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PlantGDB: a resource for comparative plant genomics.

Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V - Nucleic Acids Res. (2007)

Bottom Line: For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies.Annotation is facilitated by the integrated yrGATE module for community curation of gene models.PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.

ABSTRACT
PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.

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Transcript assemblies (PUTs) at PlantGDB, grouped by taxonomic affiliation. Sequence totals displayed here are as of 30 October 2007. Parentheses indicate the number of species/subspecies per genus. Genera highlighted in yellow are associated with a genome browser at PlantGDB; an underscore indicates chromosome-based genome browsers. An asterisk designates genera for which PlantGDB provides preprocessed GeneSeqer indices for quick access to spliced alignments.
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Figure 2: Transcript assemblies (PUTs) at PlantGDB, grouped by taxonomic affiliation. Sequence totals displayed here are as of 30 October 2007. Parentheses indicate the number of species/subspecies per genus. Genera highlighted in yellow are associated with a genome browser at PlantGDB; an underscore indicates chromosome-based genome browsers. An asterisk designates genera for which PlantGDB provides preprocessed GeneSeqer indices for quick access to spliced alignments.

Mentions: PlantGDB periodically uploads and parses all Viridiplantae sequences from GenBank (3) and Uniprot (4) into ∼70 000 individual data sets according to species or subspecies origin (Figure 1). PlantGDB's sequence data are refreshed approximately every 4 months, coinciding with alternate bimonthly GenBank version releases. GenBank and Uniprot sequences are uploaded, parsed by (sub)species, indexed for BLAST (5) and GeneSeqer (6) analysis, and loaded into MySQL tables. For all species with >10 000 published transcripts, a non-redundant set of PlantGDB-generated Unique Transcripts (PUTs) is generated using a custom assembly pipeline (http://www.plantgdb.org/prj/ESTCluster/PUT_procedure.php). PUTs are aligned to UniProt entries using BLAST, and the best matches (if any) and UniProt-associated Gene Ontology (GO) annotations (7) are stored. Currently, 116 species have PUT assemblies at PlantGDB, spanning diverse taxonomic groups (Figure 2). Users can track assembly progress in PlantGDB at http://www.plantgdb.org/prj/ESTCluster/progress.php. PlantGDB also provides genome survey sequence (GSS) assemblies for maize and sorghum (http://www.plantgdb.org/prj/GSSAssembly/). All PlantGDB sequence data (raw and processed) are available for download in a variety of file formats at http://www.plantgdb.org/download/download.php. In addition, all Zea mays sequence data at PlantGDB are uploaded monthly to MaizeGDB, the central repository for maize genetic information (http://www.maizegdb.org) (8).Figure 1.


PlantGDB: a resource for comparative plant genomics.

Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V - Nucleic Acids Res. (2007)

Transcript assemblies (PUTs) at PlantGDB, grouped by taxonomic affiliation. Sequence totals displayed here are as of 30 October 2007. Parentheses indicate the number of species/subspecies per genus. Genera highlighted in yellow are associated with a genome browser at PlantGDB; an underscore indicates chromosome-based genome browsers. An asterisk designates genera for which PlantGDB provides preprocessed GeneSeqer indices for quick access to spliced alignments.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238959&req=5

Figure 2: Transcript assemblies (PUTs) at PlantGDB, grouped by taxonomic affiliation. Sequence totals displayed here are as of 30 October 2007. Parentheses indicate the number of species/subspecies per genus. Genera highlighted in yellow are associated with a genome browser at PlantGDB; an underscore indicates chromosome-based genome browsers. An asterisk designates genera for which PlantGDB provides preprocessed GeneSeqer indices for quick access to spliced alignments.
Mentions: PlantGDB periodically uploads and parses all Viridiplantae sequences from GenBank (3) and Uniprot (4) into ∼70 000 individual data sets according to species or subspecies origin (Figure 1). PlantGDB's sequence data are refreshed approximately every 4 months, coinciding with alternate bimonthly GenBank version releases. GenBank and Uniprot sequences are uploaded, parsed by (sub)species, indexed for BLAST (5) and GeneSeqer (6) analysis, and loaded into MySQL tables. For all species with >10 000 published transcripts, a non-redundant set of PlantGDB-generated Unique Transcripts (PUTs) is generated using a custom assembly pipeline (http://www.plantgdb.org/prj/ESTCluster/PUT_procedure.php). PUTs are aligned to UniProt entries using BLAST, and the best matches (if any) and UniProt-associated Gene Ontology (GO) annotations (7) are stored. Currently, 116 species have PUT assemblies at PlantGDB, spanning diverse taxonomic groups (Figure 2). Users can track assembly progress in PlantGDB at http://www.plantgdb.org/prj/ESTCluster/progress.php. PlantGDB also provides genome survey sequence (GSS) assemblies for maize and sorghum (http://www.plantgdb.org/prj/GSSAssembly/). All PlantGDB sequence data (raw and processed) are available for download in a variety of file formats at http://www.plantgdb.org/download/download.php. In addition, all Zea mays sequence data at PlantGDB are uploaded monthly to MaizeGDB, the central repository for maize genetic information (http://www.maizegdb.org) (8).Figure 1.

Bottom Line: For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies.Annotation is facilitated by the integrated yrGATE module for community curation of gene models.PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.

ABSTRACT
PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.

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