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Pig Genome Newsletter #109
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #109
Date: Tue, 27 Sep 2011 22:39:32 -0500
Pig Genome Update # 109:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.109.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.109.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. 109 **************
* *
* October 1, 2011 *
***************************************
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1. Pig genome sequence ready for analysis
2. Congratulations to the Swine Genome Sequencing Consortium
3. PAG 2012 registration is now open
4. Genome Canada Study
5. What's new on the NAGRP animal genome web site (#3 2011)
6. As always, suggestions from the livestock community are always welcome
7. NIFA is pleased to announce that Dr Lakshmi Matukumalli has accepted
a position of National Program Leader of Animal Breeding, Genetics
and Genomics
8. Upcoming meetings ( 5 items )
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Pig genome sequence ready for analysis. The Swine Genome Sequencing
Consortium (SGSC, http://piggenome.org) is pleased to announce that the
sequence data and assembly on which the draft pig genome sequence
publications will be based are now available for analysis. This draft
pig genome sequence (Sscrofa10.2) has been released by the International
Swine Genome Sequencing Consortium under the terms of the Toronto
Statement (Nature 2009, 461: 168). Sscrofa10.2 replaces the previous
assembly, Sscrofa10, which had assembly errors. The International Swine
Genome Sequencing Consortium is coordinating genome-wide analyses, as
described in BMC Genomics 2010 11:438. Funders of the pig genome
project are acknowledged in this marker paper. The sequence data, from
which this assembly was constructed, comprise hierarchical shotgun
sequence data providing 4-6x genome coverage from BAC clones
representing a minimal tile path across the genome plus >30x genome
coverage in whole genome shotgun sequence (WGS) Illumina reads. All the
WGS data and most of the BAC data are derived from blood cells of a
single Duroc female pig (Duroc 2-14; CHORI-242 BAC library) but also
includes some data from other BAC libraries from other breeds.
The Consortium is grateful to Mario Caccamo and his colleagues at The
Genome Analysis Centre, Norwich, UK for their work in finalizing the
assembly. We are also grateful for the efforts of Martien Groenen and
colleagues, Wageningen and Bertrand Servin and colleagues, INRA,
Toulouse for their contributions to checking the quality of the multiple
iterations of the assembly over the summer. The sequence data and
assembly have been posted on the NCBI ftp site at:
ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Sus_scrofa/Sscrofa10.2/
All those who wish to analyze or use the sequence data are strongly
encouraged to access the data from this NCBI ftp site in order to ensure
that everyone is working with an identical primary dataset. Annotation
of this draft pig genome sequence (Sscrofa10.2) has been initiated by
the Ensembl team and the genome team at NCBI will also start their
annotation effort soon. The annotation currently visible in the Ensembl
and NCBI genome browsers should be used with caution - Ensembl is
currently displaying the 2009 assembly (Sscrofa9) and the information
displayed in the NCBI Map Viewer is based on the flawed assembly 10. The
Consortium is holding a series of regular Skype conference calls to
discuss and coordinate the analysis and annotation activities and to
develop the main and companion papers describing the genome sequence and
its use. We are aiming to produce substantive draft manuscripts before
the end of the year. If you wish to join these discussions then please
contact Larry Schook: schook@illinois.edu or Alan Archibald:
alan.archibald@roslin.ed.ac.uk
Congratulations to the Swine Genome Sequencing Consortium. The
mid-continent region of the Federal Laboratory Consortium recently
present its Excellence in Technology Transfer Award to Swine Genome
Sequencing Consortium that developed the Porcine SNP Beadchip, a tool
marketed as "a cost-effective and high-quality solution for
interrogating genetic variation in multiple porcine breeds." Illumina
Inc., headquartered in San Diego, licensed the technology and sells it
as part of their genetic analysis kits. Gary Rohrer accepted the award
on behalf of the team
o o o o o o o o o o o
PAG 2012 registration is now open. The website has been redesigned and
can be found at http://www.intlpag.org/web/ . This year another great
meeting is planned. The swine workshop will be Saturday January 14 and
chaired by Daniel Ciobanu. Students wishing to apply for travel funding
should go to http://www.intlpag.org/web/index.php/attend/travel-grants
o o o o o o o o o o o
Genome Canada grant to study "Maintaining healthy and more profitable
pig production." Under a new grant funded by Genome Canada, researchers
in Canada, the USA and the UK, led by Graham Plastow, Univ. Alberta,
John Harding, Univ. Saskatchewan, and Bob Kemp, PigGen Canada, will
apply genomics to help reduce the impact of the two most common diseases
in commercial pig production - Porcine Circovirus Associated Disease
(PCVAD) and Porcine Respiratory and Reproductive Syndrome (PRRS).
Scientists will study mechanisms that make pigs genetically less
susceptible to these diseases, identify new diagnostic tools for
breeders and expand the understanding of disease control mechanisms.
This should lead to new strategies for disease control in addition to
new drugs, improved vaccines, and a safer pork product by reducing the
use of antibiotics. Researchers will also study public perceptions about
the use of genomic technologies to prevent disease in pork production.
o o o o o o o o o o o
What's new on the NAGRP animal genome web site (#3 2011).
1) Announcing Release 15 of the Animal QTLdb with 14,239 total QTL in
the database: (Break down: Cattle QTL: 4,802; Chicken QTL: 2,451; Pig
QTL: 6,347; Sheep QTL: 639. New QTL added to the database since the
Release 14: Cattle: 120; Pig: 3; Sheep: 185. http://www.animalgenome.org/QTLdb/).
2) Another change is that QTL data submission to the Animal QTLdb is now
required by several journals prior to the publication of your paper. We
encourage you to submit your QTL data directly to the database through
the curator web portal (http://www.animalgenome.org/QTLdb/app.html) to
speed up the review of your paper.
3) Good news for AnGenMap listserv users - the File Share Platform can
now be used as an alternative to share non-plain-text files that are
normally not allowed as email attachments on the AnGenMap listserv (e.g.
.PDF, .doc, .xls, .ppt, .xlm, etc.)
http://www.animalgenome.org/community/angenmap/faq.php#11
4) An experimental pig genome database is under development. A number of
new functions and utilities are under development
(http://www.animalgenome.org/pig/genome/db/). If you have any new ideas
for the pig genome database to better serve your purpose, please feel
free to send your suggestions, note "pig genome database" in the
"subject:" line, to bioinfo-team@animalgenome.org
5) A local copy of the Biomart has been installed on AnimalGenome.ORG to
serve the livestock research community. Currently, queries against the
pig, cattle, chicken and horse genomes are supported. More species will
be added upon the availability of the data. See:
http://www.animalgenome.org:8181/
6) The Blast Extension Analysis Program (BEAP) has been modified to
assist users for easier setup. See the updated manual for details.
(http://www.animalgenome.org/tools/beap/)
7) The NAGRP data repository has been expanded to host supplementary
data for publications. If you are looking for an online host for
additional data to your publication, feel free to contact us at
bioinfo-team@animalgenome.org (http://www.animalgenome.org/repository/pub/)
8) The new pig genome assembly has been actively improved during the
summer. The most recent build 10.2 has been submitted to NCBI and is
available for blast analysis on the NAGRP blast server
(http://www.animalgenome.org/blast/)
As always, suggestions from the livestock community are always welcome.
We are here to serve to community. You can either call Jim Reecy at
+1-515-294-9269 or send them a note at bioinfo-team@animalgenome.org.
o o o o o o o o o o o
NIFA is pleased to announce that Dr. Lakshmi Matukumalli has accepted a
position of National Program Leader of Animal Breeding, Genetics and
Genomics within the Institute of Food Production and Sustainability,
Division of Animal Systems. Dr. Matukumalli has held positions at
George Mason University and a joint position with USDA/ARS before
joining the NIFA family. He was a key member of the bovine genome group
at ARS and made significant contributions in analyzing the bovine genome
sequence. Dr.Matukumalli can be reached at lmatukumalli@nifa.usda.gov or
by phone at 202-401-1766.
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
4th International Symposium on Animal Functional Genomics, October
10-12, 2011. Dublin, Ireland. See http://www.isafg2011.org.
The International Conference on Feed Efficiency in Swine. Hilton
Hotel/Qwest Center. Omaha, Neb. November 8-9 Cosponsored by Iowa State
University and Kansas State University. See more information, including
registration and lodging details on the event website
http://www.ans.iastate.edu/ICFES/
National Swine Improvement Federation Annual Meeting, December 1-2,
2011, Lincoln, NE, for information contact Jim Schneider at
jim.schneider@ars.usda.gov
Plant & Animal Genome Conference, PAG XX, Jan. 14-18, 2012, Town &
Country Hotel, San Diego, CA. Information available at
http://www.intl-pag.org/ .
Human Genome Meeting (HGM2012), March 11-14, 2012, Sydney, Australia.
See http://www.hgm2012.org
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Items for Pig Genome Update 110 can be sent to me by no later than December 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/pig/
cc: Muquarrab Qureshi, NAGRP Director, National Animal Genome Research Program, NIFA
===========================================================================
U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Supported by Multi-State Research | Web: http://www.animalgenome.org/pig
| Funds to the National Research | Mail: angenmap\@animalgenome.org
| Service Program: NRSP-8 |
+-----------------------------------+--------------------------------------
