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Pig Genome Newsletter #103
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #103
Date: Wed, 30 Jun 2010 15:19:36 -0500
Pig Genome Update # 103:
- PDF version is available at
http://www.animalgenome.org/pigs/newsletter/pdf/No.103.pdf
- Web version is available at
http://www.animalgenome.org/pigs/newsletter/No.103.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
__________________________________________________________________
A Bimonthly Newsletter of the U.S. Pig Genome Coordination Program
************** No. 103 **************
* *
* <angenmap@animalgenome.org> *
* July 1, 2010 *
***************************************
===========================================================================
1. Information on the next sequencing efforts are expected shortly
2. Sequencing pig genome assembly and the publications that are likely to
result will continue to be of primary importance
3. The SGSC has submitted a "marker" paper for publication
4. The SGSC would welcome the input of members of the community in the
analysis and annotation of the draft sequence
5. The International Symposium on Animal Genomics for Animal Health (AGAH)
was held in Paris, France, May 31 - June 2, 2010
6. What's new on NAGRP animal genome web site
7. Upcoming meetings ( 5 items )
===========================================================================
Information on the next sequencing efforts are expected shortly. Please
stay tuned for an announcement in the near future.
Sequencing pig genome assembly and the publications that are likely to
result will continue to be of primary importance. Pig Genome Update 101
(March 1) and Pig Genome Update 102 (May 1) were devoted to primarily
explaining the process and much of the opportunities. Please see:
http://www.animalgenome.org/pigs/newsletter/No.101.html and
http://www.animalgenome.org/pigs/newsletter/No.102.html .
o o o o o o o o o o o
The SGSC has submitted a "marker" paper for publication 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.
o o o o o o o o o o o
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]).
o o o o o o o o o o o
The International Symposium on Animal Genomics for Animal Health (AGAH)
was held in Paris, France, May 31 - June 2, 2010. The goal of the AGAH
was to identify critical needs and opportunities to advance the use of
animal genomics to solve problems in animal health. The symposium
included major talks by leaders in the field addressing both host and
microbial genomics, functional responses of hosts to infections and
nutritional and immune interventions, and host and pathogen genetic
controls of those responses. It is clear that genomic developments, such
as SNP chips, nextgen sequencing, etc., have changed the way genomics of
animal health studies can proceed. Yet there is still a need for
improved datasets with deeper phenotypes for the most important animal
diseases, both for production agriculture and developing economies. The
AGAH attracted 170 attendees from 30 countries who attended and
presented 39 oral and 70 poster presentations. It provided an excellent
opportunity to discuss current and future research with leaders in the
fields of animal and microbial genomics and animal health. The full
program is available at https://colloque.inra.fr/agah2010. The meeting
ended with a Roundtable discussion on "What are the critical
needs/future applications in animal health: input of research and links
with industry." The summary of these discussions, as well as numerous
papers from the AGAH, will be published in BMC proceedings. (Kindly
submitted by Joan Lunney).
o o o o o o o o o o o
What's new on NAGRP animal genome web site. (1)Release 11 of the Animal
QTLdb is complete. As of April 23, 2010, a total of 1643 new QTL have
been added to the Animal QTLdb since last release before the New Year.
The new data included 1532 cattle QTL and 111 pig QTL. We encourage all
users to add your own new QTL data through the Curator web form: found
at the URL: http://www.animalgenome.org/QTLdb/app.html. . (2) A major
improvement to the CateGOrizer online tool is made to improve its
performance. The improvement included faster algorithms and more
efficient ways to handle large data sets and can be seen at
URL: http://www.animalgenome.org/bioinfo/tools/catego/ . (3) Animal
QTLdb frequently asked questions has been updated with new items. The
most recent additions are to address possible confusions that some
downloaded QTL data may "appear" like "duplicates". The FAQ explained
why and provided hints as how to correctly examine the downloaded data.
(4) A generic online tool has been in development
(http://www.animalgenome.org/cgi-bin/util/2gff) to help users to convert
their mapping data file into GFF3 format, which is useful to upload to
GBrowse for map alignments of the genome features. In addition, the
same data is also available in SAM data format
http://www.animalgenome.org/cgi-bin/QTLdb/SS/index. The SAM data format
is to assist users using SAM Tools. For details using SAM tools, see:
http://samtools.sourceforge.net/. Please let us know if you have data
that are not on our input file format list. Check out the "what's new"
page (http://www.animalgenome.org/news/whatsnew.html) for more
up-to-date information (kindly provided by the NAGRP Bioinfo Team who
may be contacted at bioinfo-team@animalgenome.org).
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
International Society of Animal Genetics conference will take place in
Edinburgh (UK), July 26-30, 2010. For details see
http://www.isag.org.uk/society/conferences.asp
The 9th World Congress on Genetics Applied to Livestock Production
(WCGALP), Aug. 1-6, 2010, Leipzig, Germany. For more details visit
http://www.wcgalp2010.org/.
The 9th International Veterinary Immunology Symposium, August 16-20,
2010, Tokyo, Japan For more details visit http://9th-ivis.jtbcom.co.jp.
Plant and Animal Genome XIX Conference, January 15-19, 2011, San Diego
CA. For details see http://www.intl-pag.org/
Swine in Biomedical Research, July 17-19, 20011, Chicago IL, for details
contact larry Schook at schook@uiuc.edu
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Items for Pig Genome Update 104 can be sent to me by no later than August 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
===========================================================================
U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Supported by USDA/NIFA NRSP-8 | Web: http://www.animalgenome.org/pig
| National Animal Genome Research | Mail: angenmap@animalgenome.org
| Program |
+-----------------------------------+--------------------------------------
