PlantGDB News

2010 - What's New?

PlantGDB at Maize Genetics Conf.

PlantGDB will be represented at the 52nd Annual Maize Genetics Conference, March 18-21, 2010, Riva del Garda, Italy. Check out Poster 151, "Maize Community Annotation Project to Improve Gene Structures" in the 2010_maize_meeting_program.pdf.

New Annotation Workflow at BioExtract

The BioExtract Server has added a powerful new workflow for annotating genomic DNA, based on user-selected transcript and protein databases. The pipeline uses EVM (EVidence Modeler) to evaluate transcript- and ab initio-derived exons, and it outputs a GFF3-formatted file of optimal gene structures. A similar pipeline is available at PlantGDB for use with xGDB genome browsers (see next news item).

New Annotation Pipeline at PlantGDB

The AnnotationPipeDream tool allows users to annotate any genomic region (up to 500 kb) using any combination of transcript and protein datasets. The pipeline uses EVM (EVidence Modeler) to evaluate transcript- and ab initio-derived exons, and it outputs a GFF3-formatted file of optimal gene structures. The pipeline is currently available in the maize genome browser ZmGDB (click "Annotation Pipeline") and will soon be available for all genomes. This pipeline is also available as a customizable workflow in the BioExtract Server (see previous news item).

Community Annotation Tips

The yrGATE tool for gene structure annotation sports new context-sensitive help icons: just click any help icon () for a popup explanation of each function or tool.(Example).

2010 - previous news items

PlantGDB at PAG

PlantGDB will be at the Plant & Animal Genome meetings, Jan 8-13, 2010. Check out Poster C-928 and presentations at 4:40 PM Sunday in the Alternative Splicing Workshop and 1:30 PM Wednesday Computer Demo. Or stop by the Plant Genome DB Outreach Consortium booth and schedule a personal PlantGDB demo.

2009 news items

Brachypodium distachyon genome browser

BdGDB, a genome browser for the model grass species Brachypodium distachyon, is now available, based on the JGI v1.0 8x genome assembly. The assembly displayed comprises 271.15 Mb arranged in 5 pseudochromosomes. Display includes gene models, splice-aligned EST, cDNA, PUT assembly and Arabidopsis and rice predicated proteins (October 30, 2009).

Maize pseudochromosome browser

The pseudochromosome browser ZmGDB is now available, based on maizesequence.org Release 4a.53 and the golden path BAC assembly from AGI. Display includes gene models and yrGATE annotated genes; splice-aligned ESTs, cDNAs, NEW PUT assemblies, and sorghum and rice predicated proteins; Ds insertions; GSS assemblies; agp contigs; and masked regions. We continue to provide a separate, BAC-based ZmGDB (BAC) browser with the latest BAC data (October 16, 2009; PUTs added Nov 5).

GenBank Release 173

We have updated our sequence repository to GenBank Release 173.0, announced on August 26. We are now updating BLAST and GeneSeqer indices. (October 1, 2009).

New and Updated Transcript Assemblies (v.173)

New and refreshed transcript assemblies (PUTs) based on GenBank Release 173 are available for download and BLAST at PlantGDB.
New PUT assemblies include:

• Agrostis stolonifera (Creeping bentgrass)
• Avena barbata (slender oat)
• Cajanus cajan (pigeon pea).
• Cicer arietinum (chickpea)
• Citrus trifoliata (hardy orange)
• Festuca pratensis (meadow ryegrass)
• Glycyrrhiza uralensis (Chinese licorice)

Refreshed assemblies include:

• Mimulus guttatus (monkeyflower)
• Avena sativa (oat)
• Raphanus sativus (radish)
• Nicotiana benthamiana
• Nicotiana tabacum (tobacco)
• Malus x domestica (apple)
• Brassica napus (rapeseed)
• Phaseolus coccineus (scarlet runner bean)

View all PUT assemblies on our EST Assembly Data Page. (October 1, 2009)

Genome Updates: AtGDB, LjGDB, MtGDB, OsGDB

PlantGDB's genome browsers for Arabidopsis thaliniana (AtGDB), Medicago truncatula (MtGDB), and Oryza sativa (OsGDB) have been updated to the latest genome assembly and annotation version for each species. Splice-aligned transcript and related-species proteins from Version 171 are displayed as well as the latest transcript assemblies. In addition, the Lotus japonicus BAC-based genome browser (LjGDB) has been re-released, based on a pseudochromosome assembly available from kazuza.org (October 1, 2009).

CoGe Links

Genome Browsers at PlantGDB display spliced alignments to model species proteins, which are also listed in searchable Protein Alignment tables. These tables now provide hyperlinks to CoGe's GEvo (Genome Evolution) tool for exploring colinearity across multiple genomes. To try this, click "Protein Alignments" in the left menu of any Genome Browser, and then click a CoGe link icon in the genome-ordered list. For more details, see Genome Browser Help or ZmGDB Help (October 3, 2009).

Interface Improvements

Several features have been added to PlantGDB's genome browser interface, making it easier for users to configure tracks and display alternative data views. Genomic region, track order and view/hide configurations are now preserved within a session, and logged-in users can customize all configurations for later recall. You can give the new features a spin by visiting any PlantGDB Genome Browser home page (July 13, 2009).

CoGe alignments for maize

ZmGDB's Protein Alignment Table, displaying high quality spliced alignments of sorghum and rice gene models to maize BACs, now has direct hyperlinks to CoGe's GEvo (Genome Evolution) tool for multiple genome alignment. Click any table entry to generate real-time blastz or tblastx alignments to the matching regions of rice or sorghum at CoGe. - now loads all overlapping gene models in one GEvo window! (details) Similar links for other genomes at PlantGDBD are under development (updated July 30, 2009).

BAC/scaffold GmGDB

In addition to the pseudochromosome- based GmGDB (soybean) genome browser based on the JGI Glyma1 release, we have created an alternative GmGDB browser based on the previous scaffold-based Glyma0 assembly together with Glycine max BACS. This allows users to view legacy data as well as BAC sequences not included in the current assembly. View BAC/Scaffold GmGDB (July 13, 2009).

Primer analysis for AcDs

The new FindPrimers online tool allows rapid batchwise design of primers optimized for confirmation of Ds insertion in maize DNA (July 13, 2009)

External links

All external links at PlantGDB are now decorated with an icon indicating that the link navigates away from PlantGDB's pages. (July 30, 2009)

New and Updated Transcript Assemblies (v.171)

Three new and nine refreshed transcript assemblies (PUTs) based on GenBank Release 171 are available for download and BLAST at PlantGDB. You can access these and other assemblies through our EST Assembly Data Page (look for version 171a). First-time PUT assemblies include Elaeis guineensis (African oil palm), Gerbera hybrid cultivar (hybrid daisy), Zinnia violacea (garden zinnia). Refreshed assemblies include Adiantum capillus-veneris (maidenhair fern), Arachis hypogaea (peanut), Brassica rapa (field mustard), Cichorium intybus (chicory), Citrus clementina (clementine orange), Lotus japonicus (lotus bean), Oryza sativa Indica Group (indica rice), and Solanum lycopersicumTomato. [June 13, 2009]

AcDs Tagging Project Update

The AcDs Tagging project site for maize has been updated with new flanking sequences (fDs) and additional search and download features. Visit the Browse Insersions page for a current list of insertions placed to the maize genome, or use our fDs BLAST page to find out if your favorite maize gene has a Ds insertion. (May 22, 2009).

New feature: Add a genome track

PlantGDB's genome browsers can now display tracks served from a remote genome browser using our new DAS (Distributed Annotation Service) client. From any genome region, simply choose Configure -> Add Track from the track menu, and paste the DAS server URL. A list of DAS servers can be found on our DAS Overview page (May 5, 2009).

New feature: User control menu

PlantGDB's genome browsers have a new dropdown menu for tools and user settings. Track order can be customized with simple with drag and drop or click to hide. Check it out at ZmGDB (May 5, 2009).

Update to GenBank Release 171

We have updated our sequence repository to GenBank Release 171.0, which was announced on April 15. We are now updating BLAST and GeneSeqer indices. New and updated transcript assemblies will be available within approx. 1 month of the release (April 20, 2009).

Soybean genome browser updated

The GmGDB (soybean) genome browser has been updated to the latest assembly (20 pseudochromosomes) based on the JGI Glyma1 release. Glyma1 gene models are displayed along with splice-aligned soybean transcripts, PUT and microarray probes, and Arabidopsis and Medicago predicted proteins [April 8, 2009].

PlantGDB Website - Feedback

We appreciate all the feedback we've received since our design change in March. We are working hard to make additional improvements and bug fixes, and we continue to welcome your comments and suggestions! As always, our feedback form is the easiest way to contact us [April 7, 2009].

PlantGDB Website - Menus

The Search and Download menus have been consolidated under Sequence. To view all sequence data available at PlantGDB, go to Sequence -> Overview. The Help and About menus have been consolidated under Support. To view all support pages available at PlantGDB, go to Support -> About. [April 7, 2009].

Maize spliced alignments

ZmGDB, the genome browser for Zea mays has been udpated to has been updated to GenBank Release 169 EST/cDNA alignments. A new PUT Assembly for maize is in progress [March 11, 2009].

Maize gene models

ZmGDB now includes gene models from maizesequence.org's Version 3B.50 "Working Gene Set", displayed as a light-green track [March 11, 2009].

New DAS Server

PlantGDB's genome browsers now provide a DAS (Distributed Annotation Service) server for remotely viewing PlantGDB genome-aligned features (EST, PUT, and community annotation gene models) on a genome browser. Currently available for AtGDB and ZmGDB; see PlantGDB's DAS table for latest DAS resources and links [March 11, 2009].

AcDs Tagging Database

The AcDs Tagging pages at PlantGDB have been updated and expanded. New features include a searchable table of Ds insertions matching maize BACs, a new matching algorithm for BAC:fDs matches, and expanded support pages [March 11, 2009].

New Download Tool

Want to download all the splice-aligned ESTs, PUTs, or proteins from a genomic region? Try the new advanced search/download feature, available on all genome browsers at PlantGDB under the "Search by Region" link. You can also download gene models (transcript or protein) or a GenBank or GFF3-formatted version of the genomic region. HOT TIP: the GenBank-formatted output imports directly into Vector NTI [March 11, 2009].

New PlantGDB Design!

Starting March 11, 2009 Plantgdb.org features a new look and feel, improved navigation and support pages, and several new data features and tools (see below). We hope you enjoy exploring the new site, and encourage you to give us feedback if you encounter problems [March 11, 2009]

PlantGDB at Maize Genetics Conf.

PlantGDB was represented at the 51st Maize Genetics Conference (March 12-14, 2009) Poster #169 (What's New at PlantGDB for Maize?) [March 11, 2009].

PlantGDB at PAG XVII

PlantGDB was at Plant & Animal Genome Meeting, January 10-14, 2009. Poster #809 (PlantGDB).

Version 169a Update

Plant sequence from GenBank Release 169 (December 15, 2008) has been uploaded to PlantGDB, and sequence download repository, ftp site and BLAST and GeneSeqer indices have been updated. For more information, visit the Sequence Overview Page [Jan. 11, 2009].

Lotus japonicus genome update

LjGDB, the genome browser for Lotus japonicus, has been updated to incorporate the recently-published Lotus draft genome sequence (Sato et al., 2008) [January, 11 2009].

Soybean genome update

GmGDB, the genome browser for Glycine max, has been updated to Version 167a EST/cDNA and PUT assembly. [November, 2008].

2008

Plant sequence from GenBank Release 167 (August 2008) has been uploaded to PlantGDB, and sequence download repository, ftp site and BLAST and GeneSeqer indices have been updated [Sept. 19, 2008].

Ten new and seven refreshed transcript assemblies (PUTs) based on GenBank Release 167 are available for download and BLAST at PlantGDB. See details at our cluster progress page (look for version 167a) [Sept. 19, 2008].

First-time PUT assemblies include Actinidia chinensis (Chinese gooseberry ), Actinidia deliciosa (kiwifruit), Actinidia eriantha (kiwifruit sp.), Carica papaya (Papaya), Citrus aurantium (sour orange), Citrus reticulata (mandarin orange), Citrus x limonia (mandarin lime), Linum usitatissimum (flax), Papaver somniferum (opium poppy), Paullinia cupana var. sorbilis (guarana, a medicinal Amazonian plant).

Refreshed assemblies include Vigna unguiculata (blackeyed pea), Cryptomeria japonica (Japanese cedar), Citrus sinensis(navel orange), Glycine max (soybean), Poncirus trifoliata (hardy orange), Elaeis guineensis (African oil palm), and Nicotiana tabacum(tobacco).

New publication: Sparks, M.E. & Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics, 9, 381. [abstract] [provisional PDF] [Sept. 19, 2008]

The online GeneSeqer spliced alignment tool at PlantGDB has been updated and expanded to include any plant species transcript dataset [Sept. 19, 2008].

Papaya genome browser

Genome browser for papaya (Carica papaya L.), is now available, based on the recently-published papaya genome sequence (Ming et al., 2008). The new CpGDB displays the 3,208 sequence scaffolds (obtained from GenBank) with spliced-alignment to papaya EST, cDNA, PUT, and predicted Arabidopsis proteins. [August 15, 2008]

Advanced Search tool

The Advanced Search feature for xGDB genome browsers has been expanded to include gene models (Gbk-mRNA) as well as additional sequence retrieval options. To access Search, select a genome browser from the 'Genomes' dropdown menu, and then click 'Search' in the xGDB header menubar. See an example at GmGDB. [August 15, 2008]

GAEVAL tables

GAEVAL tables display incongruities in gene models versus alignment evidence. GAEVAL tables are now accessible for all browsers from the right menubar under 'GAEVAL Problematic Gene Models'. See an example at GmGDB, or visit the GAEVAL Help page for further details [August 15, 2008].

New FAQ Page

Visit the new FAQ (Frequently Asked Questions) help page here. [August 15, 2008]

Plant sequence from GenBank Release 167 (August 2008) has been uploaded to PlantGDB, and sequence download repository, ftp site and BLAST and GeneSeqer indices have been updated [Sept. 19, 2008].

Ten new and seven refreshed transcript assemblies (PUTs) based on GenBank Release 167 are available for download and BLAST at PlantGDB. See details at our cluster progress page (look for version 167a) [Sept. 19, 2008].

First-time PUT assemblies include Actinidia chinensis (Chinese gooseberry ), Actinidia deliciosa (kiwifruit), Actinidia eriantha (kiwifruit sp.), Carica papaya (Papaya), Citrus aurantium (sour orange), Citrus reticulata (mandarin orange), Citrus x limonia (mandarin lime), Linum usitatissimum (flax), Papaver somniferum (opium poppy), Paullinia cupana var. sorbilis (guarana, a medicinal Amazonian plant).

Refreshed assemblies include Vigna unguiculata (blackeyed pea), Cryptomeria japonica (Japanese cedar), Citrus sinensis (navel orange), Glycine max (soybean), Poncirus trifoliata (hardy orange), Elaeis guineensis (African oil palm), and Nicotiana tabacum (tobacco).

New publication: Sparks, M.E. & Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics, 9, 381. [abstract] [provisional PDF] [Sept. 19, 2008]

The online GeneSeqer spliced alignment tool at PlantGDB has been updated and expanded to include any plant species transcript dataset [Sept. 19, 2008].

Plant sequence from GenBank Release 165 (April 2008) has been uploaded to PlantGDB, and sequence download repository, ftp site and BLAST and GeneSeqer indices have been updated [June 3, 2008].

The AtGDB genome browser for Arabidopsis thaliana has been updated to TAIR 8, and the GAEVAL list of incongruent gene models has been updated. [June 3, 2008].

The ZmGDB genome browser for maize (Zea mays) has been updated to display spliced alignment to maize PUT assembly 163a, as well as to updated EST/cDNA datasets. A new track displays spliced alignment to sorghum predicted proteins from JGI. ZmGDB continues to provide daily annotation of maize BAC sequences deposited to GenBank by the Maize Genome Sequencing Consortium (www.maizesequence.org) [ June 3, 2008]

GAEVAL (Gene Annotation Evaluation) data summarizing incongruence between gene models and evidence alignments has been compiled for several genomes (Arabidopsis, rice, sorghum, soybean, Medicago, moss, poplar, maize). GAEVAL tables allow annotators to assess and prioritize the annotation needs for a genome. To access them, use the "GAEVAL Problematic Gene Models" link on each genome browser home page. See an example at GmGDB [June 3, 2008].

All-new PlantGDB Help Pages are now available at PlantGDB, including Genome Browsers, Community Annotation, FAQ, and a new Site Map. Please let us know how you like the new format and content [June 3, 2008]

A new Advanced Search feature is available for all xGDB genome browsers, featuring batch mode search and retrieval of upstream or downstream sequence data. Click the "Search" link from any genome browser home page, e.g. AtGDB [June 3, 2008]

The BioExtract Server workflow management tool (Menu>Tools>Collaborations>BioExtract) menus have been reconfigured to streamline query building [June 3, 2007].

Twenty-nine new transcript assemblies (PUTs) based on GenBank Release 165 are available for download and BLAST at PlantGDB. See details at our cluster progress page (look for version 165a) [June 3, 2008].

First-time PUT assemblies include Amborella trichopoda (a basal angiosperm), Aristolochia fimbriata (Dutchman's pipe), Catharanthus roseus (rosy periwinkle), Cenchrus ciliaris (African foxtail grass), Eucalyptus gunnii (cider tree), Limnanthes alba (meadowfoam), Liriodendron tulipifera (tulip tree), Persea americana (avacado), Phaseolus angustissimus (slimleaf limabean), Selaginella moellendorffii (spikemoss) Triticum turgidum subsp. durum (durum wheat), Vigna unguiculata (cowpea), Volvox carteri f. nagariensis (a multicellular chlorophyte alga), and Zamia vazquezii (cycad) [June 3, 2008].

New transcript assemblies (PUTs) are available for maize (Zea mays) and rice (Oryza sativa Japonica and Indica groups), based on GenBank Release 163. New PUT assemblies are also available for four solanaceous species: Solanum chacoense, S. habrochaites, S. pennellii and Nicotiana sylvestris. See complete PUT list on the Assembly Progress Page. [April 17, 2008]

GmGDB, the BAC-based browser for soybean (Glycine max), has been updated to include genomic scaffolds from the recently released soybean draft genome. The 3,317 scaffolds of assembly release Glyma0 (JGI), as well as BACs from GenBank, have been splice-aligned to EST, cDNA, PUT, probe, and predicted proteins from both Arabidopsis and Medicago. Predicted gene set Glyma0.1b from JGI is also displayed [April 17, 2008].

PpGDB, a new genome browser for moss (Physcomitrella patens) is now available, based on the recently-published moss genome sequence ( Rensing et al., 2008). The 2,106 scaffolds of assembly release v.1.1 been splice-aligned to EST, cDNA, PUT, and predicted proteins from both Arabidopsis and rice. Predicted gene set Phypa1.1 from JGI is also displayed [April 17, 2008].

AtGDB, the chromosome-based browser for Arabidopsis thaliana, has been updated to display spliced aligments to A. thaliana PUT assembly version 163a as well as EST and cDNA sequence from GenBank Release 163 [April 17, 2008].

For the latest on genome-wide mutagenesis in maize using Ac/Ds transposons, visit the updated Ac/Ds Project Page [March 7, 2008].

PlantGDB has been updated to GenBank Release 163, and new parsed sequence datasets are now available for download and BLAST. [February 7, 2008].

The ASIP (Alternative Splicing in Plants) database now includes legumes Medicago truncatula and Lotus japonicus. See also: Wang, B.-B., O'Toole, M., Brendel, V., and Young, N. (2008) Cross-species alignments reveal novel and conserved alternate splicing events in legumes. BMC Plant Biology 8:17 doi:10.1186/1471-2229-8-17 [online article] [February 20, 2008].

PtGDB, the pseudochromosome-based browser for Populus trichocarpa, has been updated to include annotated gene models from JGI [February 7, 2008].

SbGDB, the new chromosome-based genome browser for Sorghum bicolor, has been updated to include Orya sativa predicted protein spliced alignments. Data and database download are also available [January 7, 2008].

PlantGDB now offers an ftp site for bulk download of plant sequence and transcript assemblies (PUTs), in addition to our web browser-based download portal. [February 7, 2008].

New publication: Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson, M.D., Lawrence, C.J., Lushbough, C. & Brendel, V. (2007) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Research, 2007, doi: 10.1093/nar/gkm1041. [ PubMed ID: 18063570 ] [ online article ] [January 7, 2008].

13 updated and 17 new transcript assemblies (PUTs) are available for download and BLAST at PlantGDB. See details at our cluster progress page. Notably, the Arabidopsis thaliana PUT assembly has been updated to v.163 and annotated with UniProt similarity.

First-time assemblies include Artemisia annua (wormwood), Brassica oleracea (wild cabbage), Cucumis melo subsp. melo (melon), Cycas rumphii (cycad), Elaeis guineensis (oil palm), Eucalyptus globulus (bluegum tree), Ginkgo biloba, Gnetum gnemon (Spanish joint-fir), Humulus lupulus (hops), Leymus cinereus x Leymus triticoides (wild rye), Medicago sativa (alfalfa/lucerne), Raphanus raphanistrum subsp. maritimus (sea radish), R. raphanistrum subsp. raphanistrum (wild radish), Raphanus sativus (radish), and Raphanus sativus var. oleiformis (oil radish).) [February 14, 2008].

2007

VvGDB, a new chromosome-based genome browser for Vitis vinifera (wine grape), is now available, based on the recent release of the grape genome. VvGDB displays chromosome 1 - 19 alignments with V. vinifera EST, cDNA, transcript assemblies (PUT), microarray probe, and Arabidopsis predicted proteins as well as complete data and database download [November 7, 2007].

SbGDB, the genome browser for Sorghum bicolor has been updated to a chromosome-based browser following the release of the Sbi1 assembly for sorghum. SbGDB currently displays chromosome 1 - 10 alignments with sorghum EST, cDNA, GSS assembly, and transcript assemblies (PUT), with Oryza sativa predicted protein spliced alignments to come soon. Data and database download are also available [November 7, 2007].

The ZmGDB genome browser for Zea mays has a new home page and searchable BAC tables for Phase 1, 2, and 3 BACs, including chromosome number and BAC clone names [November 7, 2007].

The maize daily BAC annotation table now allows users to search for multiple BAC annotations at a time by pasting a list of BAC gi's [November 7, 2007].

The BioExtract Server workflow management tool now includes a feature for local data upload [November 7, 2007].

PlantGDB has been updated with GenBank Release 161 sequence data, and new PUT assemblies have been generated for 16 species: Allium cepa, Arachis hypogaea, Brassica napus, Brassica rapa, Centaurea maculosa, Cryptomeria japonica, Glycine max, Hordeum vulgare, Medicago truncatula, Nicotiana benthamiana, Nuphar advena, Ostreococcus lucimarinus, Picea sitchensis, Pseudotsuga menziesii, Raphanus raphanistrum, and Solanum lycopersicum. [September 15, 2007].

GmGDB, a BAC-based genome browser for Glycine max (soybean), has been updated with BAC alignments to EST, cDNA, transcript assemblies (PUT), probe, and Arabidopsis protein [September 15, 2007].

The BioExtract Server, a PlantGDB-hosted server for executing custom sequence analysis workflows, has been updated. New features include many more available Web services tools, options for adding local tools and local datasets, and a powerful new workflow management tool [September 15, 2007].

GhGDB, a new BAC-based genome browser for Gossypium hirsutum (cotton), is available with BAC alignments to EST, cDNA, transcript assemblies (PUT), probe, and Arabidopsis protein [August 15, 2007].

SlGDB, a BAC-based genome browser for Solanum lycopersicum (tomato; formerly Lycopersicum esculentum), has been updated with 314 additional BAC sequences and alignments to EST, cDNA, transcript assemblies (PUT), probe, and Arabidopsis. The LeGDB (Lycopersicum esculentum) genome browser has been deprecated [August 15, 2007].

The ZmGDB BAC annotation table for Zea mays, introduced in May, provides searchable, browsable rice protein annotations for all maize BACs. New annotation tables, with either rice or Arabidopsis protein annotations, are now available for all BAC-based genome browsers including HvGDB (Hordeum vulgare, barley), LjGDB (Lotus japonicus), SlGDB (Solanum lycopersicum, tomato), GmGDB (Glycine max, soybean), BrGDB (Brassica rapa, field mustard), TaGDB (Triticum aestivum, bread wheat), SbGDB (Sorghum bicolor, sorghum), and GhGDB (Gossypium hirsutum, cotton) [August 15, 2007].

The ZmGDB genome browser for Zea mays now links individual BACs to their equivalent at MaizeSequence.org [June 28, 2007]

The maize daily BAC annotation table has been updated with faster performance and new features, including multiple search modes and the ability to display BAC matches to Ds transposon tags. New help pages are also available. [June 18, 2007]

The MtGDB genome browser for Medicago truncatula has been updated to display pseudochromosomes aligned to PUT, probes, EST/cDNA, and Arabidopsis predicted protein alignments. [June 1, 2007].

The AtGDB genome browser for Arabidopsis thaliana has been updated to TAIR7. [June 1, 2007]

The ZmGDB genome browser for Zea mays now includes a daily update of new maize BAC sequences deposited in GenBank by the maize genome project. Alignments to PUT, GSS, EST/cDNA, rice predicted proteins, microarray probes, and fDs are displayed for each BAC. A new annotation table is available for browsing the latest BACs and annotated proteins from rice. Up-to-date maize BAC sequences are also available for download and BLAST. [May 16, 2007].

The OsGDB genome browser for Oryza sativa has been updated to TIGR genome build 5.0. A new track is available showing Arabidopsis thaliana predicted protein alignments. [May 16, 2007].

The PtGDB genome browser for Populus trichocarpa has been updated to display pseudochromosomes aligned to PUT, EST/cDNA, and Arabidopsis predicted protein alignments. [May 16, 2007].

The most recent Ds transposon insertion flanking sites (fDs) have been mapped onto current maize BACs and are available for BLAST query. [May 16, 2007]

Several new analysis tools have been added: Tracembler, which allows the user to do chromosome walks with pre-assembly trace data; MuSeq Box, a tool for generating tabular output from multiple BLAST queries; and TE Nest, for annotation and visualization of nested transposable elements in maize. [May 16, 2007]

We recently migrated PlantGDB.org to a new server for improved performance. Please let us know if you experience any problems using the site. Thank you! [May 16, 2007]

2006

PlantGDB poster presented at the 49th Maize Genetics Conference, March 22-25, 2007.

New, annotated PUT assemblies available for 100 plant species [Feb. 22] Details

New HvGDB genome browser for Hordeum vulgare (barley) [Feb. 22]

New BLAST interface: query by taxa (monocots, dicots, grasses, conifers) or any combination of 60,000 individual species) [Feb. 22]

[Nov. 2006] Plant Genome Research Outreach Portal (PGROP) now provides a map showing the location of outreach resources.

[Oct. 2006] PUT release 155a is now available. Details.

[Aug. 2006] Genome browsers are available for 11 plant species.

[Jun. 2006] The new interface alpha version for BLAST@PlantGDB to more conveniently select species-specific databases is now available for test.

[Jun. 2006] PUT release 153a is now available.

[Apr. 2006] AtGDB has been updated with PlantGDB 152a version of Arabidopsis ESTs, cDNAs, and PUTs. The number of ESTs increased about 50% from 151a version.

[Mar. 2006] PlantGDB mailing list has been released! Sign up for it now!

[Mar. 2006] PUT release 152a is now available.

[Feb. 2006] AtGDB has been updated to incorporate the TAIR version 6.0 genome release, PlantGDB 151a version of Arabidopsis ESTs, cDNAs, PUTs, and Affymetrix microarray probes.

[Feb. 2006] OsGDB has been updated to incorporate the TIGR Version 4 genome assembly and annotation as well as the PlantGDB 151a version of rice PUTs and Affymetrix microarray probes.

[Feb. 2006] ZmGDB is up to date with respect to the PlantGDB 151a version of maize BACs, ESTs, cDNAs, PUTs, and GSS contigs. The browser now also links Maize Oligonucleotide Array Project probes.

[Feb.2006] The Affymetrix Arabidopsis, soybean, tomato, Medicago, rice, sugar cane, wheat, and grape, maize and the Maize Oligonucleotide Array Project probes have been mapped to PUT version 151a contigs and linked to the PLEXdb expression database (see an example). You can search for matches against these probe sequences using our ProbeMatch tool.

[Feb. 2006] PUT release 151a is now available.

2005

[Aug. 2005] Recently updated species-specific EST assemblies are now available. Find out more!

[Aug. 2005] Announcement: New Plant Genome Program Research Solicitation available at NSF.

[Jul. 2005] The Plant Genomics Community can access our alignment data through DAS

[Jul. 2005] Annotation for Amateurs: a complete teaching module that teachers can adopt for classroom use and which is also appropriate for anyone new to gene annotation. All are invited to become a member of the growing Annotation Community!

[Apr. 2005] ZmGDB the maize counterpart to AtGDB and OsGDB

[Feb. 2005] PlantGDB now accommodates sequences from ALL plant species available at GenBank!

[Oct. 2004] Complete assembly of maize genome survey sequences (GSS)!