P0944 PGSCED: A Database for Plant Gene Structure Comparison and Evolution

Yi Wang , University of California, Davis, CA
Frank You , University of California, Davis, CA
Gerard R. Lazo , USDA-ARS Western Regional Research Center, Albany, CA
Mingcheng Luo , Department of Plant Sciences, University of California, Davis, CA
Shahryar Kianian , North Dakota State University/Plant Sciences, Fargo, ND
Yong Q. Gu , USDA-ARS- WRRC, Albany, CA
Orthologous and paralogogus genes often show degrees of difference 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 PGSCED (http://probes.pw.usda.gov/PGSCED) for plant gene structure comparison and evolution. Annotated genes were extracted from 24 plant species and classified based on Pfam motif. Phylogenetic tree was reconstructed for each gene category. The comparison of gene sequences provided fundamental information to reveal gene structure difference that will be particularly useful for studying exon/intron evolution. The PGSCED database provides a user-friendly graphical viewer that displays a gene structure pattern diagram linked to the resulting bootstrapped dendrogram for each gene family. Gene structure information can be displayed and retrieved in nucleotide sequence or in aligned protein sequence. We also developed a JavaScript viewing tool to view the evolution of orthologous gene group, which was analyzed using the GLOOME and EXALIGN program. The PGSCED database is a powerful tool for comparing gene sequences and can provide valuable implications for the evolution of gene structure in plant genomes.