@article{kalmar_oh_dean_muddiman_2020, title={Investigating host-pathogen meta-metabolic interactions of Magnaporthe oryzae infected barley using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry}, volume={412}, ISSN={["1618-2650"]}, DOI={10.1007/s00216-019-02216-z}, abstractNote={Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) mass spectrometry imaging is a useful tool for identifying important meta-metabolomic features pertinent for enhancing our understanding of biological systems. Magnaporthe oryzae (M. oryzae) is a filamentous fungus that is the primary cause of rice blast disease. True to its name, M. oryzae primarily destroys rice crops and can also destroy other cereal crops as well. In a previous study, the F-box E3 ligase protein in M. oryzae was noted to be crucial for its growth and pathogenicity. In this study, we inoculated three separate sets of barley with wild-type M. oryzae, an F-box E3 ligase protein knock out of M. oryzae, and a control solution. Over the course of the infection (8 days), we imaged each treatment after development of an advanced polarity switching method, which allowed for the detection of low and high molecular weight compounds that ionize in positive or negative polarities. A set of features from initial experiments were chosen for another analysis using tandem mass spectrometry. Serotonin, a barley defense metabolite, was a compound identified in both positive and negative modes. Serotonin was putatively identified using MS1 data including carbon estimation and sulfur counting then confirmed based on tandem mass spectrometry fragmentation patterns. Metabolites in the melanin pathway, important for infection development of M. oryzae, were also identified using MS1 data but were unable to be confirmed with MS/MS due to their low abundances.}, number={1}, journal={ANALYTICAL AND BIOANALYTICAL CHEMISTRY}, author={Kalmar, Jaclyn Gowen and Oh, Yeonyee and Dean, Ralph A. and Muddiman, David C.}, year={2020}, month={Jan}, pages={139–147} }
 @article{eyre_wang_oh_dean_2019, title={Identification and Characterization of the Core Rice Seed Microbiome}, volume={3}, ISSN={["2471-2906"]}, DOI={10.1094/PBIOMES-01-19-0009-R}, abstractNote={The use of microbes in agriculture for enhancing crop production is an emerging alternative to chemical fertilizers and pesticides; however, their effectiveness is often limited by factors such as host genotype and variability in geographic location. To address this issue, the microbiomes of six different rice (Oryza sativa) seeds, sourced from two locations in Arkansas, U.S.A. of two different genotypes and two harvest years, were characterized. The bacterial and fungal communities were identified in each of four seed compartments (grain, outer grain, husk, and outer husk) using high throughput Illumina MiSeq sequencing. More unique amplicon sequence variants were identified in the outer seed husk and least in the grain compartment for both the fungal and bacterial microbiomes, however this only resulted in a decrease in diversity for the fungal communities. Principal component analysis indicated that each tissue compartment harbored relatively distinct bacterial and fungal communities for the three innermost compartments. A bacterial and fungal core microbiome shared among the six seed types for each compartment was identified. Key bacterial genera in the core across all compartments were Sphingomonas, Methylobacterium, and taxa in the family Enterobacteriaceae, members of which have been reported to support rice growth. Compared with the bacterial core, more fungal taxa were identified, possibly resulting from the more abundant reads after filtering, and key genera identified were Alternaria, Hannaella, and members of the order Pleosporales. These core members represent valuable candidates for manipulating the rice microbiome, decreasing the use of chemicals while increasing plant performance.}, number={2}, journal={PHYTOBIOMES JOURNAL}, author={Eyre, Alexander W. and Wang, Mengying and Oh, Yeonyee and Dean, Ralph A.}, year={2019}, pages={148–157} }
 @article{oh_franck_dean_2018, title={Sequential Phosphopeptide Enrichment for Phosphoproteome Analysis of Filamentous Fungi: A Test Case Using Magnaporthe oryzae}, volume={1848}, ISBN={["978-1-4939-8723-8"]}, ISSN={["1940-6029"]}, DOI={10.1007/978-1-4939-8724-5_7}, abstractNote={A number of challenges have to be overcome to identify a complete complement of phosphorylated proteins, the phosphoproteome, from cells and tissues. Phosphorylated proteins are typically of low abundance and moreover, the proportion of phosphorylated sites on a given protein is generally low. The challenge is further compounded when the tissue from which protein can be recovered is limited. Global phosphoproteomics primarily relies on efficient enrichment methods for phosphopeptides involving affinity binding coupled with analysis by fast high-resolution mass spectrometry (MS) and subsequent identification using various software packages. Here, we describe an effective protocol for phosphopeptide enrichment using an Iron-IMAC resin in combination with titanium dioxide (TiO2) beads from trypsin digested protein samples of the filamentous fungus Magnaporthe oryzae. Representative protocols for LC-MS/MS analysis and phosphopeptide identification are also described.}, journal={PLANT PATHOGENIC FUNGI AND OOMYCETES: METHODS AND PROTOCOLS}, author={Oh, Yeonyee and Franck, William L. and Dean, Ralph A.}, year={2018}, pages={81–91} }
 @article{oh_robertson_parker_muddiman_dean_2017, title={Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae}, volume={15}, journal={Proteome Science}, author={Oh, Y. and Robertson, S. L. and Parker, J. and Muddiman, D. C. and Dean, R. A.}, year={2017} }
 @article{adhikari_oh_panthee_2017, title={Current Status of Early Blight Resistance in Tomato: An Update}, volume={18}, ISSN={1422-0067}, url={http://dx.doi.org/10.3390/ijms18102019}, DOI={10.3390/ijms18102019}, abstractNote={Early blight (EB) is one of the dreadful diseases of tomato caused by several species of Alternaria including Alternaria linariae (which includes A. solani and A. tomatophila), as well as A. alternata. In some instances, annual economic yield losses due to EB have been estimated at 79%. Alternaria are known only to reproduce asexually, but a highly-virulent isolate has the potential to overcome existing resistance genes. Currently, cultural practices and fungicide applications are employed for the management of EB due to the lack of strong resistant cultivars. Resistance sources have been identified in wild species of tomato; some breeding lines and cultivars with moderate resistance have been developed through conventional breeding methods. Polygenic inheritance of EB resistance, insufficient resistance in cultivated species and the association of EB resistance with undesirable horticultural traits have thwarted the effective breeding of EB resistance in tomato. Several quantitative trait loci (QTL) conferring EB resistance have been detected in the populations derived from different wild species including Solanum habrochaites, Solanum arcanum and S. pimpinellifolium, but none of them could be used in EB resistance breeding due to low individual QTL effects. Pyramiding of those QTLs would provide strong resistance. More research is needed to identify additional sources of useful resistance, to incorporate resistant QTLs into breeding lines through marker-assisted selection (MAS) and to develop resistant cultivars with desirable horticultural traits including high yielding potential and early maturity. This paper will review the current understanding of causal agents of EB of tomato, resistance genetics and breeding, problems associated with breeding and future prospects.}, number={10}, journal={International Journal of Molecular Sciences}, publisher={MDPI AG}, author={Adhikari, Pragya and Oh, Yeonyee and Panthee, Dilip}, year={2017}, month={Sep}, pages={2019} }
 @article{sharpee_oh_yi_franck_eyre_okagaki_valent_dean_2017, title={Identification and characterization of suppressors of plant cell death (SPD) effectors from Magnaporthe oryzae}, volume={18}, ISSN={["1364-3703"]}, DOI={10.1111/mpp.12449}, abstractNote={Phytopathogenic microorganisms, including the fungal pathogen Magnaporthe oryzae, secrete a myriad of effector proteins to facilitate infection. Utilizing the transient expression of candidate effectors in the leaves of the model plant Nicotiana benthamiana, we identified 11 suppressors of plant cell death (SPD) effectors from M. oryzae that were able to block the host cell death reaction induced by Nep1. Ten of these 11 were also able to suppress BAX-mediated plant cell death. Five of the 11 SPD genes have been identified previously as either essential for the pathogenicity of M. oryzae, secreted into the plant during disease development, or as suppressors or homologues of other characterized suppressors. In addition, of the remaining six, we showed that SPD8 (previously identified as BAS162) was localized to the rice cytoplasm in invaded and surrounding uninvaded cells during biotrophic invasion. Sequence analysis of the 11 SPD genes across 43 re-sequenced M. oryzae genomes revealed that SPD2, SPD4 and SPD7 have nucleotide polymorphisms amongst the isolates. SPD4 exhibited the highest level of nucleotide diversity of any currently known effector from M. oryzae in addition to the presence/absence polymorphisms, suggesting that this gene is potentially undergoing selection to avoid recognition by the host. Taken together, we have identified a series of effectors, some of which were previously unknown or whose function was unknown, that probably act at different stages of the infection process and contribute to the virulence of M. oryzae.}, number={6}, journal={MOLECULAR PLANT PATHOLOGY}, author={Sharpee, William and Oh, Yeonyee and Yi, Mihwa and Franck, William and Eyre, Alex and Okagaki, Laura H. and Valent, Barbara and Dean, Ralph A.}, year={2017}, month={Aug}, pages={850–863} }
 @article{parker_oh_moazami_pierce_loziuk_dean_muddiman_2016, title={Examining ubiquitinated peptide enrichment efficiency through an epitope labeled protein}, volume={512}, ISSN={["1096-0309"]}, DOI={10.1016/j.ab.2016.08.017}, abstractNote={Ubiquitination is a dynamic process that is responsible for regulation of cellular responses to stimuli in a number of biological systems. Previous efforts to study this post-translational modification have focused on protein enrichment; however, recent research utilizes the presence of the di-glycine (Gly-Gly) remnants following trypsin digestion to immuno-enrich ubiquitinated peptides. Monoclonal antibodies developed to the cleaved ubiquitin modification epitope, (tert-butoxycarbonyl) glycylglycine (Boc-Gly-Gly-NHS)1, are used to identify the Gly-Gly signature. Here, we have successfully generated the Boc-Gly-Gly-NHS modification and showed that when conjugated to a lysine containing protein, such as lysozyme, it can be applied as a standard protein to examine ubiquitinated peptide enrichment within a complex background.}, journal={ANALYTICAL BIOCHEMISTRY}, author={Parker, J. and Oh, Y. and Moazami, Y. and Pierce, J. G. and Loziuk, P. L. and Dean, R. A. and Muddiman, D. C.}, year={2016}, month={Nov}, pages={114–119} }
 @article{okagaki_nunes_sailsbery_clay_brown_john_oh_young_fitzgerald_haas_et al._2015, title={Genome sequences of three phytopathogenic species of the Magnaporthaceae family of fungi}, volume={5}, number={12}, journal={G3-Genes Genomes Genetics}, author={Okagaki, L. H. and Nunes, C. C. and Sailsbery, J. and Clay, B. and Brown, D. and John, T. and Oh, Y. and Young, N. and Fitzgerald, M. and Haas, B. J. and et al.}, year={2015}, pages={2539–2545} }
 @article{franck_gokce_randall_oh_eyre_muddiman_dean_2015, title={Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development}, volume={14}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/PR501064Q}, DOI={10.1021/pr501064q}, abstractNote={The rice pathogen, Magnaporthe oryzae, undergoes a complex developmental process leading to formation of an appressorium prior to plant infection. In an effort to better understand phosphoregulation during appressorium development, a mass spectrometry based phosphoproteomics study was undertaken. A total of 2924 class I phosphosites were identified from 1514 phosphoproteins from mycelia, conidia, germlings, and appressoria of the wild type and a protein kinase A (PKA) mutant. Phosphoregulation during appressorium development was observed for 448 phosphosites on 320 phosphoproteins. In addition, a set of candidate PKA targets was identified encompassing 253 phosphosites on 227 phosphoproteins. Network analysis incorporating regulation from transcriptomic, proteomic, and phosphoproteomic data revealed new insights into the regulation of the metabolism of conidial storage reserves and phospholipids, autophagy, actin dynamics, and cell wall metabolism during appressorium formation. In particular, protein phosphorylation appears to play a central role in the regulation of autophagic recycling and actin dynamics during appressorium formation. Changes in phosphorylation were observed in multiple components of the cell wall integrity pathway providing evidence that this pathway is highly active during appressorium development. Several transcription factors were phosphoregulated during appressorium formation including the bHLH domain transcription factor MGG_05709. Functional analysis of MGG_05709 provided further evidence for the role of protein phosphorylation in regulation of glycerol metabolism and the metabolic reprogramming characteristic of appressorium formation. The data presented here represent a comprehensive investigation of the M. oryzae phosphoproteome and provide key insights on the role of protein phosphorylation during infection-related development.}, number={6}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Franck, William L. and Gokce, Emine and Randall, Shan M. and Oh, Yeonyee and Eyre, Alex and Muddiman, David C. and Dean, Ralph A.}, year={2015}, month={May}, pages={2408–2424} }
 @article{franck_gokce_oh_muddiman_dean_2013, title={Temporal Analysis of theMagnaporthe OryzaeProteome During Conidial Germination and Cyclic AMP (cAMP)-mediated Appressorium Formation}, volume={12}, ISSN={1535-9476 1535-9484}, url={http://dx.doi.org/10.1074/MCP.M112.025874}, DOI={10.1074/mcp.m112.025874}, abstractNote={Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed the appressorium. The development of the appressorium represents the first critical stage of infectious development. A total of 3200 unique proteins were identified by nanoLC-MS/MS in a temporal study of conidial germination and cAMP-induced appressorium formation in M. oryzae. Using spectral counting based label free quantification, observed changes in relative protein abundance during the developmental process revealed changes in the cell wall biosynthetic machinery, transport functions, and production of extracellular proteins in developing appressoria. One hundred and sixty-six up-regulated and 208 down-regulated proteins were identified in response to cAMP treatment. Proteomic analysis of a cAMP-dependent protein kinase A mutant that is compromised in the ability to form appressoria identified proteins whose developmental regulation is dependent on cAMP signaling. Selected reaction monitoring was used for absolute quantification of four regulated proteins to validate the global proteomics data and confirmed the germination or appressorium specific regulation of these proteins. Finally, a comparison of the proteome and transcriptome was performed and revealed little correlation between transcript and protein regulation. A subset of regulated proteins were identified whose transcripts show similar regulation patterns and include many of the most strongly regulated proteins indicating a central role in appressorium formation. A temporal quantitative RT-PCR analysis confirmed a strong correlation between transcript and protein abundance for some but not all genes. Collectively, the data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and highlight biological processes important for pathogenicity.}, number={8}, journal={Molecular & Cellular Proteomics}, publisher={American Society for Biochemistry & Molecular Biology (ASBMB)}, author={Franck, William L. and Gokce, Emine and Oh, Yeonyee and Muddiman, David C. and Dean, Ralph A.}, year={2013}, month={May}, pages={2249–2265} }
 @article{gokce_franck_oh_dean_muddiman_2012, title={In-Depth Analysis of the Magnaporthe oryzae Conidial Proteome}, volume={11}, ISSN={["1535-3907"]}, DOI={10.1021/pr300604s}, abstractNote={The filamentous fungus Magnaporthe oryzae (M. oryzae) is the causative agent of rice blast disease and presents a significant threat to worldwide rice production. To establish the groundwork for future research on the pathogenic development of M. oryzae, a global proteomic study of conidia was performed. The filter aided sample preparation method (FASP) and anion StageTip fractionation combined with long, optimized shallow 210 min nanoLC gradients prior to mass spectrometry analysis on an Orbitrap XL was applied, which resulted in a doubling of protein identifications in comparison to our previous GeLC analysis. Herein, we report the identification of 2912 conidial proteins at a 1% protein false discovery rate (FDR) and we present the most extensive study performed on M. oryzae conidia to date. A similar distribution between identified proteins and the predicted proteome was observed when subcellular localization analysis was performed, suggesting the detected proteins build a representative portion of the predicted proteome. A higher percentage of cytoplasmic proteins (associated with translation, energy, and metabolism) were observed in the conidial proteome relative to the whole predicted proteome. Conversely, nuclear and extracellular proteins were less well represented in the conidial proteome. Further analysis by gene ontology revealed biological insights into identified proteins important for central metabolic processes and the physiology of conidia.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Gokce, Emine and Franck, William L. and Oh, Yeonyee and Dean, Ralph A. and Muddiman, David C.}, year={2012}, month={Dec}, pages={5827–5835} }
 @article{oh_franck_han_shows_gokce_muddiman_dean_2012, title={Polyubiquitin Is Required for Growth, Development and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae}, volume={7}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0042868}, DOI={10.1371/journal.pone.0042868}, abstractNote={Protein ubiquitination, which is highly selective, regulates many important biological processes including cellular differentiation and pathogenesis in eukaryotic cells. Here, we integrated pharmacological, molecular and proteomic approaches to explore the role of ubiquitination in Magnaporthe oryzae, the leading fungal disease of rice world-wide. Inhibition of ubiquitin-mediated proteolysis using the 26S proteasome inhibitor, Bortezomib, significantly attenuated conidia germination, appressorium formation and pathogenicity in M. oryzae. Gene expression analysis revealed that many genes associated with protein ubiquitination were developmentally regulated during conidia germination. Only a few, including a polyubiquitin encoding gene, MGG_01282, were more abundantly expressed during appressorium formation and under nitrogen starvation. Targeted gene deletion of MGG_01282, in addition to a significant reduction in protein ubiquitination as determined by immuno blot assays, resulted in pleiotropic effects on M. oryzae including reduced growth and sporulation, abnormal conidia morphology, reduced germination and appressorium formation, and the inability to cause disease. Mutants were also defective in sexual development and were female sterile. Using mass spectrometry, we identified 63 candidate polyubiquitinated proteins under nitrogen starvation, which included overrepresentation of proteins involved in translation, transport and protein modification. Our study suggests that ubiquitination of target proteins plays an important role in nutrient assimilation, development and pathogenicity of M. oryzae.}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Oh, Yeonyee and Franck, William L. and Han, Sang-Oh and Shows, Angela and Gokce, Emine and Muddiman, David C. and Dean, Ralph A.}, editor={Nielsen, KirstenEditor}, year={2012}, month={Aug}, pages={e42868} }
 @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} }
 @article{kim_hu_oh_park_choi_lee_dean_mitchell_2010, title={Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus}, volume={6}, ISSN={["1553-7374"]}, DOI={10.1371/journal.ppat.1000909}, abstractNote={Significant progress has been made in defining the central signaling networks in many organisms, but collectively we know little about the downstream targets of these networks and the genes they regulate. To reconstruct the regulatory circuit of calcineurin signal transduction via MoCRZ1, a Magnaporthe oryzae C2H2 transcription factor activated by calcineurin dephosphorylation, we used a combined approach of chromatin immunoprecipitation - chip (ChIP-chip), coupled with microarray expression studies. One hundred forty genes were identified as being both a direct target of MoCRZ1 and having expression concurrently differentially regulated in a calcium/calcineurin/MoCRZ1 dependent manner. Highly represented were genes involved in calcium signaling, small molecule transport, ion homeostasis, cell wall synthesis/maintenance, and fungal virulence. Of particular note, genes involved in vesicle mediated secretion necessary for establishing host associations, were also found. MoCRZ1 itself was a target, suggesting a previously unreported autoregulation control point. The data also implicated a previously unreported feedback regulation mechanism of calcineurin activity. We propose that calcium/calcineurin regulated signal transduction circuits controlling development and pathogenicity manifest through multiple layers of regulation. We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen.}, number={5}, journal={PLOS PATHOGENS}, author={Kim, Soonok and Hu, Jinnan and Oh, Yeonyee and Park, Jongsun and Choi, Jinhee and Lee, Yong-Hwan and Dean, Ralph A. and Mitchell, Thomas K.}, year={2010}, month={May} }
 @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} }
 @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{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} }