PlantGDB

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Acknowledgments

PlantGDB was initiated with support from the USA National Science Foundation Plant Genome Research Projects grants DBI-0110254, DBI-0321600 and IOS-0606909 and is currently supported by grant DBI 1126267, 'IPGA: Characterization, Modeling, Prediction, and Visualization of the Plant Transcriptome.'

- Volker Brendel (PI, Indiana University)
- Karin Dorman (Co-PI, Iowa State University)
- Shailesh Lal (Co-PI, Oakland University)
- Shannon Schlueter (Co-PI, University of North Carolina-Charlotte)
- Yasser El-Manzalawi (Senior Personnel, Iowa State University)
- Jon Duvick (Senior Personnel, Iowa State University)

The databases, web pages and tools at PlantGDB have been made possible by the efforts of many people and we want to acknowledge their efforts and thank them.

Current

PlantGDB Website and database

Ann Fu - Database Management

PlantGDB Systems Support

Mike Brekke (currently Department of Statistics, but still helping us out!)

Other acknowledgments...

PlantGDB relies on the following Javascript tools and libraries: JQuery (Mark Resnik),JQuery UI, Treeview by Jörn Zeafferer, Superfish by Joel Birch
Some of the icons on our website are from the Silk icon set at famfamfam.com

Former

PlantGDB - Brendel Group Graduate Students

Hong Lu (Iowa State University)
Shannon Schlueter (UNC-Charlotte)
Michael Sparks (USDA-ARS - Maryland)
Bing-Bing Wang (Pioneer Hi-Bred, International)
Matt Wilkerson (UNC-Chapel Hill)

PlantGDB - Other Student Programmers

Ganesha Upadhyaya (Iowa State University)
Lavanya Ram (Iowa State University, now in Houston, TX)
Ian Gartin (Iowa State University)
Sandy Huang (Iowa State Univeristy, now at Stanford)
Ganesan Mani (Iowa State University)
Brent Kronmiller (Iowa State University, now at Mendel Biotechnology, Inc.)
Mukul Sabharwal (Iowa State University, now at Microsoft)
Renish Palapetty (Iowa State University)
Travis Sanderson

PlantGDB - Staff

Qunfung Dong (University of North Texas)

PlantGDB - Systems Support

Mike Brekke
Chris Campbell

PlantGDB - Other Contributors

BioExtract - Staff

Carol Lushbough (PI)
Doug Jennewein
Brent Anderson
Joe Reynoldson
Colte Haines

New & Noteworthy

Click below or view all news | Twitter

What comes after PlantGDB? (July 1, 2015): PlantGDB's NSF funding has ended and the website is no longer being updated. However, you can check out a related project from the Brendel Lab, xGDBvm, a virtual environment for genome annotation in the cloud. xGDBvm instances are now available to registered users of iPlant Atmosphere (3-14-2012)
New Location for PlantGDB (July 23, 2012): The Brendel Group is now located at Indiana University, and the PlangGDB server has been migrated as well, and it is now hosted at the Indiana University School of Informatics and Computing. We don't anticipate any disruption in service, but if you encounter any problems with the website we encourage you to contact us using our Feedback Form. (3-14-2012)
BrGDB - Brassica rapa chromosome-based genome browser (Mar. 16)
StGDB - Solanum tuberosum new genome browser (Mar. 16, 2012): StGDB, a new genome database for the potato (Solanum tuberosum) is now available at PlantGDB (Genomes→Other→StGDB). Based on the JGI draft genome, VcGDB includes 14,971 protein-coding loci and 15,285 protein-coding transcripts on 413 scaffolds. Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-14-2012)
BrGDB - Brassica rapa chromosome-based genome browser (Mar. 16, 2012): BrGDB, the genome browser for rapeseed (Brassica rapa) is now updated at PlantGDB (Genomes→Other→BrGDB). Based on the BRAD draft genome, BrGDB includes 41,019 protein-coding transcripts on 10 chromosomes plus unanchored scaffolds (concatenated with 200 N spacer as "chr11"). Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-16-2012)
VcGDB - Volvox carteri new genome browser (Mar. 14, 2012): VcGDB, a new genome database for the multicellular green alga Volvox (Volvox carteri) is now available at PlantGDB (Genomes→Other→VcGDB). Based on the JGI draft genome, VcGDB includes 14,971 protein-coding loci and 15,285 protein-coding transcripts on 413 scaffolds. Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-14-2012)
Medicago genome updated (Feb 27, 2012): The Medicago truncatula (barrel medic) genome browser MtGDB has been updated to the new assembly / annotation version 3.5 using data deposited at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Rice genome updated (Feb 27, 2012): The Oryza sativa (rice) genome browser OsGDB has been updated to the new assembly / annotation version 7 using data deposited at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Cassava genome updated (Feb 27, 2012): The Manihot esculenta (cassava) genome browser MeGDB has been updated to the v4 assembly / v4.1 annotation that is available at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Populus annotation updated (Feb 27, 2012): The Populus trichocarpa (poplar) genome browser PtGDB has been updated to annotation version 2.2 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Mimulus annotation updated (Feb 27, 2012): The Mimulus guttatus genome browser MgGDB has been updated to annotation version 4.3 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Chlamydomonas annotation updated (Feb 27, 2012): The Chlamydomonas reinhardtii genome browser CrGDB has been updated to annotation version 4.3 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Brachopodium annotation updated (Feb 13, 2012): The Brachypodium distachyon genome browser BdGDB has been updated to annotation version Bradi1.2 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
PlantGDB NSF Grant (Jan 31, 2012): The PlantGDB website is currently being managed under a new NSF Genome Research Grant, IOS-1126267 (IPGA: Characterization, Modeling, Prediction, and Visualization of the Plant Transcriptome.) Read more about IPGA.
PlantGDB at Maize Genetics Conf. (Jan 31, 2012): PlantGDB will be represented at the 54th Annual Maize Genetics Conference, March 15-18, 2012, in Portland, Oregon USA. Check out poster P56 "Discovery, annotation and expression analysis of arginine/serine (SR) proteins in maize using the Plant Genome Database PlantGDB". (1-28-2012)
GenBank Release 187 (Jan 31): GenBank Release 187.0 sequence data (close date 12-15-2011) have been processed and are available for downloading at PlantGDB. Twenty-three new or updated transcript assemblies have been created. Please note that indexing the new sequence data has been postponed due to infrastructure issues. (2-27-2012)
New Add Track feature for Genome Browsers Dec 15, 2011: Users can add their own genome features (aligned transcripts, gene models, etc) using our User Add Track tool. All that's needed is a properly formatted gff3 file. This feature is currently available at ZmGDB and AtGDB/ and will be available soon for all GDB. (12-15-2011).

What's Coming?

Genome updates (1-31-2012): We are in the process of prioritizing genomes at PlantGDB for update. In addition, newly-available plant genomes are being prioritized for inclusion in PlantGDB's Genome Browser suite. Our goal is to maintain current data for at least 25 genomes.