PIECE: A database for plant gene structure comparison and evolution

Yi Wang, Frank M. You, Gerard R. Lazo, Ming Cheng Luo, Roger Thilmony, Sean Gordon, Shahryar F. Kianian, Yong Q. Gu

Research output: Contribution to journalArticlepeer-review

38 Scopus citations

Abstract

Gene families often show degrees of differences in terms of exon-intron structures depending on their distinct evolutionary histories. Comparative analysis of gene structures is important for understanding their evolutionary and functional relationships within plant species. Here, we present a comparative genomics database named PIECE (http://wheat.pw.usda.gov/piece) for Plant Intron and Exon Comparison and Evolution studies. The database contains all the annotated genes extracted from 25 sequenced plant genomes. These genes were classified based on Pfam motifs. Phylogenetic trees were pre-constructed for each gene category. PIECE provides a user-friendly interface for different types of searches and a graphical viewer for displaying a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. The gene structure evolution of orthologous gene groups was determined using the GLOOME, Exalign and GECA software programs that can be accessed within the database. PIECE also provides a web server version of the software, GSDraw, for drawing schematic diagrams of gene structures. PIECE is a powerful tool for comparing gene sequences and provides valuable insights into the evolution of gene structure in plant genomes.

Original languageEnglish (US)
Pages (from-to)D1159-D1166
JournalNucleic acids research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013

Bibliographical note

Funding Information:
U.S. National Science Foundation [IOS 0701916 and IOS 0822100]; United State Department of Agriculture, Agriculture Research Service CRIS project [5325-21000-014]. Funding for open access charge: US Department of Agriculture, Agriculture Research Service.

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