Browsing by Author "Shu, Shengqiang"

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    Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass
    Frazier, Taylor P.; Palmer, Nathan A.; Xie, Fuliang; Tobias, Christian M.; Donze-Reiner, Teresa J.; Bombarely, Aureliano; Childs, Kevin L.; Shu, Shengqiang; Jenkins, Jerry W.; Schmutz, Jeremy; Zhang, Baohong; Sarath, Gautam; Zhao, Bingyu Y. (2016-11-08)
    BACKGROUND: Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. RESULTS: In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from 'Alamo', a rust-resistant switchgrass cultivar, and 'Dacotah', a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar 'Summer' plants indicated that the expression of some of these RGHs was developmentally regulated. CONCLUSIONS: Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop.
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    JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom
    Sreedasyam, Avinash; Plott, Christopher; Hossain, Md Shakhawat; Lovell, John T.; Grimwood, Jane; Jenkins, Jerry W.; Daum, Christopher; Barry, Kerrie; Carlson, Joseph; Shu, Shengqiang; Phillips, Jeremy; Amirebrahimi, Mojgan; Zane, Matthew; Wang, Mei; Goodstein, David; Haas, Fabian B.; Hiss, Manuel; Perroud, Pierre-Francois; Jawdy, Sara S.; Yang, Yongil; Hu, Rongbin; Johnson, Jenifer; Kropat, Janette; Gallaher, Sean D.; Lipzen, Anna; Shakirov, Eugene; Weng, Xiaoyu; Torres-Jerez, Ivone; Weers, Brock; Conde, Daniel; Pappas, Marilia R.; Liu, Lifeng; Muchlinski, Andrew; Jiang, Hui; Shyu, Christine; Huang, Pu; Sebastian, Jose; Laiben, Carol; Medlin, Alyssa; Carey, Sankalpi; Carrell, Alyssa A.; Chen, Jin-Gui; Perales, Mariano; Swaminathan, Kankshita; Allona, Isabel; Grattapaglia, Dario; Cooper, Elizabeth A.; Tholl, Dorothea; Vogel, John P.; Weston, David J.; Yang, Xiaohan; Brutnell, Thomas P.; Kellogg, Elizabeth A.; Baxter, Ivan; Udvardi, Michael; Tang, Yuhong; Mockler, Todd C.; Juenger, Thomas E.; Mullet, John; Rensing, Stefan A.; Tuskan, Gerald A.; Merchant, Sabeeha S.; Stacey, Gary; Schmutz, Jeremy (Oxford University Press, 2023-08-01)
    Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.