November 21, 2008

Agaricus bisporus Genome Sequencing – JGI update 2008/11

JGIstatus_20081121The JGI has recently recently completed their checkpoint sequencing & assembly for Agaricus bisporus H97.

Jeremy Schmutz from the JGIs Genome Assembly Group has provided a summary report jgisummary.pdf


The H97 assembly will change when the remainder of the sequence is generated and reassembled. Contig and scaffold numbers and arrangements will change between the 4X and 8X assembly and the JGI does not provide read mapping information.
ESTs for Agaricus bisporus U1 are currently in clustering.

jgi_logoThe JGI remain interested in any resources our community has to offer to aid in the annotation, e.g. ESTs, BAC libraries, physical and genetic maps.  If research groups have suitable resources and would be prepared to share them with the project, please let me know as soon as possible.


November 14, 2008

Agaricus bisporus strains now with FGSC

Many thanks to Anton Sonnenberg who has deposited various Agaricus bisporus var. bisporus strains being used in the JGI project with the Fungal Genetics Stock Centre (FGSC)

Kevin McCluskey (Curator, FGSC) has already asigned the following FGSC accession numbers

FGSC#          Designation
10389           Agaricus bisporus var. bisporus H97 (homokaryon)        
10390           Agaricus bisporus var. bisporus H39 (homokaryon)
10391           Agaricus bisporus var. bisporus Horst U1 (heterokaryon)



October 30, 2008

JGI Genome Portal Tutorial Site

Andy Bailey has kindly drawn my attention to the online JGI annotation tutorial:

JGItutorial

http://genome.jgi-psf.org/Tutorial/Tutorial.home.html

http://genome.jgi-psf.org/help/

As our Agaricus bisporus sequencing project progresses, and with the promise of 4x sequence in Q1-2009, this is a probably a good time for genome novices (like myself) to get familiar with the JGI tools. 

Other JGI-led training should take place as the project advances.


October 13, 2008

EST data sets sent to JGI

Agaricus bisporus Genome Sequencing - Project updates


[29 Sept 2008] 

Warwick sequence database (ca 1700 seqs) sent to the JGI, these comprise

1-813 EMBL nucleotide database sequences related to Agaricus bisporus

814-1066 miscellaneous cDNA library sequences

1067-1513 SSH differential expression during mushroom development (vegetative mycelium to initials)

1517-1592 SSH infection (fungal pathogen) response genes

1592-1773 SSH infection (viral) response genes


[13 Oct 2008] 

Many thanks to Dr. Jurriaan J. Mes (Agrotechnology and Food Sciences, Group Wageningen UR) who has kindly provided an additional data set of ca 1200 SSH sequences


PLEASE NOTE - There is still time to include additional data sets - interested parties with suitable data should contact me at their earliest convenience


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’ *


September 05, 2008

Agaricus bisporus Genome Sequencing: Latest news from the JGI (September 2008)

The three Agaricus bisporus var. bisporus H97 sequencing libraries (3kb, 6-8kb & fosmids) have recently passed QC. H97 will now be scheduled for the ~4X checkpoint sequencing & assembly. The estimated time frame for the availability of the assembly from the 4X dataset is between Jan-Mar 2009.

Additionally, titration runs on three 454 EST libraries for Agaricus bisporus U1 are completed. All three samples passed QC and JGI will proceed with bulk runs.

JGI_20080905

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


July 14, 2008

Basidiomycete Research Networks – Discussions

basidioresnet_nm_20080714.pdf
This document collectively summarises discussion points from two recent meetings, Basidio3 & GCBB7, and is intended to stimulate downstream community activity and discussion.

Activity should be inclusive and participation of all basidiomycete groups is encouraged to ensure that decisions/actions are representative.

The ‘Basidiomycete Research Networks – Discussion Document’ is not restricted to participants in the Basidio3 & GCBB7 meetings.
Please distribute to others within the basidiomycete research community and/or refer to this discussion page.

Snipped URL for this discussion page: http://snurl.com/2yfmr Please distribute to your colleagues


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