PIECE 2.0: an update for the plant gene structure comparison and evolution database. Issue Volume 45:Issue D1(2017) (13th October 2016)

• Record Type: Journal Article
• Authors: Wang, Yi; Xu, Ling; Thilmony, Roger; You, Frank M.; Gu, Yong Q.; Coleman-Derr, Devin
• Is Part Of: Nucleic acids research. Volume 45:Issue D1(2017)
• Page Start: D1015
• Page End: D1020
• Publication Date: 2016-10-13
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkw935
• Languages: English
• ISSNs: 0305-1048

Abstract

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.