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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: Piece2.0: an update for the pant gene structure comparison and evolution database

Author
item WANG, YI - University Of California
item LING, XU - University Of California
item THILMONY, ROGER - University Of California
item YOU, FRANK - University Of California
item GU, YONG - University Of California
item Coleman-Derr, Devin

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2016
Publication Date: 10/13/2016
Citation: Wang, Y., Ling, X., Thilmony, R., You, F., Gu, Y., Coleman-Derr, D.A. 2016. Piece2.0: an update for the pant gene structure comparison and evolution database. Nucleic Acids Research. 45:1015-1020.

Interpretive Summary: Gene structure in eukaryotic organisms is complex, often including multiple intron and exon sequences. The nature of these intron-exon boundaries contains important clues into the evolution of eukaryotic genomes. The PIECE tool provides biologists with the essential tools for performing comparative analyses of intron-exon structure across a wide variety of plants species. This update to the tool increases the number of plant genomes represented in the database, and improves the depth and breadth of analytical tools available to the user.

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 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). 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.