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United States Department of Agriculture

Agricultural Research Service

Research Project: AN INTEGRATED DATABASE AND BIOINFORMATICS RESOURCE FOR SMALL GRAINS Title: Piece: a Database for Plant Gene Structure Comparison and Evolution

Authors
item Wang, Yi -
item You, Frank -
item Lazo, Gerard
item Luo, Mingcheng -
item Thilmony, Roger
item Gordon, Sean
item Gu, Yong
item Kianian, Shahryar

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 19, 2012
Publication Date: November 14, 2012
Citation: Wang, Y., You, F., Lazo, G.R., Luo, M., Thilmony, R.L., Gordon, S.P., Gu, Y.Q., Kianian, S. 2012. PIECE: A database for plant gene structure comparison and evolution. Nucleic Acids Research. D1159-D1166.

Interpretive Summary: In plants, a typical gene structure contains two elements; the exon and the intron. 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 understanding roles of gene structure, protein functionality, and evolutionary change of genes among species. 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 extracted over 947,630 annotated genes from 25 sequenced plant species available in the public database. These genes were classified based on functional motifs and used for construction of a database that is specifically designed for gene structure and evolution analyses. This application database termed PIECES for Plant Intron and Exon Comparison and Evolution studies provides a user-friendly interface for different types of search and graphical viewer for displaying a gene structure pattern by comparing homologous genes in other plant species. Multiple bioinformatics software packages were integrated into this application database to allow users to select different viewing interfaces. PIECE is a powerful bioinformatics tool which allows plant biologists to compare gene sequences from different plant species and gain valuable insights into the evolution of gene structure in plant genomes.

Technical 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 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.

Last Modified: 12/20/2014
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