Pig Genome Update No. 104angenmap@animalgenome.orgSeptember 1, 2010 |
Editors note: My apologies for the late newsletter but we held the presses for the important news below!!
Build 10 for the Sus scrofa reference genome sequence will be released
Monday, September 20. Thanks to the efforts of many people and great
collaboration across the world, the sequence and accompanying
information will be in a final version and released from The Genome
Analysis Centre (TGAC)'s FTP site (ftp.tgac.bbsrc.ac.uk ; User: pig10 ;
Password: Sscrofa10). This final version will be based on the latest
freeze of the physical map. The assembly is the result of the
integration of all the sequenced clones and contigs produced by
SOAPdenovo and Cortex whole genome shotgun (WGS) assemblies. These WGS
assemblies were generated using Illumina reads sequenced at BGI and the
Sanger Institute (~40X coverage). As part of the release AGP files with
information about the source of every contig will be provided. The WGS
contigs will be submitted to EMBL/Genbank, and after that the WGS
contigs will be renamed in the AGP with the corresponding accession
numbers. This assembly provides an almost complete coverage of the pig
genome. Additional details will be presented in the coming weeks.
(Kindly provided by Mario Caccamo (TGAC) and the International Swine
Genome Sequencing Committee)
The "marker" paper has recently been published in which the Consortium
sets outs its plans for the analysis and publication of a draft pig
genome sequence. These plans were presented to participants in the Pig
Genome III conference held at the Wellcome Trust Sanger Institute, 2-4
November 2009 when a series of analysis working groups were established.
Please see BMC Genomics 2010, 11:438
http://www.biomedcentral.com/1471-2164/11/438 .
The SGSC would welcome the input of members of the community in the
analysis and annotation of the draft sequence. "Annotation" comprises
manual correction and improvement of the gene models for individual
genes on a gene-by-gene basis. We are using the Wellcome Trust Sanger
Institute's Otterlace tools for these manual annotation tasks - training
can be provided as necessary. Individuals who make significant
contributions to the manual annotation effort will be recognized through
authorships of the relevant paper(s). "Analysis" comprises global
analyses of particular aspects of genomic structure (e.g. repetitive
sequences, segmental duplications,..) or of gene families (e.g. the
immunoglobulin superfamily) or of genes with effects on specific traits
(e.g. immunity, reproduction, olfaction). The outputs from "analysis"
groups will be a few sentences or paragraphs in the main sequence paper
plus possibly a companion paper that describes and discusses the
specific analyses in greater detail. Authorship would be recognized in
accordance with scientific convention. The paper describing the draft
cattle genome sequence (Science 324, 522) provides an indication of
"analysis" groupings - the text of the paper illustrates the outputs
from such analyses. Members of the community who wish to contribute to the
analysis and annotation of the draft pig genome sequence should contact the
relevant analysis group leader or the coordinators, for example, if they
wish to establish additional analysis groupings (Larry Schook
schook@illinois.edu] or Alan Archibald [alan.archibald@roslin.ed.ac.uk] .
What a summer!! Are you jet lagged and meeting blurry?? Several
meetings were held this summer but the big two meetings ISAG and WCGALP
came back to back and focused on genomics and included a great deal on
the pig. Both were outstanding venues with kind hosts and great
programs. Over 630 people attended ISAG where talks focused on
everything related to genomics and genetics of your favorite species
including the pig. The WCGALP in Leipzig was also a great event with
nearly 1,400 people and far ranging talking including bioinformatics,
quantitative genetics and genomics and what is next on the horizon. For
those that like to plan ahead ISAG has chosen Australia for its meeting
2 years from now and China 4 years from now. WCGALP has chosen
Vancouver, BC for its next venue 4 years from now.
Another big meeting was the EEAP meeting in Crete. For those that
missed out the complete "Book of Abstracts" of the Annual Meeting held
in Heraklion, Crete (Greece), is available as PDF file on the EAAP
website at: http://www.eaap.org/Crete/Heraklion_2010_Abstracts.pdf
PAG 2011 Swine Workshop. The current Chair of the Swine Subcommittee,
Chris Tuggle, along with Cathy Ernst and Larry Schook, are planning the
2011 Swine Workshop for the PAG meetings which are held every year in
January in San Diego. In 2011, the Swine Workshop will be on January
15. The information for PAG is here:http://www.intl-pag.org/ and the
2011 Swine workshop is here:http://www.intl-pag.org/19/19-swine.html .
Their plans are to hold a joint Workshop with the Cattle/Sheep group in
the morning and then continue meeting in the afternoon, as a Swine only
group, as was done in 2010. This year they will also incorporate the
Swine Genome Sequencing Workshop, which will not be meeting separately
in 2011 at PAG. To fill this program, they plan to emphasize the
exciting developments in the genome sequence and its analysis and
annotation. Please contact Chris Tuggle cktuggle@iastate.edu) if you
have suggestions.
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
- Plant and Animal Genome XIX Conference, January 15-19, 2011, San Diego CA. For details seehttp://www.intl-pag.org/
- Gordon Research Conference in Quantitative Genetics & Genomics, Feb. 20-25, 2011, Hotel Galvez, Galveston, TX. See http://www.grc.org/programs.aspx?year=2011&program=quantgen
- Swine in Biomedical Research, July 17-19, 2011, Chicago IL, for details contact Larry Schook at schook@uiuc.edu
Items for Pig Genome Update 105 can be sent to me by no later than October 15 please.
Max Rothschild
U.S. Pig Genome Coordinator
2255 Kildee Hall, Department of Animal Science
Iowa State University
Ames, Iowa 50011
Phone: 515-294-6202, Fax: 515-294-2401
mfrothsc@iastate.edu
http://www.animalgenome.org/pigs/
cc: Muquarrab Qureshi, NAGRP Director, National Animal Genome Research Program, NIFA
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