PIECE


27742820	PIECE 2.0: an update for the plant gene structure comparison and evolution database. [PMID: 27742820] Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D. 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. © Crown copyright 2016. Nucleic Acids Res. 2017:45(D1) \| 16 Citations (from Europe PMC, 2025-03-22)
23180792	PIECE: a database for plant gene structure comparison and evolution. [PMID: 23180792] Wang Y, You FM, Lazo GR, Luo MC, Thilmony R, Gordon S, Kianian SF, Gu YQ. 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. Nucleic Acids Res. 2013:41(Database issue) \| 28 Citations (from Europe PMC, 2025-03-22)

PIECE 2.0: an update for the plant gene structure comparison and evolution database. [PMID: 27742820]

Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D.

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. © Crown copyright 2016.

Nucleic Acids Res. 2017:45(D1) | 16 Citations (from Europe PMC, 2025-03-22)

PIECE: a database for plant gene structure comparison and evolution. [PMID: 23180792]

Wang Y, You FM, Lazo GR, Luo MC, Thilmony R, Gordon S, Kianian SF, Gu YQ.

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.

Nucleic Acids Res. 2013:41(Database issue) | 28 Citations (from Europe PMC, 2025-03-22)

URL:	http://wheat.pw.usda.gov/piece/
Full name:	Plant Intron Exon Comparison and Evolution database
Description:	IECE is a plant gene structure comparison and evolution database with 25 species. Annotated genes were extracted from the species and classified based on Pfam motif. Phylogenetic tree was reconstructed for each gene category integrated exon-intron and protein motif information. Both the sequences and gene structure information for each identified gene are freely available for online access on the PIECE website.
Year founded:	2013
Last update:	2017-01-01
Version:	v 2.0
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA
Data object:	Plant
Database category:	Phylogeny and homology
Major species:	Arabidopsis thaliana Glycine max Oryza sativa Populus trichocarpa
Keywords:	gene structure Phylogenetic tree

University/Institution:	USDA-ARS
Address:	Crop Improvement and Genetics Research Unit
City:	Albany
Province/State:	California
Country/Region:	United States
Contact name (PI/Team):	Yi Wang
Contact email (PI/Helpdesk):	yi.wang@ars.usda.gov

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