that encode for conserved hypothetical proteins; some of these have been functionally characterized in other Pseudomonads and have been demonstrated to play important roles in disease. PSPTO_3957 encodes a conserved hypothetical protein of unknown function. To evaluate the role of PSPTO_3957 in P. syringae pv. tomato DC3000, a PSPTO_3957 deletion mutant was constructed. Here, we show that PSPTO_3957 does not influence growth on rich media, motility or biofilm formation but is necessary for nitrate assimilation and full virulence in P. syringae. Our results have revealed an important role for PSPTO_3957 in the biology of P. syringae. Given the conservation of this protein among many bacteria, this protein might serve as an attractive target for disease management of this and other bacterial plant pathogens.}, number={8}, journal={FEMS Microbiology Letters}, publisher={Oxford University Press (OUP)}, author={D'Amico, Katherine and Filiatrault, Melanie J.}, year={2017}, month={Apr} }
 @article{chakravarthy_butcher_liu_d’amico_coster_filiatrault_2017, title={Virulence of <i>Pseudomonas syringae</i> pv. <i>tomato</i> DC3000 Is Influenced by the Catabolite Repression Control Protein Crc}, volume={30}, ISSN={0894-0282 1943-7706}, url={http://dx.doi.org/10.1094/MPMI-09-16-0196-R}, DOI={10.1094/MPMI-09-16-0196-R}, abstractNote={Pseudomonas syringae infects diverse plant species and is widely used as a model system in the study of effector function and the molecular basis of plant diseases. Although the relationship between bacterial metabolism, nutrient acquisition, and virulence has attracted increasing attention in bacterial pathology, it is largely unexplored in P. syringae. The Crc (catabolite repression control) protein is a putative RNA-binding protein that regulates carbon metabolism as well as a number of other factors in the pseudomonads. Here, we show that deletion of crc increased bacterial swarming motility and biofilm formation. The crc mutant showed reduced growth and symptoms in Arabidopsis and tomato when compared with the wild-type strain. We have evidence that the crc mutant shows delayed hypersensitive response (HR) when infiltrated into Nicotiana benthamiana and tobacco. Interestingly, the crc mutant was more susceptible to hydrogen peroxide, suggesting that, in planta, the mutant may be sensitive to reactive oxygen species generated during pathogen-associated molecular pattern–triggered immunity (PTI). Indeed, HR was further delayed when PTI-induced tissues were challenged with the crc mutant. The crc mutant did not elicit an altered PTI response in plants compared with the wild-type strain. We conclude that Crc plays an important role in growth and survival during infection.}, number={4}, journal={Molecular Plant-Microbe Interactions®}, publisher={Scientific Societies}, author={Chakravarthy, Suma and Butcher, Bronwyn G. and Liu, Yingyu and D’Amico, Katherine and Coster, Matthew and Filiatrault, Melanie J.}, year={2017}, month={Apr}, pages={283–294} }
 @article{butcher_chakravarthy_d’amico_stoos_filiatrault_2016, title={Disruption of the carA gene in Pseudomonas syringae results in reduced fitness and alters motility}, volume={16}, ISSN={1471-2180}, url={http://dx.doi.org/10.1186/s12866-016-0819-z}, DOI={10.1186/s12866-016-0819-z}, abstractNote={Pseudomonas syringae infects diverse plant species and is widely used in the study of effector function and the molecular basis of disease. Although the relationship between bacterial metabolism, nutrient acquisition and virulence has attracted increasing attention in bacterial pathology, there is limited knowledge regarding these studies in Pseudomonas syringae. The aim of this study was to investigate the function of the carA gene and the small RNA P32, and characterize the regulation of these transcripts.Disruption of the carA gene (ΔcarA) which encodes the predicted small chain of carbamoylphosphate synthetase, resulted in arginine and pyrimidine auxotrophy in Pseudomonas syringae pv. tomato DC3000. Complementation with the wild type carA gene was able to restore growth to wild-type levels in minimal medium. Deletion of the small RNA P32, which resides immediately upstream of carA, did not result in arginine or pyrimidine auxotrophy. The expression of carA was influenced by the concentrations of both arginine and uracil in the medium. When tested for pathogenicity, ΔcarA showed reduced fitness in tomato as well as Arabidopsis when compared to the wild-type strain. In contrast, mutation of the region encoding P32 had minimal effect in planta. ΔcarA also exhibited reduced motility and increased biofilm formation, whereas disruption of P32 had no impact on motility or biofilm formation.Our data show that carA plays an important role in providing arginine and uracil for growth of the bacteria and also influences other factors that are potentially important for growth and survival during infection. Although we find that the small RNA P32 and carA are co-transcribed, P32 does not play a role in the phenotypes that carA is required for, such as motility, cell attachment, and virulence. Additionally, our data suggests that pyrimidines may be limited in the apoplastic space of the plant host tomato.}, number={1}, journal={BMC Microbiology}, publisher={Springer Science and Business Media LLC}, author={Butcher, Bronwyn G. and Chakravarthy, Suma and D’Amico, Katherine and Stoos, Kari Brossard and Filiatrault, Melanie J.}, year={2016}, month={Aug} }
 @article{park_bao_butcher_d’amico_xu_stodghill_schneider_cartinhour_filiatrault_2014, title={Analysis of the small RNA spf in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000}, volume={160}, ISSN={1350-0872 1465-2080}, url={http://dx.doi.org/10.1099/mic.0.076497-0}, DOI={10.1099/mic.0.076497-0}, abstractNote={Bacteria contain small non-coding RNAs (ncRNAs) that are typically responsible for altering transcription, translation or mRNA stability. ncRNAs are important because they often regulate virulence factors and susceptibility to various stresses. Here, the regulation of a recently described ncRNA of Pseudomonas syringae DC3000, spot 42 (now referred to as spf ), was investigated. A putative RpoE binding site was identified upstream of spf in strain DC3000. RpoE is shown to regulate the expression of spf . Also, deletion of spf results in increased sensitivity to hydrogen peroxide compared with the wild-type strain, suggesting that spf plays a role in susceptibility to oxidative stress. Furthermore, expression of alg8 is shown to be influenced by spf , suggesting that this ncRNA plays a role in alginate biosynthesis. Structural and comparative genomic analyses show this ncRNA is well conserved among the pseudomonads. The findings provide new information on the regulation and role of this ncRNA in P. syringae .}, number={5}, journal={Microbiology}, publisher={Microbiology Society}, author={Park, So Hae and Bao, Zhongmeng and Butcher, Bronwyn G. and D’Amico, Katherine and Xu, Yun and Stodghill, Paul and Schneider, David J. and Cartinhour, Samuel and Filiatrault, M. J.}, year={2014}, month={May}, pages={941–953} }
 @article{d'amico_horton_maynard_stehman_oakes_powell_2015, title={Comparisons of Ectomycorrhizal Colonization of Transgenic American Chestnut with Those of the Wild Type, a Conventionally Bred Hybrid, and Related Fagaceae Species}, volume={81}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/AEM.02169-14}, DOI={10.1128/AEM.02169-14}, abstractNote={ABSTRACT American chestnut ( Castanea dentata [Marsh.] Borkh.) dominated the eastern forests of North America, serving as a keystone species both ecologically and economically until the introduction of the chestnut blight, Cryphonectria parasitica , functionally eradicated the species. Restoration efforts include genetic transformation utilizing genes such as oxalate oxidase to produce potentially blight-resistant chestnut trees that could be released back into the native range. However, before such a release can be undertaken, it is necessary to assess nontarget impacts. Since oxalate oxidase is meant to combat a fungal pathogen, we are particularly interested in potential impacts of this transgene on beneficial fungi. This study compares ectomycorrhizal fungal colonization on a transgenic American chestnut clone expressing enhanced blight resistance to a wild-type American chestnut, a conventionally bred American-Chinese hybrid chestnut, and other Fagaceae species. A greenhouse bioassay used soil from two field sites with different soil types and land use histories. The number of colonized root tips was counted, and fungal species were identified using morphology, restriction fragment length polymorphism (RFLP), and DNA sequencing. Results showed that total ectomycorrhizal colonization varied more by soil type than by tree species. Individual fungal species varied in their colonization rates, but there were no significant differences between colonization on transgenic and wild-type chestnuts. This study shows that the oxalate oxidase gene can increase resistance against Cryphonectria parasitica without changing the colonization rate for ectomycorrhizal species. These findings will be crucial for a potential deregulation of blight-resistant American chestnuts containing the oxalate oxidase gene.}, number={1}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={D'Amico, Katherine M. and Horton, Thomas R. and Maynard, Charles A. and Stehman, Stephen V. and Oakes, Allison D. and Powell, William A.}, editor={Cullen, D.Editor}, year={2015}, month={Jan}, pages={100–108} }
 @article{park_butcher_anderson_pellegrini_bao_d’amico_filiatrault_2013, title={Analysis of the small RNA P16/RgsA in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000}, volume={159}, ISSN={1350-0872 1465-2080}, url={http://dx.doi.org/10.1099/mic.0.063826-0}, DOI={10.1099/mic.0.063826-0}, abstractNote={Bacteria contain small non-coding RNAs (ncRNAs) that are responsible for altering transcription, translation or mRNA stability. ncRNAs are important because they regulate virulence factors and susceptibility to various stresses. Here, the regulation of a recently described ncRNA of Pseudomonas syringae pv. tomato DC3000, P16, was investigated. We determined that RpoS regulates the expression of P16. We found that deletion of P16 results in increased sensitivity to hydrogen peroxide compared to the wild-type strain, suggesting that P16 plays a role in the bacteria's susceptibility to oxidative stress. Additionally the P16 mutant displayed enhanced resistance to heat stress. Our findings provide new information on the regulation and role of this ncRNA in P. syringae.}, number={Pt_2}, journal={Microbiology}, publisher={Microbiology Society}, author={Park, So Hae and Butcher, Bronwyn G. and Anderson, Zoe and Pellegrini, Nola and Bao, Zhongmeng and D’Amico, Katherine and Filiatrault, Melanie J.}, year={2013}, month={Feb}, pages={296–306} }
 @article{d'amico_horton_maynard_powell_2011, title={Assessing ectomycorrhizal associations and transgene expression in transgenic Castanea dentata}, volume={5}, ISSN={1753-6561}, url={http://dx.doi.org/10.1186/1753-6561-5-S7-O54}, DOI={10.1186/1753-6561-5-S7-O54}, abstractNote={Background American chestnut (Castanea dentata) once dominated the forests of the eastern United States until the introduction of a Chinese fungal pathogen Cryphonectria parasitica(causal agent of the chestnut blight) decimated the species. This tree was important not only ecologically, but also played a significant role economically. Restoration programs are implementing a variety of techniques, including genetic transformation, to develop a blight resistant tree that can be reintroduced into the native chestnut range (S.A. Merkle, 2007, Tree Genetics and Genomics, 3, 111-18). Specific genes involved in plant defense responses are being introduced into American chestnut via Agrobacterium-mediated transformation, with the hope that one gene or a combination of genes will aid in chestnut defense against blight (L.D. Polin, 2006, Plant Cell, Tissue, and Organ Culture, 84, 69-79). One gene of particular interest to the transgenic project is oxalate oxidase, a defense related gene from wheat that has also been shown to enhance the defense response of other plants when introduced through genetic transformation (H. Liang, 2001, Plant Molecular Biology, 45, 619-29). American chestnut transformation with a binary vector containing oxalate oxidase has produced a number of transgenic events, many of which have already been regenerated plants (unpublished data). Before releasing any transgenic plant it is necessary to assess any non-target impacts the introduced genes may have on associated microbial communities. C. parasiticais a fungal pathogen, so we are particularly interested in studying the effects of any transgene on the symbiotic relationship between the host plant and mycorrhizaeforming fungi. Prior studies have examined the potential impact of transgenic plants on ectomycorrhizal fungi (K. L. Oliver, 2008, Applied and Environmental Microbiology, 74, 5340-48).}, number={S7}, journal={BMC Proceedings}, publisher={Springer Science and Business Media LLC}, author={D'Amico, Katherine and Horton, Thomas and Maynard, Charles and Powell, William}, year={2011}, month={Sep} }
 @article{d’amico_horton_maynard_powell_2010, title={Comparing ectomycorrhizal colonization on transgenic, hybrid, and wildtype Castanea dentata}, volume={100}, number={11S}, journal={Phytopathology}, author={D’Amico, K. and Horton, T.R. and Maynard, C.A. and Powell, W.A.}, year={2010} }