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Pig Genome Newsletter #111
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #111
Date: Fri, 30 Mar 2012 09:35:01 -0500
Pig Genome Update # 111:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.111.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.111.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
_________________________________________________________________
A Periodic Newsletter of the U.S. Pig Genome Coordination Program
************** No. 111 **************
* *
* April 1, 2012 *
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1. The Swine Genome Sequencing Consortium continues to make good progress
2. The Swine Genome Sequencing Consortium has released the pig genome
sequence data
3. The pig genome sequence paper
4. The Consortium remains open to new groups
5. Sunny San Diego and PAG-XX
6. NRSP-8 rewrite is beginning soon
7. Upcoming meetings ( 6 items )
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The Swine Genome Sequencing Consortium continues to make good progress
towards the goal of publishing a good quality annotated reference genome
sequence for the pig. The genome assembly (Sscrofa10.2) which is the
template for the Consortium's analysis and annotation efforts and the basis
for the pig genome sequence paper was deposited at NCBI in late August 2011
(ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Sus_scrofa/Sscrofa10.2/).
This is the definitive source for the analyses. The NCBI genome team have
released an annotated copy of this draft genome sequence (see
ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/GFF/ ). This annotated pig
genome sequence is available in the NCBI Genome Browser. Members of the
Consortium have also been working with the Ensembl team. The Ensembl team
recently completed their Gene Build for Sscrofa10.2. The Ensembl gene models
are based on sequence evidence including alignments with expressed sequences
comprising not only cDNA and EST information in the public databases but
also more than 250 Gigabases of RNA-seq data generated by members of the
Consortium. The preliminary Ensembl analysis is available on the Pre-Ensembl
site (http://pre.ensembl.org/Sus_scrofa/Info/Index ) and the full annotated
genome will be available in the Ensembl genome browser in Ensembl release 67
in a few weeks time (the version currently visible in the Ensembl genome
browser is an older assembly - Sscrofa9).
o o o o o o o o o o o
The Swine Genome Sequencing Consortium has released the pig genome sequence
data in a timely manner as the project has progressed in accordance with the
principles of the Toronto Statement on Pre-publication data sharing (see:
Toronto International Data Release Workshop Authors: Prepublication data
sharing. Nature 2009, 461:168-70.). Briefly, The Toronto Statement places
obligations on the producers of such data sets, including genome sequence
data, in respect of prepublication release of the data and confirms the
principle that allows the data producers (i.e. the Consortium) to publish
the first global analyses of the data set. In 2010 the Consortium published
its plans for its first global analyses of the genome sequence and for
publication (see: Archibald et al 2010 BMC Genomics 11: 438
http://www.biomedcentral.com/1471-2164/11/438).
o o o o o o o o o o o
The pig genome sequence paper is in draft and a wide range of companion
papers are currently in draft, under review or in press. It is envisaged
that the main paper will not only describe the main and pig-specific
features of the draft genome sequence and its utility in agricultural and
biomedical uses of pigs but also explore how the sequence together with
sequences of Wild Boar and other Suids generated by Martien Groenen and
colleagues informs our understanding of speciation and domestication.
o o o o o o o o o o o
The Consortium remains open to new groups joining the efforts to
characterise and publish the pig genome. Interested scientists / groups
should contact either Larry Schook (schook@uillinois.edu) or Alan Archibald
(alan.archibald@roslin.ed.ac.uk). (kindly provided by Alan Archibald on
behalf of the Swine Genome Sequencing Consortium)
o o o o o o o o o o o
Sunny San Diego and PAG-XX drew a new record crowd of over 2800 attendees.
An excellent swine workshop followed by a PRRS meeting made for a great
start. There were some super plenary talks e presented by Lee Hood, Stephen
Quake, Carlos Bustamante and Robert Williams, among others. Next year's
PAG-XXI/NRSP-8 will be January 12-16, 2013, once again in San Diego. Note
that in March, 2013 there will also be a new 2.5 day conference, PAG-ASIA,
in Singapore (see www.intl-pag.org ).
o o o o o o o o o o o
NRSP-8 rewrite is beginning soon. The NRSP-8 is scheduled to end in
September of 2013, so if it is to continue, it must be revised and
resubmitted for review by NIFA and the Experiment Stations again this year.
The approximate deadline is this September for submitting the revised
project. New draft objectives for NRSP-8 will be circulated shortly. All
members of NRSP-8 may receive requests to contribute to assembling past
accomplishments and publications and for input into the new proposals.
Please respond promptly, as we're on a tight deadline and this will be a
huge help to the writing teams. (kindly provided by J. Dodgson)
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
33rd International Society for Animal Genetics Conference in Cairns,
Australia on July.15-20, 2012. For details see http://www.isag.us/2012/
International Conference of Quantitative Genetics in Edinburgh, Scotland on
June 17-22, 2012. For details please see http://www.icqg2012.org.uk/
American Society of Animal Science (ASAS), Dairy Science (ADSA), and
Canadian Society of Animal Science (CSA) Joint Annual Meeting in Phoenix, AZ
on July 15 - 19, 2012. For details see http://www.jtmtg.org/2012/
PAG-XXI/NRSP-8 will be January 12-16, 2013, for details see
http://www.intlpag.org/web/
Gordon Research Conferences: Quantitative Genetics & Genomics, Genetics of
Complex Disease, February 17-22, 2013, Galveston, TX for details see
http://www.grc.org/programs.aspx?year=2013&program=quantgen
PAG Asia to be held in Singapore, March 2013. For details see
http://www.intlpag.org/web
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Items for Pig Genome Update 112 can be sent to me by no later than June 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
http://www.animalgenome.org/pig/
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Supported by Multi-State Research Funds to the National Research Service
Program: NRSP-8. National Animal Genome Research Program, Muquarrab Qureshi,
NAGRP Director, NIFA
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Web: http://www.animalgenome.org/pig | Mail: angenmap@animalgenome.org
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