@article{crouch_beirn_boehm_carbone_clarke_kerns_malapi-wight_mitchell_venu_tredway_2021, title={Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including Clarireedia jacksonii and C. monteithiana}, volume={105}, ISSN={["1943-7692"]}, DOI={10.1094/PDIS-06-20-1296-A}, abstractNote={Fungi in the genus Clarireedia are widespread and destructive pathogens of grasses worldwide, and are best known as the causal agents of dollar spot disease in turfgrass. Here we report genome assemblies of seven Clarireedia isolates, including ex-types of the two most widespread species, C. jacksonii and C. monteithiana. These datasets provide a valuable resource for ongoing studies of the dollar spot pathogens that include population diversity, host/pathogen interactions, marker development and disease control.}, number={3}, journal={PLANT DISEASE}, author={Crouch, Jo Anne and Beirn, Lisa A. and Boehm, Michael J. and Carbone, Ignazio and Clarke, Bruce B. and Kerns, James P. and Malapi-Wight, Martha and Mitchell, Thomas K. and Venu, R. C. and Tredway, Lane P.}, year={2021}, month={Mar}, pages={691–694} }
 @article{nunes_gowda_sailsbery_xue_chen_brown_oh_mitchell_dean_2011, title={Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae}, volume={12}, DOI={10.1186/1471-2164-12-288}, abstractNote={Abstract Background Emerging knowledge of the impact of small RNAs as important cellular regulators has prompted an explosion of small transcriptome sequencing projects. Although significant progress has been made towards small RNA discovery and biogenesis in higher eukaryotes and other model organisms, knowledge in simple eukaryotes such as filamentous fungi remains limited. Results Here, we used 454 pyrosequencing to present a detailed analysis of the small RNA transcriptome (~ 15 - 40 nucleotides in length) from mycelia and appressoria tissues of the rice blast fungal pathogen, Magnaporthe oryzae . Small RNAs mapped to numerous nuclear and mitochondrial genomic features including repetitive elements, tRNA loci, rRNAs, protein coding genes, snRNAs and intergenic regions. For most elements, small RNAs mapped primarily to the sense strand with the exception of repetitive elements to which small RNAs mapped in the sense and antisense orientation in near equal proportions. Inspection of the small RNAs revealed a preference for U and suppression of C at position 1, particularly for antisense mapping small RNAs. In the mycelia library, small RNAs of the size 18 - 23 nt were enriched for intergenic regions and repetitive elements. Small RNAs mapping to LTR retrotransposons were classified as LTR retrotransposon-siRNAs (LTR-siRNAs). Conversely, the appressoria library had a greater proportion of 28 - 35 nt small RNAs mapping to tRNA loci, and were classified as tRNA-derived RNA fragments (tRFs). LTR-siRNAs and tRFs were independently validated by 3' RACE PCR and northern blots, respectively. Conclusions Our findings suggest M. oryzae small RNAs differentially accumulate in vegetative and specialized-infection tissues and may play an active role in genome integrity and regulating growth and development.}, journal={BMC Genomics}, author={Nunes, C. C. and Gowda, M. and Sailsbery, J. and Xue, M. F. and Chen, F. and Brown, D. E. and Oh, Y. and Mitchell, T. K. and Dean, Ralph}, year={2011} }
 @misc{meng_brown_ebbole_torto-alalibo_oh_deng_mitchell_dean_2009, title={Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae}, volume={9}, ISSN={["1471-2180"]}, DOI={10.1186/1471-2180-9-s1-s8}, abstractNote={Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly.A similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked.In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site http://amigo.geneontology.org/cgi-bin/amigo/go.cgi. Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html. The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System.Our analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae.}, journal={BMC MICROBIOLOGY}, author={Meng, Shaowu and Brown, Douglas E. and Ebbole, Daniel J. and Torto-Alalibo, Trudy and Oh, Yeon Yee and Deng, Jixin and Mitchell, Thomas K. and Dean, Ralph A.}, year={2009}, month={Feb} }
 @article{craven_velez_cho_lawrence_mitchell_2008, title={Anastomosis is required for virulence of the fungal necrotroph Alternaria brassicicola}, volume={7}, ISSN={["1535-9786"]}, DOI={10.1128/EC.00423-07}, abstractNote={ABSTRACT}, number={4}, journal={EUKARYOTIC CELL}, author={Craven, Kelly D. and Velez, Heriberto and Cho, Yangrae and Lawrence, Christopher B. and Mitchell, Thomas K.}, year={2008}, month={Apr}, pages={675–683} }
 @misc{oh_donofrio_pan_coughlan_brown_meng_mitchell_dean_2008, title={Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae}, volume={9}, ISSN={["1474-760X"]}, DOI={10.1186/gb-2008-9-5-r85}, abstractNote={Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood.We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection.We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.}, number={5}, journal={GENOME BIOLOGY}, author={Oh, Yeonyee and Donofrio, Nicole and Pan, Huaqin and Coughlan, Sean and Brown, Douglas E. and Meng, Shaowu and Mitchell, Thomas and Dean, Ralph A.}, year={2008} }
 @article{meng_patel_heist_betts_tucker_galadima_donofrio_brown_mitchell_li_et al._2007, title={A systematic analysis of T-DNA insertion events in Magnaporthe oryzae}, volume={44}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2007.04.002}, abstractNote={We describe here the analysis of random T-DNA insertions that were generated as part of a large-scale insertional mutagenesis project for Magnaporthe oryzae. Chromosomal regions flanking T-DNA insertions were rescued by inverse PCR, sequenced and used to search the M. oryzae genome assembly. Among the 175 insertions for which at least one flank was rescued, 137 had integrated in single-copy regions of the genome, 17 were in repeated sequences, one had no match to the genome, and the remainder were unassigned due to illegitimate T-DNA integration events. These included in order of abundance: head-to-tail tandem insertions, right border excision failures, left border excision failures and insertion of one T-DNA into another. The left borders of the T-DNA were frequently truncated and inserted in sequences with micro-homology to the left terminus. By contrast the right borders were less prone to degradation and appeared to have been integrated in a homology-independent manner. Gross genome rearrangements rarely occurred when the T-DNAs integrated in single-copy regions, although most insertions did cause small deletions at the target site. Significant insertion bias was detected, with promoters receiving two times more T-DNA hits than expected, and open reading frames receiving three times fewer. In addition, we found that the distribution of T-DNA inserts among the M. oryzae chromosomes was not random. The implications of these findings with regard to saturation mutagenesis of the M. oryzae genome are discussed.}, number={10}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Meng, Yan and Patel, Gayatri and Heist, Melanie and Betts, Melania F. and Tucker, Sara L. and Galadima, Natalia and Donofrio, Nicole M. and Brown, Doug and Mitchell, Thomas K. and Li, Lei and et al.}, year={2007}, month={Oct}, pages={1050–1064} }
 @article{betts_tucker_galadima_meng_patel_li_donofrio_floyd_nolin_brown_et al._2007, title={Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae}, volume={44}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2007.05.001}, abstractNote={Towards the goal of disrupting all genes in the genome of Magnaporthe oryzae and identifying their function, a collection of >55,000 random insertion lines of M. oryzae strain 70-15 were generated. All strains were screened to identify genes involved in growth rate, conidiation, pigmentation, auxotrophy, and pathogenicity. Here, we provide a description of the high throughput transformation and analysis pipeline used to create our library. Transformed lines were generated either by CaCl2/PEG treatment of protoplasts with DNA or by Agrobacterium tumefaciens-mediated transformation (ATMT). We describe the optimization of both approaches and compare their efficiency. ATMT was found to be a more reproducible method, resulting in predominantly single copy insertions, and its efficiency was high with up to 0.3% of conidia being transformed. The phenotypic data is accessible via a public database called MGOS and all strains are publicly available. This represents the most comprehensive insertional mutagenesis analysis of a fungal pathogen.}, number={10}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Betts, Melania F. and Tucker, Sara L. and Galadima, Natalia and Meng, Yan and Patel, Gayatri and Li, Lei and Donofrio, Nicole and Floyd, Anna and Nolin, Shelly and Brown, Doug and et al.}, year={2007}, month={Oct}, pages={1035–1049} }
 @article{torto-alalibo_tripathy_smith_arredondo_zhou_li_chibucos_qutob_gijzen_mao_et al._2007, title={Expressed sequence tags from Phytophthora sojae reveal genes specific to development and infection}, volume={20}, ISSN={["1943-7706"]}, DOI={10.1094/MPMI-20-7-0781}, abstractNote={ Six unique expressed sequence tag (EST) libraries were generated from four developmental stages of Phytophthora sojae P6497. RNA was extracted from mycelia, swimming zoospores, germinating cysts, and soybean (Glycine max (L.) Merr.) cv. Harosoy tissues heavily infected with P. sojae. Three libraries were created from mycelia growing on defined medium, complex medium, and nutrient-limited medium. The 26,943 high-quality sequences obtained clustered into 7,863 unigenes composed of 2,845 contigs and 5,018 singletons. The total number of P. sojae unigenes matching sequences in the genome assembly was 7,412 (94%). Of these unigenes, 7,088 (90%) matched gene models predicted from the P. sojae sequence assembly, but only 2,047 (26%) matched P. ramorum gene models. Analysis of EST frequency from different growth conditions and morphological stages revealed genes that were specific to or highly represented in particular growth conditions and life stages. Additionally, our results indicate that, during infection, the pathogen derives most of its carbon and energy via glycolysis of sugars in the plant. Sequences identified with putative roles in pathogenesis included avirulence homologs possessing the RxLR motif, elicitins, and hydrolytic enzymes. This large collection of P. sojae ESTs will serve as a valuable public genomic resource. }, number={7}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Torto-Alalibo, Trudy A. and Tripathy, Sucheta and Smith, Brian M. and Arredondo, Felipe D. and Zhou, Lecong and Li, Hua and Chibucos, Marcus C. and Qutob, Dinah and Gijzen, Mark and Mao, Chunhong and et al.}, year={2007}, month={Jul}, pages={781–793} }
 @article{cho_cramer_kim_davis_mitchell_figuli_pryor_lemasters_lawrence_2007, title={The Fus3/Kss1 MAP kinase homolog Amk1 regulates the expression of genes encoding hydrolytic enzymes in Alternaria brassicicola}, volume={44}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2006.11.015}, abstractNote={Mitogen-activated protein (MAP) kinases have been shown to be required for virulence in diverse phytopathogenic fungi. To study its role in pathogenicity, we disrupted the Amk1 MAP kinase gene, a homolog of the Fus3/Kss1 MAP kinases in Saccharomyces cerevisiae, in the necrotrophic Brassica pathogen, Alternaria brassicicola. The amk1 disruption mutants showed null pathogenicity on intact host plants. However, amk1 mutants were able to colonize host plants when they were inoculated on a physically damaged host surface, or when they were inoculated along with nutrient supplements. On intact plants, mutants expressed extremely low amounts of several hydrolytic enzyme genes that were induced over 10-fold in the wild-type during infection. These genes were also dramatically induced in the mutants on wounded plants. These results imply a correlation between virulence and the expression level of specific hydrolytic enzyme genes plus the presence of an unidentified pathway controlling these genes in addition to or in conjunction with the Amk1 pathway.}, number={6}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Cho, Yangrae and Cramer, Robert A., Jr. and Kim, Kwang-Hyung and Davis, Josh and Mitchell, Thomas K. and Figuli, Patricia and Pryor, Barry M. and Lemasters, Emily and Lawrence, Christopher B.}, year={2007}, month={Jun}, pages={543–553} }
 @article{jeong_mitchell_dean_2007, title={The Magnaporthe grisea snodprot1 homolog, MSPI, is required for virulence}, volume={273}, ISSN={["1574-6968"]}, DOI={10.1111/j.1574-6968.2007.00796.x}, abstractNote={Secreted proteins play central roles in plant-microbe interactions acting as signals, toxins, and effectors. One important group of small secreted proteins is the snodprot1 family, members of which have demonstrated phytotoxic properties. A split-marker transformation system was applied for gene deletion of the snodprot1 homolog, MSP1, in the rice blast fungus Magnaporthe grisea. msp1 mutants were phenotypically indistinguishable from wild type and elaborated apparently normal appressoria. However, the deletion mutants were greatly reduced in virulence primarily due to impaired growth in planta. Western blot analysis showed that the protein was secreted and not associated with the fungal cell wall. When purified MSP1 protein was applied to wounded leaf tissue, no apparent phytotoxic effects were noted. This is the first report to the authors' knowledge that directly implicates a snodprot1 protein as a virulence factor.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Jeong, Jun Seop and Mitchell, Thomas K. and Dean, Ralph A.}, year={2007}, month={Aug}, pages={157–165} }
 @article{taylor_mitchell_daub_2006, title={An oxidoreductase is involved in cercosporin degradation by the bacterium Xanthomonas campestris pv. zinniae}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.00483-06}, abstractNote={ABSTRACT}, number={9}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Taylor, Tanya V. and Mitchell, Thomas K. and Daub, Margaret E.}, year={2006}, month={Sep}, pages={6070–6078} }
 @article{cramer_la rota_cho_thon_craven_knudson_mitchell_lawrence_2006, title={Bioinformatic analysis of expressed sequence tags derived from a compatible Alternaria brassicicola-Brassica oleracea interaction}, volume={7}, ISSN={["1364-3703"]}, DOI={10.1111/J.1364-3703.2006.00324.X}, abstractNote={SUMMARY}, number={2}, journal={MOLECULAR PLANT PATHOLOGY}, author={Cramer, RA and La Rota, CM and Cho, Y and Thon, M and Craven, KD and Knudson, DL and Mitchell, TK and Lawrence, CB}, year={2006}, month={Mar}, pages={113–124} }
 @article{donofrio_oh_lundy_pan_brown_jeong_coughlan_mitchell_dean_2006, title={Global gene expression during nitrogen starvation in the rice blast fungus, Magnaporthe grisea}, volume={43}, ISSN={["1087-1845"]}, DOI={10.1016/j.fgb.2006.03.005}, abstractNote={Efficient regulation of nitrogen metabolism likely plays a role in the ability of fungi to exploit ecological niches. To learn about regulation of nitrogen metabolism in the rice blast pathogen Magnaporthe grisea, we undertook a genome-wide analysis of gene expression under nitrogen-limiting conditions. Five hundred and twenty genes showed increased transcript levels at 12 and 48 h after shifting the fungus to media lacking nitrate as a nitrogen source. Thirty-nine of these genes have putative functions in amino acid metabolism and uptake, and include the global nitrogen regulator in M. grisea, NUT1. Evaluation of seven nitrogen starvation-induced genes revealed that all were expressed during rice infection. Targeted gene replacement on one such gene, the vacuolar serine protease, SPM1, resulted in decreased sporulation and appressorial development as well as a greatly attenuated ability to cause disease. Data are discussed in the context of nitrogen metabolism under starvation conditions, as well as conditions potentially encountered during invasive growth in planta.}, number={9}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Donofrio, N. M. and Oh, Y. and Lundy, R. and Pan, H. and Brown, D. E. and Jeong, J. S. and Coughlan, S. and Mitchell, T. K. and Dean, R. A.}, year={2006}, month={Sep}, pages={605–617} }
 @article{walker_mitchell_marek_2006, title={Influence of temperature and time of year on colonization of bermudagrass roots by Ophiosphaerella herpotricha}, volume={90}, ISSN={["1943-7692"]}, DOI={10.1094/PD-90-1326}, abstractNote={ The influence of temperature on the infection of bermudagrass seedlings by Ophiosphaerella herpotricha and colonization of plants in the field was investigated. Bermudagrass seedlings (cv. Jackpot) inoculated with O. herpotricha exhibited dark lesions after 8 days. Root lesion length was greatest at 17°C and was similar for all temperatures examined below 21°C. Seedlings grown at 25 or 30°C had small lesions that remained similar in size when evaluated at 8 and 10 days post inoculation. Colonization of bermudagrass roots from field plots were examined in July, October, and November of 2003 and 2004. In 2003, no differences between sampling dates were observed for plants sampled from the edge of the spring patch in 5.4-cm increments to a total distance of 21.6 cm. In 2004, July and October samples were similar; however, an increase in root colonization was found between the October and November samplings. These studies suggest that infection and colonization of bermudagrass roots by O. herpotricha occurs over a wide range of cool soil temperatures, occurs in the spring, and can be variable in the autumn. }, number={10}, journal={PLANT DISEASE}, author={Walker, N. R. and Mitchell, T. K. and Marek, S. M.}, year={2006}, month={Oct}, pages={1326–1330} }
 @article{soderlund_haller_pampanwar_ebbole_farman_orbach_wang_wing_xu_brown_et al._2006, title={MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions}, volume={19}, ISSN={["1943-7706"]}, DOI={10.1094/MPMI-19-1055}, abstractNote={ The MGOS (Magnaporthe grisea Oryza sativa) web-based database contains data from Oryza sativa and Magnaporthe grisea interaction experiments in which M. grisea is the fungal pathogen that causes the rice blast disease. In order to study the interactions, a consortium of fungal and rice geneticists was formed to construct a comprehensive set of experiments that would elucidate information about the gene expression of both rice and M. grisea during the infection cycle. These experiments included constructing and sequencing cDNA and robust long-serial analysis gene expression libraries from both host and pathogen during different stages of infection in both resistant and susceptible interactions, generating >50,000 M. grisea mutants and applying them to susceptible rice strains to test for pathogenicity, and constructing a dual O. sativa-M. grisea microarray. MGOS was developed as a central web-based repository for all the experimental data along with the rice and M. grisea genomic sequence. Community-based annotation is available for the M. grisea genes to aid in the study of the interactions. }, number={10}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, author={Soderlund, Carol and Haller, Karl and Pampanwar, Vishal and Ebbole, Daniel and Farman, Mark and Orbach, Marc J. and Wang, Guo-Liang and Wing, Rod and Xu, Jin-Rong and Brown, Doug and et al.}, year={2006}, month={Oct}, pages={1055–1061} }
 @article{thon_pan_diener_papalas_taro_mitchell_dean_2006, title={The  role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae}, volume={7}, number={2}, journal={Genome Biology}, author={Thon, M. R. and Pan, H. Q. and Diener, S. and Papalas, J. and Taro, A. and Mitchell, T. K. and Dean, R. A.}, year={2006} }
 @article{craven_peterson_windham_mitchell_martin_2005, title={Molecular identification of the turf grass rapid blight pathogen}, volume={97}, ISSN={["1557-2536"]}, DOI={10.3852/mycologia.97.1.160}, abstractNote={Rapid blight is a newly described disease on turf grasses, primarily found on golf courses using suboptimal water for irrigation purposes. On the basis of shared morphological characteristics, it has been proposed that the rapid blight pathogen belongs to a genus of stramenopiles, Labyrinthula, which had been known to cause disease of marine plants only. We have collected 10 isolates from four species of turf grass in five states and sequenced portions of the SSU (18S) rDNA gene from each to provide a definitive taxonomic placement for rapid blight pathogens. We also included sequences from Labyrinthuloides yorkensis, Schizochytrium aggregatum, Aplanochytrium sp., Thraustochytrium striatum, Achlya bisexualis and several nonturf-grass isolates of Labyrinthula. We found that rapid blight isolates indeed are placed firmly within the genus Labyrinthula and that they lack detectable genetic diversity in the 18S rDNA region. We propose that the rapid blight pathogens share a recent common ancestor and might have originated from a single, infected population.}, number={1}, journal={MYCOLOGIA}, author={Craven, KD and Peterson, PD and Windham, DE and Mitchell, TK and Martin, SB}, year={2005}, pages={160–166} }
 @article{donofrio_rajagopalon_brown_diener_windham_nolin_floyd_mitchell_galadima_tucker_et al._2005, title={PACLIMS: A component LIM system for high-throughput functional genomic analysis}, volume={6}, journal={BMC Bioinformatics}, author={Donofrio, N. and Rajagopalon, R. and Brown, D. and Diener, S. and Windham, D. and Nolin, S. and Floyd, A. and Mitchell, T. and Galadima, N. and Tucker, S. and et al.}, year={2005} }
 @article{dean_talbot_ebbole_farman_mitchell_orbach_thon_kulkarni_xu_pan_et al._2005, title={The genome sequence of the rice blast fungus Magnaporthe grisea}, volume={434}, ISSN={["1476-4687"]}, DOI={10.1038/nature03449}, abstractNote={Magnaporthe grisea is the most destructive pathogen of rice worldwide and the principal model organism for elucidating the molecular basis of fungal disease of plants. Here, we report the draft sequence of the M. grisea genome. Analysis of the gene set provides an insight into the adaptations required by a fungus to cause disease. The genome encodes a large and diverse set of secreted proteins, including those defined by unusual carbohydrate-binding domains. This fungus also possesses an expanded family of G-protein-coupled receptors, several new virulence-associated genes and large suites of enzymes involved in secondary metabolism. Consistent with a role in fungal pathogenesis, the expression of several of these genes is upregulated during the early stages of infection-related development. The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation.}, number={7036}, journal={NATURE}, author={Dean, RA and Talbot, NJ and Ebbole, DJ and Farman, ML and Mitchell, TK and Orbach, MJ and Thon, M and Kulkarni, R and Xu, JR and Pan, HQ and et al.}, year={2005}, month={Apr}, pages={980–986} }
 @article{diener_dunn-coleman_foreman_houfek_teunissen_solingen_dankmeyer_mitchell_ward_dean_2004, title={Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei}, volume={230}, ISSN={["1574-6968"]}, DOI={10.1016/S0378-1097(03)00916-9}, abstractNote={Trichoderma reesei is a filamentous fungus widely used as an efficient protein producer and known to secrete large quantities of biomass degrading enzymes. Much work has been done aimed at improving the secretion efficiency of this fungus. It is generally accepted that the major bottlenecks in secretion are protein folding and ornamentation steps in this pathway. In an attempt to identify genes involved in these steps, the 5' ends of 21888 cDNA clones were sequenced from which a unique set of over 5000 were also 3' sequenced. Using annotation tools Gene Ontology terms were assigned to 2732 of the sequences. Homologs to the majority of Aspergillus niger's Srg genes as well as a number of homologs to genes involved in protein folding and ornamentation pathways were identified.}, number={2}, journal={FEMS MICROBIOLOGY LETTERS}, author={Diener, SE and Dunn-Coleman, N and Foreman, P and Houfek, TD and Teunissen, PJM and Solingen, P and Dankmeyer, L and Mitchell, TK and Ward, M and Dean, RA}, year={2004}, month={Jan}, pages={275–282} }
 @article{diener_dunn-coleman_foreman_houfek_teunissen_solingen_dankmeyer_mitchell_ward_dean_2004, title={Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei (vol 230, pg 275, 2004)}, volume={235}, DOI={10.1111/j.1574-6968.2004.tb09588.x}, number={1}, journal={FEMS Microbiology Letters}, author={Diener, S. E. and Dunn-Coleman, N. and Foreman, P. and Houfek, T. D. and Teunissen, P. J. M. and Solingen, P. Van and Dankmeyer, L. and Mitchell, T. K. and Ward, M. and Dean, Ralph}, year={2004}, pages={209} }
 @article{diener_chellappan_mitchell_dunn-coleman_ward_dean_2004, title={Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization}, volume={41}, ISSN={["1096-0937"]}, DOI={10.1016/j.fgb.2004.08.007}, abstractNote={Trichoderma reesei is an important industrial fungus known for its ability to efficiently secrete large quantities of protein as well as its wide variety of biomass degrading enzymes. Past research on this fungus has primarily focused on extending its protein production capabilities, leaving the structure of its 33 Mb genome essentially a mystery. To begin to address these deficiencies and further our knowledge of T. reesei's secretion and cellulolytic potential, we have created a genomic framework for this fungus. We constructed a BAC library containing 9216 clones with an average insert size of 125 kb which provides a coverage of 28 genome equivalents. BAC ends were sequenced and annotated using publicly available software which identified a number of genes not seen in previously sequenced EST datasets. Little evidence was found for repetitive sequence in T. reesei with the exception of several copies of an element with similarity to the Podospora anserina transposon, PAT. Hybridization of 34 genes involved in biomass degradation revealed five groups of co-located genes in the genome. BAC clones were fingerprinted and analyzed using fingerprinted contigs (FPC) software resulting in 334 contigs covering 28 megabases of the genome. The assembly of these FPC contigs was verified by congruence with hybridization results.}, number={12}, journal={FUNGAL GENETICS AND BIOLOGY}, author={Diener, SE and Chellappan, MK and Mitchell, TK and Dunn-Coleman, N and Ward, M and Dean, RA}, year={2004}, month={Dec}, pages={1077–1087} }
 @article{takano_choi_mitchell_okuno_dean_2003, title={Large scale parallel analysis of gene expression during infection-related morphogenesis of Magnaporthe grisea}, volume={4}, ISSN={["1464-6722"]}, DOI={10.1046/J.1364-3703.2003.00182.X}, abstractNote={SUMMARY}, number={5}, journal={MOLECULAR PLANT PATHOLOGY}, author={Takano, Y and Choi, WB and Mitchell, TK and Okuno, T and Dean, RA}, year={2003}, month={Sep}, pages={337–346} }
 @misc{mitchell_thon_jeong_brown_deng_dean_2003, title={The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens}, volume={159}, ISSN={["0028-646X"]}, DOI={10.1046/j.1469-8137.2003.00787.x}, abstractNote={Summary}, number={1}, journal={NEW PHYTOLOGIST}, author={Mitchell, TK and Thon, MR and Jeong, JS and Brown, D and Deng, JX and Dean, RA}, year={2003}, month={Jul}, pages={53–61} }
 @article{foreman_brown_dankmeyer_dean_diener_dunn-coleman_goedegebuur_houfek_england_kelley_et al._2003, title={Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei}, volume={278}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M304750200}, abstractNote={The filamentous fungus Trichoderma reesei produces and secretes profuse quantities of enzymes that act synergistically to degrade cellulase and related biomass components. We partially sequenced over 5100 random T. reesei cDNA clones. Among the sequences whose predicted gene products had significant similarity to known proteins, 12 were identified that encode previously unknown enzymes that likely function in biomass degradation. Microarrays were used to query the expression levels of each of the sequences under different conditions known to induce cellulolytic enzyme synthesis. Most of the genes encoding known and putative biomass-degrading enzymes were transcriptionally co-regulated. Moreover, despite the fact that several of these enzymes are not thought to degrade cellulase directly, they were coordinately overexpressed in a cellulase overproducing strain. A variety of additional sequences whose function could not be ascribed using the limited sequence available displayed analogous behavior and may also play a role in biomass degradation or in the synthesis of biomass-degrading enzymes. Sequences exhibiting additional regulatory patterns were observed that might reflect roles in regulation of cellulase biosynthesis. However, genes whose products are involved in protein processing and secretion were not highly regulated during cellulase induction.}, number={34}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Foreman, PK and Brown, D and Dankmeyer, L and Dean, R and Diener, S and Dunn-Coleman, NS and Goedegebuur, F and Houfek, TD and England, GJ and Kelley, AS and et al.}, year={2003}, month={Aug}, pages={31988–31997} }
 @article{mitchell_alejos-gonzalez_gracz_danehower_daub_chilton_2003, title={Xanosporic acid, an intermediate in bacterial degradation of the fungal phototoxin cercosporin}, volume={62}, ISSN={["0031-9422"]}, DOI={10.1016/S0031-9422(02)00517-4}, abstractNote={The red fungal perylenequinone phototoxin cercosporin is oxidized by Xanthomonas campestris pv zinniae to a non-toxic, unstable green metabolite xanosporic acid, identified via its lactone as 1,12-bis(2'R-hydroxypropyl)-4,9-dihydroxy-6,7-methylenedioxy-11-methoxy-3-oxaperylen-10H-10-one-2-carboxylic acid. Xanosporolactone was isolated in approximately 2:1 ratio of M:P atropisomers.}, number={5}, journal={PHYTOCHEMISTRY}, author={Mitchell, TK and Alejos-Gonzalez, F and Gracz, HS and Danehower, DA and Daub, ME and Chilton, WS}, year={2003}, month={Mar}, pages={723–732} }
 @article{mitchell_chilton_daub_2002, title={Biodegradation of the polyketide toxin cercosporin}, volume={68}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.68.9.4173-4181.2002}, abstractNote={ABSTRACT}, number={9}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Mitchell, TK and Chilton, WS and Daub, ME}, year={2002}, month={Sep}, pages={4173–4181} }
 @article{martin_blackmon_rajagopalan_houfek_sceeles_denn_mitchell_brown_wing_dean_2002, title={MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea}, volume={30}, ISSN={["0305-1048"]}, DOI={10.1093/nar/30.1.121}, abstractNote={We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.}, number={1}, journal={NUCLEIC ACIDS RESEARCH}, author={Martin, SL and Blackmon, BP and Rajagopalan, R and Houfek, TD and Sceeles, RG and Denn, SO and Mitchell, TK and Brown, DE and Wing, RA and Dean, RA}, year={2002}, month={Jan}, pages={121–124} }