All entries for June 2009

Annotation of Agaricus bisporus genome: community contributions

Sequence 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

: 15 Jun 2009 15:56 |  Tags: Agaricus Bisporus Annotation Genome Sequencing |  Comments (0) |  Close comments |  Report a problem

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

The 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

: 10 Jun 2009 09:49 |  Tags: Genomes Img Jgi Microbiome |  Comments (0) |  Close comments |  Report a problem

Agaricus bisporus linkage maps sent to JGI

Anton 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.

: 04 Jun 2009 14:58 |  Tags: Agaricus Bisporus Genome Sequencing Linkage Maps |  Comments (0) |  Close comments |  Report a problem

British Mycological Society (BMS) Survey

The 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)

: 02 Jun 2009 11:30 |  Tags: Bms Mycology |  Comments (0) |  Close comments |  Report a problem

DOE JGI Releases Expanded Version of Phytozome.net

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

An 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

: 01 Jun 2009 11:29 |  Tags: Biofuel Genome Sequencing Jgi |  Comments (0) |  Close comments |  Report a problem