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Latest update: January 20, 2010

Transcript Assembly Update

New and refreshed transcript assemblies (PUTs) based on GenBank Release 175 are available for download and BLAST at PlantGDB.
New PUT assemblies include:

• Fragaria x ananassa (garden strawberry)
• Jatropha curcas (Barbados nut)
• Mimulus guttatus var. nasutus (common monkeyflower)
• Mimulus lewisii (purple monkeyflower)
• Phyllostachys edulis (tortoiseshell bamboo)
• Pisum sativum (garden pea)
• Pinus contorta (lodgepole pine)
• Quercus petraea (sessile oak).
• Quercus robur (English oak)
• Solanum melongena (eggplant)
• Solanum torvum (turkeyberry)

Refreshed assemblies include:

• Brachypodium distachyon (Brachypodium)
• Bruguiera gymnorhiza (large-leafed mangrove)
• Cicer arietinum (chickpea)
• Coffea arabica (coffee)
• Cucumis sativus (cucumber)
• Festuca arundinacea (tall fescue)
• Musa acuminata (banana)
• Picea abies (Norway spruce)
• Picea glauca (white spruce)
• Phaseolus coccineus (scarlet runner bean)
• Picea sitchensis (Sitka spruce)
• Solanum habrochaites (wild tomato)
• Solanum pennellii (wild tomato)

View all PUT assemblies on our EST Assembly Data Page. (January 21, 2010)

GenBank Release 175

GenBank Release 175.0 sequence data are now available on our Download Page. PUT assemblies are currently being updated (January 15, 2010).

New Help Links

Need help understanding what you see on a page? Click the help icon, , for a popup explanation and additional resources. We will be rolling this system out across PlantGDB soon; for now, it's implemented for Genome Browsers (Example).

Links to CIWOG

CIWOGPlants is a database of common introns from 29,967 orthologous gene clusters from eight plant species*. PlantGDB now links to CIWOG alignments: from the gene model record page (see example), click on the @ CIWOG (loose) link under "Additional Resource Links" to search the CIWOG database for this gene model (January 6, 2010)
*Briefings in Bioinformatics 10:631 (2009) (abstract)

Genome browser video

A new 6 minute video tutorial, "How to use genome browsers at PlantGDB", is available from the Home page, Help & Tutorials, or any Genome browser page (December 26, 2009).

Parallel GeneSeqer

GeneSeqer has been installed on USD's high performance computer system, and a Parallel GeneSeqer web interface is available for larger runs (December 26, 2009).

PtGDB (Populus trichocarpa) update

PlantGDB's genome browser for Populus trichocarpa (PtGDB) has been updated to incoporate JGI poptr v1.1 gene model annotations and up-to-date PlantGDB spliced alignments to cDNA, EST, and related species proteins (December 10, 2009).

Annotation video

Check out the new gene structure annotation video, available from Help and Tutorials page or any genome browser. This 4.5 minute video demonstrates the yrGATE annotation tool in action (December 2, 2009).

Maize genome annotation

Community-annotated maize gene models at ZmGDB (see an example) can now be viewed at MaizeGDB and maizesequence, by means of Distributed Annotation Service (DAS). (November 20, 2009).

Manihot esculenta (cassava) genome browser

The recently-released Manihot esculenta draft genome consists of 11,243 scaffolds spanning 416Mb. PlantGDB will release a cassava genome browser incorporating EST, cDNA, PUT and related-species protein alignments as well as published gene models (expected Jamuary, 2010).