H97 Genome Browser Portal Training

	A two part training exercise in the use of the Agaricus bisporus var. bisporus H97 Genome Portal has been organised by the JGI. All collaborators involved in the H97 annotation effort are welcome to participate in the two 'dial-in' conference call sessions.
	Session I -- Mon, Nov 23, 8:00--9:30am Pacific Standard Time (16:00 -- GMT) will cover use of the Browser, Protein and Annotation pages Session II -- Wed, Nov 25 (8:00am PST / 16:00 GMT) will cover the KEGG/KOG/GO browsers, track editor and the clustering tools

Participants may find it beneficial to view the manual curation exercises available on the JGI pages <here>

Collaborators who would like to take part in this training (and have not already registered) should contact Mike C in advance of the event for further instructions

Michael Challen : 18 Nov 2009 09:44 |  Tags: Agaricus Annotation Genome Sequencing Jgi |  Comments (0) |  Close comments |  Report a problem

Revised Agaricus bisporus var. bisporus (H97) v2.0 genome assembly

The JGI have announced the pre-release of an improved Agaricus bisporus var. bisporus (H97) 8.50x genome assembly, which integrates linkage mapping data.

We are grateful to Anton Sonnenberg, Marie Foulongne and Rick Kerrigan for sharing data and their work mapping various markers to the v2 scaffolds.

This H97 v2.0 genome browser is now available for community annotation inputs.

In order to access the browser and make annotations, users will need to register with the JGI and the project team will need to approve the request. If you are interested in joining the annotation effort please contact the Agaricus genome team.

Michael Challen : 05 Nov 2009 16:06 |  Tags: Agaricus Bisporus Genome Sequencing H97 Jgi |  Comments (0) |  Close comments |  Report a problem

Pre–release of Agaricus bisporus var. bisporus (H97) v1.0 genome assembly

The JGI have announced the pre-release (or ‘internal’ release) of the Agaricus bisporus var. bisporus (H97) 8.50x  genome assembly following automated annotation.

The H97 v1.0 genome browser is now available for community annotation inputs.

In order to access the browser and make annotations, users will need to register with the JGI and the project team will need to approve the request.
If you are interested in joining the annotation effort please contact the Agaricus genome team.

Summary of A. bisporus var. bisporus H97 v1 assembly:

JGI predicted 10,387 genes with the following average properties:

Genes were predicted by the following methods:

Genes were validated by the following evidence:

H97 JGI Project status http://bit.ly/9h4nS | Community annotation plans agaricusgenomeseqactivities_8

Michael Challen : 02 Oct 2009 16:54 |  Tags: Agaricus Bisporus Annotation Genome Sequencing Jgi |  Comments (0) |  Close comments |  Report a problem

Agaricus bisporus 8x Assembly Revised

The JGI have issued a revision of the 8X genome assembly for Agaricus bisporus (H97, lead homokaryon).  Jeremy Schmutz of the JGI has provided an assembly report/update JGIupdate_200908

This is an update to the initial draft release (2009 03) and incorporates two additional breaks based on the linkage mapping data provided by Anton Sonnenberg and colleagues. Many thanks to Anton and Jeremy Schmutz for their work on this. 

This draft genome will now go into genome improvement, additional joins may yet be made to complete the chromosomes.

JGI project summaries are available at  http://snipurl.com/ex7l2

Agaricus bisporus 8x Revised Assembly [project ID 4084801 / August 2009]

Michael Challen : 10 Aug 2009 15:12 |  Tags: Agaricus Bisporus Genome Sequencing Jgi |  Comments (0) |  Close comments |  Report a problem

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 ]

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

Michael Challen : 21 Jul 2009 11:51 |  Tags: Agaricus Bisporus Blast Genome Sequencing |  Comments (0) |  Close comments |  Report a problem

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

Michael Challen : 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

Michael Challen : 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.

Michael Challen : 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)

Michael Challen : 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

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