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Research Project: Enabling Improved Environmental Stress Tolerance in Crops through Novel Computational Strategies and Tool Development

Location: Plant Gene Expression Center

Title: High-resolution phylogenic microbial community profiling

item Singer, Esther - JOINT GENOME INSTITUTE
item Bushnell, Brian - JOINT GENOME INSTITUTE
item Coleman-derr, Devin
item Bowers, Robert - JOINT GENOME INSTITUTE
item Cheng, Jan-feng - JOINT GENOME INSTITUTE
item Copeland, Alex - JOINT GENOME INSTITUTE

Submitted to: The ISME Journal: Multidisciplinary Journal of Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2015
Publication Date: N/A
Citation: N/A

Interpretive Summary: Post-transcriptional regulation of N-gene expression during seedling growth. The plant resistance (R) gene, Necrotic (N), mediates innate immunity against tobacco mosaic virus (TMV), however the regulation of N-mediated virus resistance during plant growth is not well-understood. We previously showed that miR6019/6020 silence N gene expression. In this study we investigated the role of miRNA silencing in fine-tuning expression of N and TMV resistance during seedling development. We found that while N effectively restricts TMV to infected leaves of 6-week old tobacco seedlings, TMV is not restricted to infected leaves of 1-week old seedlings and virus spreads triggering lethal systemic necrosis. Using an N promoter-reporter gene fusion we found that the N-promoter drives similar levels of reporter gene expression in one- and six-week old seedlings, whereas N transcript levels were 10-fold higher in six week-old seedlings compared to one-week old seedlings. We explored the role of miRNA regulation of N expression during seedling growth. Using a MIR6019/6020 promoter-reporter gene fusion and sRNA sequencing we found MIR6019/6020 expression and miRNA levels were approximately three-fold lower in six-week old compared to one-week old seedlings. Yeast one-hybrid analysis identified candidate transcriptional repressors and activators that potentially regulate MIR6019/6020 expression. High-throughput transcriptome sequence profiling of sRNAs and NLR targets support a broader role for small RNAs in regulation of NLRs as plants develop. This study provides insight into the mechanistic basis of miRNA regulation of R-genes during growth and defense.

Technical Abstract: PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 ( or PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution