ArticleNucleic acids research2013
PIECE: a database for plant gene structure comparison and evolution.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 65 citations in OpenAlex.
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- SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm.Nucleic acids research · 2020Article
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- Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs.Genetics and molecular biology · 2018Article
- PrLPAAT4, a Putative Lysophosphatidic Acid Acyltransferase from Paeonia rockii, Plays an Important Role in Seed Fatty Acid Biosynthesis.Molecules (Basel, Switzerland) · 2017Article
- Functional divergence and origin of the DAG-like gene family in plants.Scientific reports · 2017Article
- PIECE 2.0: an update for the plant gene structure comparison and evolution database.Nucleic acids research · 2017Article
- Characterization of the maize lipoxygenase gene family in relation to aflatoxin accumulation resistance.PloS one · 2017Article
- Computational Tools for Genomic Studies in Plants.Current genomics · 2016Article
- Evolutionary and Expression Analysis Provides Evidence for the Plant Glutamate-like Receptors Family is Involved in Woody Growth-related Function.Scientific reports · 2016Article
- JuncDB: an exon-exon junction database.Nucleic acids research · 2016Article
- Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.).PloS one · 2016Article
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- GSDS 2.0: an upgraded gene feature visualization server.Bioinformatics (Oxford, England) · 2015Article
- Genome-wide investigation and transcriptome analysis of the WRKY gene family in Gossypium.Molecular genetics and genomics : MGG · 2015Article
- Genome-wide identification and comparative analysis of the heat shock transcription factor family in Chinese white pear (Pyrus bretschneideri) and five other Rosaceae species.BMC plant biology · 2015Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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