PIECE 2.0: an update for the plant gene structure comparison and evolution database

Nucleic Acids Res. 2017 Jan 4;45(D1):1015-1020. doi: 10.1093/nar/gkw935. Epub 2016 Oct 13.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / methods
  • Databases, Genetic*
  • Evolution, Molecular*
  • Exons*
  • Genes, Plant*
  • Genome, Plant
  • Genomics / methods*
  • Introns*
  • Plants / genetics*
  • Search Engine
  • User-Computer Interface
  • Web Browser