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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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Screenshots from ZmGDB and yrGATE illustrate the use of online tools for gene discovery and community gene annotation. (A) A web-accessible table of Z. mays BACs (alternately shaded) displaying (left to right) the BAC GI, BAC clone name, followed by the ID, start/end coordinates and functional annotation of splice-aligned TIGR-predicted proteins from O. sativa and finally the ZmGDB entry date. All fields are searchable and each row is linked via column 1 to a genome browser view of the BAC region. This table is currently updated daily at ZmGDB (http://www.plantgdb.org/ZmGDB/DisplayGeneAnn.php). (Similar tables are available for eight other BAC-based xGDB browsers.) Note that a region of BAC GI 156523432 is aligned to three paralogous rice predicted polypeptides, annotated as ‘autophagy-related protein 8 precursor’. Clicking on the BAC GI ‘156523432’ in table column 1 (circled) brings up a BAC/Clone Context View of the specified region (B), showing spliced alignments to the rice predicted polypeptides (black), along with other alignment data, in this case maize cDNAs (blue) and maize ESTs (red). Note the evidence for alternative splicing among the maize ESTs (circles) suggesting at least two alternate transcripts (labeled 1 and 2). The user has the option to explore and annotate this variation using yrGATE. (C) Launching the yrGATE annotation tool displays scrolling list of evidence scores and supporting exons for all exon coordinates at a locus (alternative splice coordinates for 1 and 2 are circled). The user can build a complete gene model on screen by selecting each desired exon and then compare the resulting open reading frame to known proteins using BLAST (data not shown). (D) The chosen gene model is displayed graphically and will be published on the ZmGDB browser following curation by PlantGDB staff. Shown here are yrGATE models for the two putative splice variants, with translation start/stop positions indicated by triangles. (E) Predicted protein sequence for the two yrGATE gene models. This example illustrates how xGDB and yrGATE can be used to identify and publish gene model predictions quickly and easily, enhancing the community genome knowledge base for maize as well as facilitating hypothesis-driven research.
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Figure 3: Screenshots from ZmGDB and yrGATE illustrate the use of online tools for gene discovery and community gene annotation. (A) A web-accessible table of Z. mays BACs (alternately shaded) displaying (left to right) the BAC GI, BAC clone name, followed by the ID, start/end coordinates and functional annotation of splice-aligned TIGR-predicted proteins from O. sativa and finally the ZmGDB entry date. All fields are searchable and each row is linked via column 1 to a genome browser view of the BAC region. This table is currently updated daily at ZmGDB (http://www.plantgdb.org/ZmGDB/DisplayGeneAnn.php). (Similar tables are available for eight other BAC-based xGDB browsers.) Note that a region of BAC GI 156523432 is aligned to three paralogous rice predicted polypeptides, annotated as ‘autophagy-related protein 8 precursor’. Clicking on the BAC GI ‘156523432’ in table column 1 (circled) brings up a BAC/Clone Context View of the specified region (B), showing spliced alignments to the rice predicted polypeptides (black), along with other alignment data, in this case maize cDNAs (blue) and maize ESTs (red). Note the evidence for alternative splicing among the maize ESTs (circles) suggesting at least two alternate transcripts (labeled 1 and 2). The user has the option to explore and annotate this variation using yrGATE. (C) Launching the yrGATE annotation tool displays scrolling list of evidence scores and supporting exons for all exon coordinates at a locus (alternative splice coordinates for 1 and 2 are circled). The user can build a complete gene model on screen by selecting each desired exon and then compare the resulting open reading frame to known proteins using BLAST (data not shown). (D) The chosen gene model is displayed graphically and will be published on the ZmGDB browser following curation by PlantGDB staff. Shown here are yrGATE models for the two putative splice variants, with translation start/stop positions indicated by triangles. (E) Predicted protein sequence for the two yrGATE gene models. This example illustrates how xGDB and yrGATE can be used to identify and publish gene model predictions quickly and easily, enhancing the community genome knowledge base for maize as well as facilitating hypothesis-driven research.

Mentions: The xGDB browser Context View (Figure 3B) displays current gene model annotation together with high quality, cognate and non-cognate GeneSeqer alignments of ESTs, cDNAs, and PUTs to genomic sequence. Similarly, Oryza sativa predicted polypeptides from TIGR (http://rice.tigr.org/tdb/e2k1/osa1/) (13) and/or Arabidopsis thaliana predicted polypeptides from TAIR (http://www.arabidopsis.org/) (14) are splice-aligned to genomic sequence using GenomeThreader (15) and displayed in the same window. For species with microarray probe sequence, these are downloaded from the microarray database at PLEXdb (16), aligned relative to PUT assemblies and displayed. Significantly, users can view spliced alignments in a genomic region at the nucleotide level and also retrieve quality scores and provenance information for any spliced alignment displayed at xGDB. Additional sequence alignments, including GSS contigs and repeat masked regions, are displayed for some genomes. A subset of xGDB annotation data are accessible through the Distributed Annotation System (DAS) (http://www.biodas.org/). These data can be downloaded for further analysis, or alternatively imported into another genome browser capable of importing DAS formatted data.Figure 3.


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)

Screenshots from ZmGDB and yrGATE illustrate the use of online tools for gene discovery and community gene annotation. (A) A web-accessible table of Z. mays BACs (alternately shaded) displaying (left to right) the BAC GI, BAC clone name, followed by the ID, start/end coordinates and functional annotation of splice-aligned TIGR-predicted proteins from O. sativa and finally the ZmGDB entry date. All fields are searchable and each row is linked via column 1 to a genome browser view of the BAC region. This table is currently updated daily at ZmGDB (http://www.plantgdb.org/ZmGDB/DisplayGeneAnn.php). (Similar tables are available for eight other BAC-based xGDB browsers.) Note that a region of BAC GI 156523432 is aligned to three paralogous rice predicted polypeptides, annotated as ‘autophagy-related protein 8 precursor’. Clicking on the BAC GI ‘156523432’ in table column 1 (circled) brings up a BAC/Clone Context View of the specified region (B), showing spliced alignments to the rice predicted polypeptides (black), along with other alignment data, in this case maize cDNAs (blue) and maize ESTs (red). Note the evidence for alternative splicing among the maize ESTs (circles) suggesting at least two alternate transcripts (labeled 1 and 2). The user has the option to explore and annotate this variation using yrGATE. (C) Launching the yrGATE annotation tool displays scrolling list of evidence scores and supporting exons for all exon coordinates at a locus (alternative splice coordinates for 1 and 2 are circled). The user can build a complete gene model on screen by selecting each desired exon and then compare the resulting open reading frame to known proteins using BLAST (data not shown). (D) The chosen gene model is displayed graphically and will be published on the ZmGDB browser following curation by PlantGDB staff. Shown here are yrGATE models for the two putative splice variants, with translation start/stop positions indicated by triangles. (E) Predicted protein sequence for the two yrGATE gene models. This example illustrates how xGDB and yrGATE can be used to identify and publish gene model predictions quickly and easily, enhancing the community genome knowledge base for maize as well as facilitating hypothesis-driven research.
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Related In: Results  -  Collection

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Figure 3: Screenshots from ZmGDB and yrGATE illustrate the use of online tools for gene discovery and community gene annotation. (A) A web-accessible table of Z. mays BACs (alternately shaded) displaying (left to right) the BAC GI, BAC clone name, followed by the ID, start/end coordinates and functional annotation of splice-aligned TIGR-predicted proteins from O. sativa and finally the ZmGDB entry date. All fields are searchable and each row is linked via column 1 to a genome browser view of the BAC region. This table is currently updated daily at ZmGDB (http://www.plantgdb.org/ZmGDB/DisplayGeneAnn.php). (Similar tables are available for eight other BAC-based xGDB browsers.) Note that a region of BAC GI 156523432 is aligned to three paralogous rice predicted polypeptides, annotated as ‘autophagy-related protein 8 precursor’. Clicking on the BAC GI ‘156523432’ in table column 1 (circled) brings up a BAC/Clone Context View of the specified region (B), showing spliced alignments to the rice predicted polypeptides (black), along with other alignment data, in this case maize cDNAs (blue) and maize ESTs (red). Note the evidence for alternative splicing among the maize ESTs (circles) suggesting at least two alternate transcripts (labeled 1 and 2). The user has the option to explore and annotate this variation using yrGATE. (C) Launching the yrGATE annotation tool displays scrolling list of evidence scores and supporting exons for all exon coordinates at a locus (alternative splice coordinates for 1 and 2 are circled). The user can build a complete gene model on screen by selecting each desired exon and then compare the resulting open reading frame to known proteins using BLAST (data not shown). (D) The chosen gene model is displayed graphically and will be published on the ZmGDB browser following curation by PlantGDB staff. Shown here are yrGATE models for the two putative splice variants, with translation start/stop positions indicated by triangles. (E) Predicted protein sequence for the two yrGATE gene models. This example illustrates how xGDB and yrGATE can be used to identify and publish gene model predictions quickly and easily, enhancing the community genome knowledge base for maize as well as facilitating hypothesis-driven research.
Mentions: The xGDB browser Context View (Figure 3B) displays current gene model annotation together with high quality, cognate and non-cognate GeneSeqer alignments of ESTs, cDNAs, and PUTs to genomic sequence. Similarly, Oryza sativa predicted polypeptides from TIGR (http://rice.tigr.org/tdb/e2k1/osa1/) (13) and/or Arabidopsis thaliana predicted polypeptides from TAIR (http://www.arabidopsis.org/) (14) are splice-aligned to genomic sequence using GenomeThreader (15) and displayed in the same window. For species with microarray probe sequence, these are downloaded from the microarray database at PLEXdb (16), aligned relative to PUT assemblies and displayed. Significantly, users can view spliced alignments in a genomic region at the nucleotide level and also retrieve quality scores and provenance information for any spliced alignment displayed at xGDB. Additional sequence alignments, including GSS contigs and repeat masked regions, are displayed for some genomes. A subset of xGDB annotation data are accessible through the Distributed Annotation System (DAS) (http://www.biodas.org/). These data can be downloaded for further analysis, or alternatively imported into another genome browser capable of importing DAS formatted data.Figure 3.

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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Related in: MedlinePlus