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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #335484

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: PIECE 2.0: an update for the plant gene structure comparison and evolution database

Author
item Wang, Yi - University Of California
item Xu, L - University Of California
item Thilmony, Roger
item You, Frank - Agriculture And Agri-food Canada
item Gu, Yong
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., Xu, L., Thilmony, R.L., You, F., Gu, Y.Q., Coleman-Derr, D.A. 2016. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Research. 45(D1):1015-1020. https://doi.org/10.1093/nar/gkw935.

Interpretive Summary: In plants, a typical gene structure contains two elements, exons and introns. Exons are the DNA sequences that are transcribed and represented in the mature forms of RNA (mRNA) which serve as template for synthesis of the encoded protein. Introns that interrupt the exons in gene sequences are also transcribed, but removed from the mature RNA transcripts by RNA splicing. Comparative analysis of exon-intron organization is important for predicting the protein products of genes and for understanding how genes change by evolution. However, bioinformatics tools that can be directly applied for comparative analyses of gene structures among different plant species are not widely available. In this study, we updated our previous Plant Intron Exon Comparison and Evolution (PIECE) database. The updated PIECE2.0 database contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. We also added several new useful features to improve web performance and database utility. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.

Technical Abstract: PIECE (Plant Intron Exon Comparision 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. Database URL: http://probes.pw.usda.gov/AIM