@article{noar_thomas_2022, title={Genetic Characteristics and Metabolic Interactions between Pseudocercospora fijiensis and Banana: Progress toward Controlling Black Sigatoka}, url={https://www.mdpi.com/2223-7747/11/7/948/htm}, DOI={https://doi.org/10.3390/plants11070948}, abstractNote={The international importance of banana and severity of black Sigatoka disease have led to extensive investigations into the genetic characteristics and metabolic interactions between the Dothideomycete Pseudocercospora fijiensis and its banana host. P. fijiensis was shown to have a greatly expanded genome compared to other Dothideomycetes, due to the proliferation of retrotransposons. Genome analysis suggests the presence of dispensable chromosomes that may aid in fungal adaptation as well as pathogenicity. Genomic research has led to the characterization of genes and metabolic pathways involved in pathogenicity, including: secondary metabolism genes such as PKS10-2, genes for mitogen-activated protein kinases such as Fus3 and Slt2, and genes for cell wall proteins such as glucosyl phosphatidylinositol (GPI) and glycophospholipid surface (Gas) proteins. Studies conducted on resistance mechanisms in banana have documented the role of jasmonic acid and ethylene pathways. With the development of banana transformation protocols, strategies for engineering resistance include transgenes expressing antimicrobial peptides or hydrolytic enzymes as well as host-induced gene silencing (HIGS) targeting pathogenicity genes. Pseudocercospora fijiensis has been identified as having high evolutionary potential, given its large genome size, ability to reproduce both sexually and asexually, and long-distance spore dispersal. Thus, multiple control measures are needed for the sustainable control of black Sigatoka disease.}, journal={Plants}, author={Noar, R.D. and Thomas, E.}, year={2022}, month={Mar} }
 @misc{noar_thomas_daub_2022, title={Genetic Characteristics and Metabolic Interactions between Pseudocercospora fijiensis and Banana: Progress toward Controlling Black Sigatoka}, volume={11}, ISSN={["2223-7747"]}, url={https://www.mdpi.com/2223-7747/11/7/948}, DOI={10.3390/plants11070948}, abstractNote={The international importance of banana and severity of black Sigatoka disease have led to extensive investigations into the genetic characteristics and metabolic interactions between the Dothideomycete Pseudocercospora fijiensis and its banana host. P. fijiensis was shown to have a greatly expanded genome compared to other Dothideomycetes, due to the proliferation of retrotransposons. Genome analysis suggests the presence of dispensable chromosomes that may aid in fungal adaptation as well as pathogenicity. Genomic research has led to the characterization of genes and metabolic pathways involved in pathogenicity, including: secondary metabolism genes such as PKS10-2, genes for mitogen-activated protein kinases such as Fus3 and Slt2, and genes for cell wall proteins such as glucosyl phosphatidylinositol (GPI) and glycophospholipid surface (Gas) proteins. Studies conducted on resistance mechanisms in banana have documented the role of jasmonic acid and ethylene pathways. With the development of banana transformation protocols, strategies for engineering resistance include transgenes expressing antimicrobial peptides or hydrolytic enzymes as well as host-induced gene silencing (HIGS) targeting pathogenicity genes. Pseudocercospora fijiensis has been identified as having high evolutionary potential, given its large genome size, ability to reproduce both sexually and asexually, and long-distance spore dispersal. Thus, multiple control measures are needed for the sustainable control of black Sigatoka disease.}, number={7}, journal={PLANTS-BASEL}, author={Noar, Roslyn D. and Thomas, Elizabeth and Daub, Margaret E.}, year={2022}, month={Apr} }
 @article{thomas_noar_daub_2021, title={A polyketide synthase gene cluster required for pathogenicity of Pseudocercospora fijiensis on banana}, volume={16}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0258981}, DOI={10.1371/journal.pone.0258981}, abstractNote={Pseudocercospora fijiensis is the causal agent of the highly destructive black Sigatoka disease of banana. Previous research has focused on polyketide synthase gene clusters in the fungus, given the importance of polyketide pathways in related plant pathogenic fungi. A time course study of expression of the previously identified PKS7-1, PKS8-2, and PKS10-2 gene clusters showed high expression of all three PKS genes and the associated clustered genes in infected banana plants from 2 weeks post-inoculation through 9 weeks. Engineered transformants silenced for PKS8-2 and PKS10-2 were developed and tested for pathogenicity. Inoculation of banana plants with silencing transformants for PKS10-2 showed significant reduction in disease symptoms and severity that correlated with the degree of silencing in the conidia used for inoculation, supporting a critical role for PKS10-2 in disease development. Unlike PKS10-2, a clear role for PKS8-2 could not be determined. Two of four PKS8-2 silencing transformants showed reduced disease development, but disease did not correlate with the degree of PKS8-2 silencing in the transformants. Overall, the degree of silencing obtained for the PKS8-2 transformants was less than that obtained for the PKS10-2 transformants, which may have limited the utility of the silencing strategy to identify a role for PKS8-2 in disease. Orthologous PKS10-2 clusters had previously been identified in the related banana pathogens Pseudocercospora musae and Pseudocercospora eumusae. Genome analysis identified orthologous gene clusters to that of PKS10-2 in the newly sequenced genomes of Pseudocercospora fuligena and Pseudocercospora cruenta, pathogens of tomato and cowpea, respectively. Our results support an important role for the PKS10-2 polyketide pathway in pathogenicity of Pseudocercospora fijiensis, and suggest a possible role for this pathway in disease development by other Pseudocercospora species.}, number={10}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Thomas, Elizabeth and Noar, Roslyn D. and Daub, Margaret E.}, editor={Wilson, Richard A.Editor}, year={2021}, month={Oct}, pages={e0258981} }
 @article{thomas_herrero_eng_gomaa_gillikin_noar_beseli_daub_2020, title={Engineering Cercospora disease resistance via expression of Cercospora nicotianae cercosporin-resistance genes and silencing of cercosporin production in tobacco}, volume={15}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0230362}, DOI={10.1371/journal.pone.0230362}, abstractNote={Fungi in the genus Cercospora cause crop losses world-wide on many crop species. The wide host range and success of these pathogens has been attributed to the production of a photoactivated toxin, cercosporin. We engineered tobacco for resistance to Cercospora nicotianae utilizing two strategies: 1) transformation with cercosporin autoresistance genes isolated from the fungus, and 2) transformation with constructs to silence the production of cercosporin during disease development. Three C. nicotianae cercosporin autoresistance genes were tested: ATR1 and CFP, encoding an ABC and an MFS transporter, respectively, and 71cR, which encodes a hypothetical protein. Resistance to the pathogen was identified in transgenic lines expressing ATR1 and 71cR, but not in lines transformed with CFP. Silencing of the CTB1 polyketide synthase and to a lesser extent the CTB8 pathway regulator in the cercosporin biosynthetic pathway also led to the recovery of resistant lines. All lines tested expressed the transgenes, and a direct correlation between the level of transgene expression and disease resistance was not identified in any line. Resistance was also not correlated with the degree of silencing in the CTB1 and CTB8 silenced lines. We conclude that expression of fungal cercosporin autoresistance genes as well as silencing of the cercosporin pathway are both effective strategies for engineering resistance to Cercospora diseases where cercosporin plays a critical role.}, number={3}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Thomas, Elizabeth and Herrero, Sonia and Eng, Hayde and Gomaa, Nafisa and Gillikin, Jeff and Noar, Roslyn and Beseli, Aydin and Daub, Margaret E.}, editor={Wilson, Richard A.Editor}, year={2020}, month={Mar}, pages={e0230362} }
 @misc{swiderska-burek_daub_thomas_jaszek_pawlik_janusz_2020, title={Phytopathogenic Cercosporoid Fungi-From Taxonomy to Modern Biochemistry and Molecular Biology}, volume={21}, ISSN={["1422-0067"]}, DOI={10.3390/ijms21228555}, abstractNote={Phytopathogenic cercosporoid fungi have been investigated comprehensively due to their important role in causing plant diseases. A significant amount of research has been focused on the biology, morphology, systematics, and taxonomy of this group, with less of a focus on molecular or biochemical issues. Early and extensive research on these fungi focused on taxonomy and their classification based on in vivo features. Lately, investigations have mainly addressed a combination of characteristics such as morphological traits, host specificity, and molecular analyses initiated at the end of the 20th century. Some species that are important from an economic point of view have been more intensively investigated by means of genetic and biochemical methods to better understand the pathogenesis processes. Cercosporin, a photoactivated toxin playing an important role in Cercospora diseases, has been extensively studied. Understanding cercosporin toxicity in relation to reactive oxygen species (ROS) production facilitated the discovery and regulation of the cercosporin biosynthesis pathway, including the gene cluster encoding pathway enzymes. Furthermore, these fungi may be a source of other biotechnologically important compounds, e.g., industrially relevant enzymes. This paper reviews methods and important results of investigations of this group of fungi addressed at different levels over the years.}, number={22}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Swiderska-Burek, Urszula and Daub, Margaret E. and Thomas, Elizabeth and Jaszek, Magdalena and Pawlik, Anna and Janusz, Grzegorz}, year={2020}, month={Nov} }
 @article{noar_thomas_daub_2019, title={A novel polyketide synthase gene cluster in the plant pathogenic fungus Pseudocercospora fijiensis}, volume={14}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0212229}, DOI={10.1371/journal.pone.0212229}, abstractNote={Pseudocercospora fijiensis, causal agent of black Sigatoka of banana, produces polyketide synthase (PKS) pathways shown to be important in disease development by related Dothideomycete fungi. Genome analysis of the P. fijiensis PKS8-1 gene identified it as part of a gene cluster including genes encoding two transcription factors, a regulatory protein, a glyoxylase/beta-lactamase-like protein, an MFS transporter, a cytochrome P450, two aldo/keto reductases, a dehydrogenase, and a decarboxylase. Genome analysis of the related pathogens Pseudocercospora musae, Pseudocercospora eumusae, and Pseudocercospora pini-densiflorae, identified orthologous clusters containing a nearly identical combination of genes. Phylogenetic analysis of PKS8-1 identified homology to PKS proteins in the monodictyphenone and cladofulvin pathways in Aspergillus nidulans and Cladosporium fulvum, respectively. Analysis of clustered genes showed that the PKS8-1 cluster shares genes for enzymes involved in the production of the emodin intermediate in the monodictyphenone and cladofulvin pathways, but differs in many genes, suggesting production of a different metabolic product. Time course analysis of gene expression in infected banana showed up-regulation of PKS8-1 and four of eight clustered genes as early as 2 weeks post-inoculation and remaining high through 9 weeks. Overexpression of the pathway through constitutive expression of an aflR-like transcription factor gene in the cluster resulted in increased expression in culture of PKS8-1 as well as the four clustered genes that are up-regulated in infected plants. No differences were seen in timing or severity of disease symptoms with the overexpression strains relative to controls, however gene expression analysis showed no difference in expression in planta by an overexpression strain relative to controls. Thus constitutive expression of the aflR-like gene is not sufficient to upregulate the pathway above normal expression in planta. Pathway expression during all phases of disease development and conservation of the pathway in related Pseudocercospora species support a role for this pathway in disease.}, number={2}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Noar, Roslyn D. and Thomas, Elizabeth and Daub, Margaret E.}, editor={Lespinet, OlivierEditor}, year={2019}, month={Feb}, pages={e0212229} }
 @article{noar_thomas_xie_carter_ma_daub_2019, title={A polyketide synthase gene cluster associated with the sexual reproductive cycle of the banana pathogen, Pseudocercospora fijiensis}, volume={14}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0220319}, DOI={10.1371/journal.pone.0220319}, abstractNote={Disease spread of Pseudocercospora fijiensis, causal agent of the black Sigatoka disease of banana, depends on ascospores produced through the sexual reproductive cycle. We used phylogenetic analysis to identify P. fijiensis homologs (PKS8-4 and Hybrid8-3) to the PKS4 polyketide synthases (PKS) from Neurospora crassa and Sordaria macrospora involved in sexual reproduction. These sequences also formed a clade with lovastatin, compactin, and betaenone-producing PKS sequences. Transcriptome analysis showed that both the P. fijiensis Hybrid8-3 and PKS8-4 genes have higher expression in infected leaf tissue compared to in culture. Domain analysis showed that PKS8-4 is more similar than Hybrid8-3 to PKS4. pPKS8-4:GFP transcriptional fusion transformants showed expression of GFP in flask-shaped structures in mycelial cultures as well as in crosses between compatible and incompatible mating types. Confocal microscopy confirmed expression in spermagonia in leaf substomatal cavities, consistent with a role in sexual reproduction. A disruption mutant of pks8-4 retained normal pathogenicity on banana, and no differences were observed in growth, conidial production, and spermagonia production. GC-MS profiling of the mutant and wild type did not identify differences in polyketide metabolites, but did identify changes in saturated fatty acid methyl esters and alkene and alkane derivatives. To our knowledge, this is the first report of a polyketide synthase pathway associated with spermagonia.}, number={7}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Noar, Roslyn D. and Thomas, Elizabeth and Xie, De-Yu and Carter, Morgan E. and Ma, Dongming and Daub, Margaret E.}, editor={Lespinet, OlivierEditor}, year={2019}, month={Jul}, pages={e0220319} }
 @inproceedings{oakley_thomas_daub_2017, title={Assessment of key genes in Cercospora nicotianae that encode resistance to cercosporin}, author={Oakley, B. and Thomas, E. and Daub, M.E.}, year={2017} }
 @inproceedings{green_thomas_daub_2017, title={Effects of culture medium on growth and gene expression in the plant pathogen Mycosphaerella fijiensis}, author={Green, A. and Thomas, E. and Daub, M.E.}, year={2017} }
 @article{beseli_amnuaykanjanasin_herrero_thomas_daub_2015, title={Membrane transporters in self resistance of Cercospora nicotianae to the photoactivated toxin cercosporin}, volume={61}, ISSN={0172-8083 1432-0983}, url={http://dx.doi.org/10.1007/s00294-015-0486-x}, DOI={10.1007/s00294-015-0486-x}, abstractNote={The goal of this work is to characterize membrane transporter genes in Cercospora fungi required for autoresistance to the photoactivated, active-oxygen-generating toxin cercosporin they produce for infection of host plants. Previous studies implicated a role for diverse membrane transporters in cercosporin resistance. In this study, transporters identified in a subtractive cDNA library between a Cercospora nicotianae wild type and a cercosporin-sensitive mutant were characterized, including two ABC transporters (CnATR2, CnATR3), an MFS transporter (CnMFS2), a uracil transporter, and a zinc transport protein. Phylogenetic analysis showed that only CnATR3 clustered with transporters previously characterized to be involved in cercosporin resistance. Quantitative RT-PCR analysis of gene expression under conditions of cercosporin toxicity, however, showed that only CnATR2 was upregulated, thus this gene was selected for further characterization. Transformation and expression of CnATR2 in the cercosporin-sensitive fungus Neurospora crassa significantly increased cercosporin resistance. Targeted gene disruption of CnATR2 in the wild type C. nicotianae, however, did not decrease resistance. Expression analysis of other transporters in the cnatr2 mutant under conditions of cercosporin toxicity showed significant upregulation of the cercosporin facilitator protein gene (CFP), encoding an MFS transporter previously characterized as playing an important role in cercosporin autoresistance in Cercospora species. We conclude that cercosporin autoresistance in Cercospora is mediated by multiple genes, and that the fungus compensates for mutations by up-regulation of other resistance genes. CnATR2 may be a useful gene, alone or in addition to other known resistance genes, for engineering Cercospora resistance in crop plants.}, number={4}, journal={Current Genetics}, publisher={Springer Science and Business Media LLC}, author={Beseli, Aydin and Amnuaykanjanasin, Alongkorn and Herrero, Sonia and Thomas, Elizabeth and Daub, Margaret E.}, year={2015}, month={Apr}, pages={601–620} }
 @article{gkarmiri_finlay_alström_thomas_cubeta_högberg_2015, title={Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica}, volume={16}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-015-1758-z}, DOI={10.1186/s12864-015-1758-z}, abstractNote={Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq. Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10 % of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log2 fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation. This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Gkarmiri, Konstantia and Finlay, Roger D. and Alström, Sadhna and Thomas, Elizabeth and Cubeta, Marc A. and Högberg, Nils}, year={2015}, month={Aug} }
 @article{cubeta_thomas_dean_jabaji_neate_tavantzis_toda_vilgalys_bharathan_fedorova-abrams_et al._2014, title={Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP}, volume={2}, ISSN={2169-8287}, url={http://dx.doi.org/10.1128/genomeA.01072-14}, DOI={10.1128/genomeA.01072-14}, abstractNote={ABSTRACT
          
            The soil fungus
            Rhizoctonia solani
            is a pathogen of agricultural crops. Here, we report on the 51,705,945 bp draft consensus genome sequence of
            R. solani
            strain Rhs1AP. A comprehensive understanding of the heterokaryotic genome complexity and organization of
            R. solani
            may provide insight into the plant disease ecology and adaptive behavior of the fungus.
          }, number={5}, journal={Genome Announcements}, publisher={American Society for Microbiology}, author={Cubeta, Marc A. and Thomas, Elizabeth and Dean, Ralph A. and Jabaji, Suha and Neate, Stephen M. and Tavantzis, Stellos and Toda, Takeshi and Vilgalys, Rytas and Bharathan, Narayanaswamy and Fedorova-Abrams, Natalie and et al.}, year={2014}, month={Oct} }
 @inproceedings{baumgardner_thomas_daub_2014, title={Engineering Cercospora disease-resistant plants using fungal resistance genes}, author={Baumgardner, A. and Thomas, E. and Daub, M.E.}, year={2014} }
 @article{losada_pakala_fedorova_joardar_shabalina_hostetler_pakala_zafar_thomas_rodriguez-carres_et al._2014, title={Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3}, volume={352}, ISSN={["1574-6968"]}, DOI={10.1111/1574-6968.12387}, abstractNote={The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Losada, Liliana and Pakala, Suman B. and Fedorova, Natalie D. and Joardar, Vinita and Shabalina, Svetlana A. and Hostetler, Jessica and Pakala, Suchitra M. and Zafar, Nikhat and Thomas, Elizabeth and Rodriguez-Carres, Marianela and et al.}, year={2014}, month={Mar}, pages={165–173} }
 @inproceedings{george_thomas_2013, title={Effective science instruction for young children}, author={George, A. and Thomas, E.}, year={2013} }
 @inproceedings{maldonado_thomas_daub_2013, title={Engineering Cercospora disease-resistant plants using fungal toxin-resistance genes}, author={Maldonado, N. and Thomas, E. and Daub, M.E.}, year={2013} }
 @article{thomas_pakala_joardar_nierman_cubeta_2013, place={Austin, TX}, title={Transcriptional profiling of sclerotia formation in the soil fungus Rhizoctonia solani}, volume={103}, number={S2}, journal={Phytopathology}, publisher={American Phytopathological Society and Mycological Society of America Annual Meeting}, author={Thomas, E. and Pakala, S. and Joardar, V. and Nierman, W.C. and Cubeta, M.A.}, year={2013}, pages={144–145} }
 @inproceedings{thomas_taylor_figueroa-contreras_zhang_ivors_cubeta_2012, title={Investigation of sclerotial morphogenesis in the soil fungus Rhizoctonia solani}, author={Thomas, E. and Taylor, N. and Figueroa-Contreras, M. and Zhang, Z. and Ivors, K.L. and Cubeta, M.A.}, year={2012} }
 @article{thomas_pakala_fedorova_nierman_cubeta_2012, title={Triallelic SNP-mediated genotyping of regenerated protoplasts of the heterokaryotic fungus Rhizoctonia solani}, volume={158}, ISSN={["1873-4863"]}, DOI={10.1016/j.jbiotec.2012.01.024}, abstractNote={The aneuploid and heterokaryotic nuclear condition of the soil fungus Rhizoctonia solani have provided challenges in obtaining a complete genome sequence. To better aid in the assembly and annotation process, a protoplast and single nucleotide polymorphism (SNP)-based method was developed to identify regenerated protoplasts with a reduced nuclear genome. Protocol optimization experiments showed that enzymatic digestion of mycelium from a 24 h culture of R. solani increased the proportion of protoplasts with a diameter of ≤7.5 μm and 1–4 nuclei. To determine whether strains regenerated from protoplasts with a reduced number of nuclei were genetically different from the parental strain, triallelic SNPs identified from variance records of the genomic DNA sequence reads of R. solani were used in PCR-based genotyping assays. Results from 16 of the 24 SNP-based PCR assays provided evidence that one of the three alleles was missing in the 11 regenerated protoplast strains, suggesting that these strains represent a reduced genomic complement of the parental strain. The protoplast and triallelic SNP-based method used in this study may be useful in strain development and analysis of other basidiomycete fungi with complex nuclear genomes.}, number={3}, journal={JOURNAL OF BIOTECHNOLOGY}, author={Thomas, Elizabeth and Pakala, Suman and Fedorova, Natalie D. and Nierman, William C. and Cubeta, Marc A.}, year={2012}, month={Apr}, pages={144–150} }
 @inproceedings{pakala_thomas_rodriguez-carres_dean_schwartz_zhou_vilgalys_joardar_hostetler_zafar_et al._2011, title={Sequencing and assembling the mitochondrial DNA genome of the soil fungus Rhizoctonia solani}, booktitle={Proceedings of the 26th Fungal Genetics Conference}, author={Pakala, S. and Thomas, E. and Rodriguez-Carres, M. and Dean, R. and Schwartz, D. and Zhou, S. and Vilgalys, R. and Joardar, V. and Hostetler, J. and Zafar, N. and et al.}, year={2011} }
 @article{thomas_thropp_2011, title={Some Effects of Abiotic Stress on Infection of Dyer's Woad (<i>Isatis tinctoria L.</i>) by <i>Puccinia thlaspeos</i> C. Schub.: Implications for Biological Control}, volume={6}, ISSN={1557-4989}, url={http://dx.doi.org/10.3844/ajabssp.2011.45.51}, DOI={10.3844/ajabssp.2011.45.51}, abstractNote={Problem statement: The rust pathogen, Puccinia thlaspeos, is being studied as a potential biocontrol agent for the noxious weed dyer’s woad. Although its disease etiology is well understood, very little has been learned about the effect of environmental stresses on infection. Approach: Dyer’s woad plants were exposed to different levels of oxidative stress, salinity stress, osmotic stress, dehydration, and cold stress before being inoculated with the rust pathogen. Rust infections were subsequently detected in asymptomatic tissue using rust-selective primers with the polymerase chain reaction. Results: Mild abiotic stress appears to enable dyer’s woad plants to develop cross-tolerance to the rust pathogen. Plants exposed to the mildest level of salinity were only 60% infected. Those exposed to the lowest osmotic stress were only 50% infected while plants exposed to the shortest period of dehydration, or cold stress were both only 70% infected. Control plants were 100% infected for all experiments. On the other hand, exposing plants to mild oxidative stress did not lower infection while the highest level of oxidative stress significantly lowered infection to 55%. Conclusion: Crosstolerance to multiple stresses often a desirable trait for plants of economic importance, is a cause for concern in biocontrol of weeds because of its potential to adversely impact the efficacy of mycoherbicides.}, number={1}, journal={American Journal of Agricultural and Biological Sciences}, publisher={Science Publications}, author={Thomas, E. and Thropp, B.R.}, year={2011}, month={Jan}, pages={45–51} }
 @article{kropp_thomas_2011, title={Suppression of Salicylic Acid-Mediated Plant Defense Responses During Initial Infection of Dyer's Woad by Puccinia thlaspeos}, volume={6}, ISSN={1557-4989}, url={http://dx.doi.org/10.3844/ajabssp.2011.307.316}, DOI={10.3844/ajabssp.2011.307.316}, abstractNote={Problem statement: Puccinia thlaspeos is a microcyclic rust pathogen that is being investigated as a potential biocontrol agent of the noxious weed, dyer’s woad (Isatis tinctoria). Although, the initial events in the colonization of dyer’s woad by the rust pathogen has been elucidated using scanning electron microscopy and PCR, little is known regarding the susceptibility response of this plant to its rust pathogen. Approach: The induction kinetics and amplitude of the Salicylic Acid (SA)-responsive Pathogenesis-Related (PR) genes, PR-1, β-1, 3-glucanase and ChiA in the compatible interaction between the rust pathogen Puccinia thlaspeos and dyer’s woad were examined during the first 72 h of the infection process. Furthermore SA, an inducer of plant defense response was applied to infected plants in order to reprogram the host defense response at periods that coincided with key events of the infection process. Results: PR genes were upregulated following host penetration by the pathogen. A subsequent pathogen-mediated suppression of PR genes was seen that corresponded with haustorium formation. This was followed by a second up-regulation of these genes that was, in turn, followed by a second long-term pathogen-induced suppression of the defense response that appears to allow successful infections in dyer’s woad. Exogenous application of SA to uninoculated plants led to activation of defense responses by 8 h after treatment. In treatments where inoculated plants were treated with SA, responses differed depending on the timing of SA application. Application of SA at times corresponding to the pre-haustorial and posthaustorial phases of infection triggered an up-regulation of defense genes and increased protection against the pathogen. However, the application of SA during haustorium formation could not override the pathogen-mediated suppression of defense responses and consequently, did not offer the host increased protection. Conclusion: Although pathogen-induced PR expression was observed during rust infection of dyer’s woad, it appears to be insufficient to inhibit fungal growth during the compatible interaction between dyer’s woad and the rust pathogen. Suppression of pathogeninduced host defense responses during and after haustorium formation is postulated to be vital in the establishment of biotrophy in this system.}, number={3}, journal={American Journal of Agricultural and Biological Sciences}, publisher={Science Publications}, author={Kropp, B.R. and Thomas, E.}, year={2011}, month={Mar}, pages={307–316} }
 @article{thomas_kropp_2009, title={Analysis of isolation and expression analysis of ItCYP79B2 during rust infection of dyer's woad (Isatis tinctoria) by Puccinia thlaspeos}, volume={31}, ISSN={["1715-2992"]}, DOI={10.1080/07060660909507578}, abstractNote={Dyer's woad (Isatis tinctoria) has been shown to have unusually high quantities of indole glucosinolates. It is known that production of glucosinolates and their hydrolysis products is part of a plant's defense response to pathogens and insects. In Arabidopsis thaliana, which, like dyer's woad, is in the family Brassicaceae, the gene sequences encoding CYP79B2 and CYP79B3 catalyze the conversion of tryptophan to indole-3-acetaldoxime during the biosynthesis of indole glucosinolates. In this study, a sequence encoding CYP79B2 was isolated from dyer's woad. ItCYP79B2 from I. tinctoria shows 97% sequence identity with CYP79B2 and 89% sequence identity with CYP79B3 from A. thaliana. Thus, it can be inferred that the I. tinctoria sequence, like that of A. thaliana, is involved in the biosynthesis of indole glucosinolates. The kinetics and amplitude of ItCYP79B2 expression during the first 72 h after infection by the pathogenic rust fungus Puccinia thlaspeos were also studied. There was a significant down-regulation of ItCYP79B2 during the first 8 h after infection of the host that coincides with fungal penetration. This was followed by induction of ItCYP79B2, coinciding with the formation of haustoria. However, after haustoria formation, ItCYP9B2 was again suppressed during the time period coinciding with successful asymptomatic systemic colonization of the host. The results of this study indicates that suppression of a gene involved in indole glucosinolate production during the penetration and post-haustorial phases of infection plays a role in pathogen establishment. They also imply that the pathogen possesses mechanisms for circumventing the elevated expression of this gene during the haustorial phase}, number={1}, journal={CANADIAN JOURNAL OF PLANT PATHOLOGY}, author={Thomas, E. and Kropp, B. R.}, year={2009}, pages={103–107} }
 @misc{thomas_kropp_2007, title={Induction kinetics of defense-related genes in rust infected dyer’s woad}, author={Thomas, E. and Kropp, B.R.}, year={2007} }
 @article{kropp_thomas_pounder_anderson_1996, title={Increased emergence of spring wheat after inoculation with Pseudomonas chlororaphis isolate 2E3 under field and laboratory conditions}, volume={23}, ISSN={0178-2762 1432-0789}, url={http://dx.doi.org/10.1007/bf00336064}, DOI={10.1007/bf00336064}, number={2}, journal={Biology and Fertility of Soils}, publisher={Springer Science and Business Media LLC}, author={Kropp, B. R. and Thomas, E. and Pounder, J. I. and Anderson, A. J.}, year={1996}, month={Aug}, pages={200–206} }
 @inproceedings{thomas_kropp_1996, title={Potential phytotoxicity of Biocontrol agent O6 on wheat}, author={Thomas, E. and Kropp, B.R.}, year={1996} }