All 19 entries tagged Jgi, MCs Basidio Blogging

May 20, 2010

Public Release of Agaricus bisporus var. burnettii JB137–S8 Genome Sequence

The JGI have announced the public release of Agaricus bisporus var. burnettii JB137-S8 genome assembly and annotation, which can be accessed at the following URL: http://jgi.doe.gov/Agabi_varbur_1

Annotation of the Agaricus bisporus var burnettii (v. 052010) assembly was produced through the JGI annotation pipeline, using a variety of homlogy-based and ab initio gene predictors. ESTs from Agaricus bisporus var bisporus were used. After filtering for EST support, completeness and homology support, a total of 11,289 genes were structurally and functionally annotated.

Statistics on the assembly and annotation of JB137-S8 in comparison to the Agaricus bisporus var bisporus H97 genome are shown in the JGI tables below. Further details can be found on the Info page:
http://genome.jgi-psf.org/Agabi_varbur_1/Agabi_varbur_1.info.html

Community annotation and analysis of the Agaricus bisporus H97 and JB137-S8 genomes are continuing. Additional contributions are invariably welcomed, please contact MC if you would like to join the community effort.

Please respect the community rules and JGI data release policy for publication rights of the genome-wide analyses:
http://genome.jgi-psf.org/Agabi_varbur_1/Agabi_varbur_1.download.html

: 20 May 2010 11:18 | Tags: Agaricus Agaricus Bisporus Genome Sequencing Jb137-S8 Jgi Var Burnettii | Comments (0) | Close comments | Report a problem

May 06, 2010

'MycoCosm' portal for JGI Fungal Genomes and Exploration of Fungal Diversity

Writing about web page http://genome.jgi-psf.org/pages/fungi/home.jsf

Genome sequences for Agaricus bisporus var bisporus (H97) and var burnettii (JB137-S8) are available through the JGI's 'MycoCosm' portal.

Fungal Genome sequences and other opportunities to explore Fungal Diversity are layered over a Fungal Tree of Life GUI. This resource should rapidly expand as fungal genomes continue to pour out of the JGI sequencing pipeline.

It's never been easier to explore fungal genomes: Go on, click on a branch!

jgi_logo

: 06 May 2010 10:31 | Tags: Agaricus Bisporus Genome Sequencing H97 Jb137-S8 Jgi Mycocosm | Comments (0) | Close comments | Report a problem

May 04, 2010

Pre–release of Agaricus bisporus var. burnettii JB137–S8 genome

A pre-release of Agaricus bisporus var. burnettii JB137-S8 genome assembly and annotation is available to the community through the JGI portal.

This pre-release is currently restricted access and a JGI login is required. If you want to access the JB137-S8 portal contact MC for further instructions. It is expected that the Agaricus bisporus var. burnettii JB137-S8 genome
portal will available to the public after 14 May 2010.

Statistics on the assembly and annotation of JB137-S8 in comparison to the Agaricus bisporus var bisporus H97 genome are shown in the JGI tables below:

: 04 May 2010 10:54 | Tags: Agaricus Bisporus Basidiomycete Genome Sequencing Jb137-S8 Jgi Var Burnettii | Comments (0) | Close comments | Report a problem

Public Release of Agaricus bisporus var bisporus H97 Genome Sequence

The Agaricus bisporus var bisporus H97 genome is now available to the public via the JGI portal. Annotations of the v2.0 assembly are available at http://genome.jgi-psf.org/Agabi_varbisH97_2

Detailed statistics on the assembly and annotation of the A. bisporus var bisporus H97 genome can be found on the Info page of the JGI portal: http://genome.jgi-psf.org/Agabi_varbisH97_2/Agabi_varbisH97_2.info.html

Community annotation and analysis of the Agaricus bisporus genomes are continuing. Additional contributions are invariably welcomed, please contact MC if you would like to join the community effort.

Please respect the community rules and JGI data release policy for publication rights of the genome-wide analyses:
http://genome.jgi-psf.org/Agabi_varbisH97_2/Agabi_varbisH97_2.download.html

: 04 May 2010 10:15 | Tags: Agaricus Bisporus Genome Sequencing H97 Jgi | Comments (0) | Close comments | Report a problem

January 18, 2010

Agaricus bisporus var. burnettii JB137–S8 draft genome

The JGI have released a draft genome sequence for a second Agaricus homokaryon JB137-S8 (the tetrasporic Agaricus bisporus var. burnettii).
JB137-S8 genome was sequenced using 454/Illumina technology and assembled by comparisons with the lead H97 genome (Agaricus bisporus var. bisporus).

A brief summary of the JB137-S8 assembly and a dotplot comparison between the var. bisporus and var. burnettii genomes are attached.

JGI are currently progressing annotation of the JB137-S8 genome, after which the standard browser and tools for comparative analysis will become available. Collaborators interested in accessing JB137-S8 data prior to that time should contact MC for further information.

Agaricus bisporus var. burnettii JB137-S8
Main genome scaffold total:	2016
Main genome contig total:	2527
Main genome scaffold sequence total:	32.6 MB
Main genome contig sequence total:	31.2 MB
Main genome scaffold N/L50:	8/1.23 MB
Main genome contig N/L50:	39/0.163 MB
Number of scaffolds > 50 KB:	52
% main genome in scaffolds > 50 KB:	87.9%

: 18 Jan 2010 16:08 | Tags: Agaricus Bisporus Genome Sequencing Jb137-S8 Jgi | Comments (0) | Close comments | Report a problem

November 18, 2009

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

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

November 05, 2009

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.

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

October 02, 2009

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:

Genome Size:	30.3 Mbp
Total number of Scaffolds:	27
Total number of EST clusters:	79,271
Total number of trimmed ESTs:	1,140,141

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

Gene length (bp):	1771.79
Transcript length (bp):	1413.32
Protein length (aa):	426.20
Exons per gene:	6.10
Exon length (bp):	232.25
Intron length (bp):	71.72

Genes were predicted by the following methods:

EST-derived:	3070 (29.6%)
Homology-based:	4242 (40.8%)
ab initio:	3075 (29.6%)

Genes were validated by the following evidence:

nr protein alignments:	8638 (83%)
Pfam alignments:	5357 (52%)
Completeness (5'M-3'*):	9376 (90%)

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

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

August 10, 2009

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]

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

June 10, 2009

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

All 19 entries tagged Jgi