PIECE: a database for plant gene structure comparison and evolution

Wang, Yi; You, Frank M.; Lazo, Gerard R.; Luo, Ming‐Cheng; Thilmony, Roger; Gordon, Sean P.; Kianian, Shahryar F.; Gu, Yong

doi:10.1093/nar/gks1109

Cited by 56 publications

(30 citation statements)

References 28 publications

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“…Comparative analyses of exon-intron organization are very important to understand rules of gene structure and organization, protein functionality and evolutionary changes among species (Wang et al , 2012). Our analysis demonstrated that the putative DGAT3 and WS/DGAT genes of most analyzed species present a high degree of conservation with the well-characterized A. thaliana DGAT3 and WS/DGAT genes, respectively.…”

Section: Discussionmentioning

confidence: 99%

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Diversity and evolution of plant diacylglycerol acyltransferase (DGATs) unveiled by phylogenetic, gene structure and expression analyses

et al. 2016

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Since the first diacylglycerol acyltransferase (DGAT) gene was characterized in plants, a number of studies have focused on understanding the role of DGAT activity in plant triacylglycerol (TAG) biosynthesis. DGAT enzyme is essential in controlling TAGs synthesis and is encoded by different genes. DGAT1 and DGAT2 are the two major types of DGATs and have been well characterized in many plants. On the other hand, the DGAT3 and WS/DGAT have received less attention. In this study, we present the first general view of the presence of putative DGAT3 and WS/DGAT in several plant species and report on the diversity and evolution of these genes and its relationships with the two main DGAT genes (DGAT1 and DGAT2). According to our analyses DGAT1, DGAT2, DGAT3 and WS/DGAT are very divergent genes and may have distinct origin in plants. They also present divergent expression patterns in different organs and tissues. The maintenance of several types of genes encoding DGAT enzymes in plants demonstrates the importance of DGAT activity for TAG biosynthesis. Evolutionary history studies of DGATs coupled with their expression patterns help us to decipher their functional role in plants, helping to drive future biotechnological studies.

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Section: Discussionmentioning

confidence: 99%

“…We use the GSDraw web server, an interface for gene structure annotation available in PIECE database (Wang et al , 2012). Basically, we submitted a query sequence set (in multi-FASTA format) consisting of genomic and CDS to GSDraw and retrieved the gene structures with conserved protein motifs and phylogenetic trees.…”

Section: Methodsmentioning

confidence: 99%

Diversity and evolution of plant diacylglycerol acyltransferase (DGATs) unveiled by phylogenetic, gene structure and expression analyses

et al. 2016

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“…A number of web server applications for gene structure analysis have been developed, such as FancyGene (16), GSDraw (5), GenePainter (17) and GSDS (18). Among them, GSDraw is the one that can use sequence data (genomic, CDS and transcript sequences) to extract the gene structure, protein motif, and phylogenetic information, and then process the information together to draw the display diagram.…”

Section: New Featurementioning

confidence: 99%

“…PIECE (Plant Intron Exon Comparison and Evolution) is an intron–exon database that provides a powerful platform to compare gene structure among plant species (5). It was released in 2012 and published in the 2013 Nucleic Acids Research database issue.…”

Section: Introductionmentioning

confidence: 99%

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

Wang

Thilmony

et al. 2016

Nucleic Acids Res

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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.

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“…However, it can only display a single gene at a time. GSDraw (Wang et al, 2013) produces customizable, high-quality images with the capability of custom motifs. In addition, GSDraw provides users with a phylogenetic tree.…”

Section: Introductionmentioning

confidence: 99%

Transcript structure and domain display: a customizable transcript visualization tool

Watanabe

Homayouni

et al. 2016

Bioinformatics

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Summary: Transcript Structure and Domain Display (TSDD) is a publicly available, web-based program that provides publication quality images of transcript structures and domains. TSDD is capable of producing transcript structures from GFF/GFF3 and BED files. Alternatively, the GFF files of several model organisms have been pre-loaded so that users only needs to enter the locus IDs of the transcripts to be displayed. Visualization of transcripts provides many benefits to researchers, ranging from evolutionary analysis of DNA-binding domains to predictive function modeling. Availability and implementation: TSDD is freely available for non-commercial users at

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PIECE: a database for plant gene structure comparison and evolution

Cited by 56 publications

References 28 publications

Diversity and evolution of plant diacylglycerol acyltransferase (DGATs) unveiled by phylogenetic, gene structure and expression analyses

Diversity and evolution of plant diacylglycerol acyltransferase (DGATs) unveiled by phylogenetic, gene structure and expression analyses

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

Transcript structure and domain display: a customizable transcript visualization tool

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