All 4 entries tagged Agaricus

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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
AssemblyStats_20100520 AnnotationStats_20100520
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


November 18, 2009

H97 Genome Browser Portal Training

Gportal_thumb 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.

jgi_logo

  • 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


    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’ *


    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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