July 21, 2009

iNquiry Blast server available for Agaricus 8x

An iNquiry Bioinformatics server has been set up at Warwick to facilitate (limited) Blast based* searches of the Agaricus bisporus genome (nt database). This facility should help the community in preliminary screening of the current 8x genome scaffolds prior to the JGI forthcoming sequence release, and permit identification of interesting sequences in advance of their annotations using the JGI genome portal.

*BLASTALL  [ blastn \ tblastn \ tblastx \ psitblastn ]

inquiry_001.jpg inquiry_002.jpg inquiry_004.jpg

Access can be granted to any participants in the genome annotation and interested parties should contact Mike Challen for further information

June 15, 2009

Annotation of Agaricus bisporus genome: community contributions

JGI_20090615Sequence of the Agaricus bisporus H97 haploid genome (ca. 8.5 x coverage) is expected to enter a period of ‘hand-on’ community annotation within the next couple of months.
Anybody interested in participating in the annotation effort should read our community circular genomecircular_20090615.pdf and contact MC for further information

June 10, 2009

Integrated Microbial Genomes system/with Microbiome Samples (IMG/M) v2.8

img/m-001The JGI have announced an update to their Integrated Microbial Genomes system/with Microbiome Samples (IMG/M). Version 2.8 includes reference genomes from IMG 2.8 (http://img.jgi.doe.gov) and 113 GEBA genomes (http://img.jgi.doe.gov/geba).

New metagenome datasets include:
1 Endophytic microbiome from rice; 8 Yellowstone hot pool microbial communities;
7 Marine planktonic communities from Hawaii Ocean Time-series; 1 Bioreactor wastewater terephthalate-degrading community sample

The IMG/M (Nucleic Acids Research, 2008, Vol. 36, Database Issue) provides tools for analyzing functional capability of microbial communities based on their metagenome sequence, in the context of reference isolate genomes included from the Integrated Microbial Genomes system.

Interested parties can check out IMG/M 2.8 at http://img.jgi.doe.gov/cgi-bin/m/main.cgi

June 04, 2009

Agaricus bisporus linkage maps sent to JGI

linkage_mapAnton Sonnenberg (PRI Wageningen) has recently submitted a detailed Agaricus bisporus linkage map to the JGI, based mainly on data provided by PRI and Marie Foulongne (INRA Bordeaux). 
Data on known repeat elements, from Rick Kerrigan and Anton, has also been sent to the JGI.
It is hoped that these data will help resolve chromosomal groups in current scaffolds, advancing the ‘genome improvement’ that is taking place prior to machine annotation.

June 02, 2009

British Mycological Society (BMS) Survey

BMS-logoThe British Mycological Society (BMS) is dedicated to the promotion of fungal science and is currently eliciting views of all mycologists on how the Society can best serve the Mycological Community.

If you work with fungi (including lichens, Myxomycota and Oomycota) please take a few minutes to complete the survey which can be found at the following link: http://bit.ly/185BFm (deadline Fri 5th June)

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.


November 24, 2008

Agaricus bisporus var. burnettii JB137–S8 deposited at FGSC

Follow-up to Agaricus bisporus strains now with FGSC from MCs Basidio Blogging

Thanks also to Rick Kerrigan who has deposited the JB137-S8 homokaryon with the FGSC collection. This represents a full compliment of strains involved in the JGI genome sequencing of Agaricus bisporus

FGSC#         Designation
10392         Agaricus bisporus var. burnettii JB137-S8 (homokaryon)     

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