@article{wang_eyre_thon_oh_dean_2020, title={Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds}, volume={11}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2020.559728}, abstractNote={Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Wang, Mengying and Eyre, Alexander W. and Thon, Michael R. and Oh, Yeonyee and Dean, Ralph A.}, year={2020}, month={Sep} }
 @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{okagaki_sailsbery_eyre_dean_2016, title={Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi}, volume={17}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-016-2491-y}, abstractNote={Magnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (take-all disease), and Magnaporthe poae (summer patch disease). Recently, the sequenced and assembled genomes for these three fungi were reported. Here, the genomes were compared for orthologous genes in order to identified genes that are unique to the Magnaporthaceae family of fungi. In addition, ortholog clustering was used to identify a core proteome for the Magnaporthaceae, which was examined for diversifying and purifying selection and evidence of two-speed genome evolution.A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. We found 1149 clusters that were unique to the Magnaporthaceae family of fungi with 295 of those containing genes from all three species. Gene clusters involved in metabolic and enzymatic activities were highly represented in the Magnaporthaceae specific clusters. Also highly represented in the Magnaporthaceae specific clusters as well as in the species specific genes were transcriptional regulators. In addition, we examined the relationship between gene evolution and distance to repetitive elements found in the genome. No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed.Taken together, these data show that at the genome level, there is no evidence to suggest multi-speed genome evolution or that proximity to repetitive elements play a role in diversification of genes.}, journal={BMC GENOMICS}, author={Okagaki, Laura H. and Sailsbery, Joshua K. and Eyre, Alexander W. and Dean, Ralph A.}, year={2016}, month={Feb} }
 @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={SummaryPhytopathogenic 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{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} }