title: PIECE 2.0: an update for the plant gene structure comparison and evolution database.
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.
authors.affiliation: USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.|Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.|USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.|USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.
authors.forename: Ling
authors.initials: L
authors.lastname: Xu
authors.affiliation: USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.
authors.forename: Roger
authors.initials: R
authors.lastname: Thilmony
authors.affiliation: Cereal Research Centre, Agriculture and Agri-Food Canada, Morden R6M 1Y5 MB, Canada.
authors.forename: Frank M
authors.initials: FM
authors.lastname: You
authors.affiliation: USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA yong.gu@ars.usda.gov.
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA devin.coleman-derr@ars.usda.gov.|USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA.
authors.forename: Devin
authors.initials: D
authors.lastname: Coleman-Derr
mesh_terms: D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005091:Exons; D017343:Genes, Plant; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D007438:Introns; D010944:Plants / Q000235:genetics*; D057386:Search Engine; D014584:User-Computer Interface; D064878:Web Browser