All 9 entries tagged Jgi

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June 01, 2009

DOE JGI Releases Expanded Version of Phytozome.net

DOE JGI Releases Expanded Version of Phytozome.net: Clearinghouse for Comparative Plant Genomics Data

phytozomeAn enhanced version of Phytozome.net, a web portal for comparative plant genomics geared to advance biofuel, food, feed, and fiber research, has been released by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI).

Phytozome provides a central “hub” for web access to a rapidly growing number of plant genomes, and includes tools for visualization of plant genomes and associated annotations, sequence analysis, and bulk, as well as targeted, plant data retrieval.  The gene families available in Phytozome, defined at several evolutionarily significant epochs, provide a framework for the transfer of functional information to important biofuel and agricultural crops from model plant systems, as well as allowing users to explore land plant evolution.

The 4.0 release of Phytozome now spans 14 plant genomes, including 8 that have been sequenced at the DOE JGI

Press Release - http://www.jgi.doe.gov/News/news_09_05_28.html



March 31, 2009

Agaricus bisporus 8x Release [project ID 4084801 / March 2009]

JGI have recently announced that the 8X sequencing & draft assembly for Agaricus bisporus (H97, lead homokaryon) is complete.


JGI_20090331 This assembly will now undergo a machine annotation with Igor Grigoriev’s JGI team (ca. 3-4 months). Draft assembly/annotation will then transfer to the community for hands-on detailed annotations (ca. 6 months). When these steps are complete, the Agaricus bisporus draft genome assembly and annotation will become publicly available via the JGI web portal, and both the assembly & annotation will be deposited in GenBank.
An extensive Agaricus bisporus U1 (H97 x H39 heterokaryon) EST data set has also been clustered to the genome.
Jeremy Schmutz of the JGI has provided an assembly report jgiupdate_8x_200903_blog.pdf

Library construction for the second homokaryon, Agaricus bisporus var. burnettii JB137-S8 is now in progress.

JGI project summaries http://snipurl.com/ex7l2



February 18, 2009

Genomic DNA of A. bisporus var. burnettii JB137–S8 sent to JGI

gDNA JB137-S8Thanks are due (again) to Rick Kerrigan and his team at Sylvan Inc. who have prepared and submitted  gDNA of Agaricus bisporus var. burnettii JB137-S8 to the JGI. This second homokaryon will most likely be sequenced using Illumina-454 technologies when the lead homokaryotic H97 genome reaches 8x coverage.

Further information on the Agaricus bisporus strains being sequenced in the JGI project is available in our original proposal, which is available at http://www.warwick.ac.uk/go/agaricusgenome





January 28, 2009

JGI Fourth Annual User Meeting

Writing about web page http://www.jgi.doe.gov/meetings/usermtg09/index.html

The JGI have recently announced details of their 4th Annual User Meeting

JGI_20090128Genomics of Energy & Environment

U.S. Department of Energy / Joint Genome Institute (JGI)
Marriott Hotel in Walnut Creek, California. March 25-27, 2009

Significantly, the event includes a 'Eukaryotic Annotation Workshop' aimed at PIs and collaborators of eukaryotic projects with genomes annotated or expected for annotation in 2009, as well as new members of user communities interested in Community Annotation.

http://www.jgi.doe.gov/meetings/usermtg09/index.html


October 30, 2008

JGI Genome Portal Tutorial Site

Andy Bailey has kindly drawn my attention to the online JGI annotation tutorial:

JGItutorial

http://genome.jgi-psf.org/Tutorial/Tutorial.home.html

http://genome.jgi-psf.org/help/

As our Agaricus bisporus sequencing project progresses, and with the promise of 4x sequence in Q1-2009, this is a probably a good time for genome novices (like myself) to get familiar with the JGI tools. 

Other JGI-led training should take place as the project advances.


October 13, 2008

EST data sets sent to JGI

Agaricus bisporus Genome Sequencing - Project updates


[29 Sept 2008] 

Warwick sequence database (ca 1700 seqs) sent to the JGI, these comprise

1-813 EMBL nucleotide database sequences related to Agaricus bisporus

814-1066 miscellaneous cDNA library sequences

1067-1513 SSH differential expression during mushroom development (vegetative mycelium to initials)

1517-1592 SSH infection (fungal pathogen) response genes

1592-1773 SSH infection (viral) response genes


[13 Oct 2008] 

Many thanks to Dr. Jurriaan J. Mes (Agrotechnology and Food Sciences, Group Wageningen UR) who has kindly provided an additional data set of ca 1200 SSH sequences


PLEASE NOTE - There is still time to include additional data sets - interested parties with suitable data should contact me at their earliest convenience


September 26, 2008

Agaricus bisporus Genome Sequence – JGI Calling for Community EST Data

The JGI are now calling for community EST’s (and other sequence, linkage, mapping related to H97) to support the forthcoming annotation effort.

JGI will be interested in any resources the community has to offer to aid in the annotation, e.g. ESTs, BAC libraries, physical and genetic maps.

jgi_logo
http://snipurl.com/3uxgu-mpc [JGI Genomes]

*JGI News Update (Thu, 18 Sep 2008)*
The A. bisporus cDNA libs are in the 454 sequencing queue and JGI should have sequence within a couple weeks

The JGI can include external ESTs with their ESTs for clustering.
JGI need ESTs (not assembled consensus sequences) in fasta format with qual scores if available.
They would prefer that ESTs are vector and adaptor trimmed (and qual trimmed if no qual file is available).
The JGI will screen out rRNA and prokaryotic seqs (for Euk projects) and separate out organelle ESTs if available for this specific genus species.
If there are EST pairing information patterns in the read names they would like to know.

If you have any Agaricus bisporus data you might like to contribute to the project, please contact me at your earliest convenience

*PLEASE NOTE – all data will enter the public domain, the JGI will not separate ‘private ESTs’ *


September 05, 2008

Agaricus bisporus Genome Sequencing: Latest news from the JGI (September 2008)

The three Agaricus bisporus var. bisporus H97 sequencing libraries (3kb, 6-8kb & fosmids) have recently passed QC. H97 will now be scheduled for the ~4X checkpoint sequencing & assembly. The estimated time frame for the availability of the assembly from the 4X dataset is between Jan-Mar 2009.

Additionally, titration runs on three 454 EST libraries for Agaricus bisporus U1 are completed. All three samples passed QC and JGI will proceed with bulk runs.

JGI_20080905

July 16, 2008

Agaricus bisporus Genome Sequencing – Project Update July 2008

Recent news from the JGI project manager:

The Agaricus bisporus H97 whole genome shotgun 3kb library has been constructed and passed QC. The 8 & 40kb gDNA libraries are also in construction.
Three EST libraries have been constructed from our RNA pools and are currently at QC production sequencing.
JGI will notify us when all three libraries for whole genome sequencing have passed QC and when to expect our 4X assembly.

Project background
http://www.warwick.ac.uk/go/agaricusgenome
http://www.jgi.doe.gov/sequencing/why/99189.html

JGI_20070715


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