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Pig Genome Newsletter #102
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #102
Date: Mon, 03 May 2010 13:24:30 -0500
Pig Genome Update # 102:
- PDF version is available at
http://www.animalgenome.org/pigs/newsletter/pdf/No.102.pdf
- Web version is available at
http://www.animalgenome.org/pigs/newsletter/No.102.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. 102 **************
* *
* <angenmap@animalgenome.org> *
* May 1, 2010 *
***************************************
===========================================================================
1. Sequencing pig genome assembly
2. Updates on the process are continuing
3. The SGSC has submitted a marker paper for publication
4. The SGSC would welcome the input of members of the community
5. Swine Genome Sequencing Consortium genome sequence analysis groups
6. Companion Manuscripts
7. SGSC Genome Manuscript Steering Committee
8. What's new on NAGRP animal genome web site
9. Upcoming meetings ( 4 items )
===========================================================================
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) was devoted to primarily explaining the process and much of
the opportunities. Please see:
http://www.animalgenome.org/pigs/newsletter/No.101.html
Updates on the process are continuing. The pig genome is being sequenced
and characterized under the auspices of the Swine Genome Sequencing
Consortium (SGSC). In accordance with the Bermuda and Fort Lauderdale
agreements and the more recent Toronto Statement the data have been
released into pubic sequence repositories in a timely manner and in
advance of publication. An assembly (Sscrofa9) covering about 90% of
the pig genome has been annotated in Ensembl automated pipelines and was
released with Ensembl 56 in September 2009. Another announcement of
SScrofa9b is expected soon. The publication of the pig genome sequence
will be based on the next assembly (Sscrofa10) which will incorporate
additional data providing greater coverage and greater contiguity.
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 and 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
Swine Genome Sequencing Consortium genome sequence analysis groups
(Analysis groups and Lead contacts)
- Assembly
Alan Archibald (alan.archibald@roslin.ed.ac.uk)
- Structural variation, segmental duplication, copy number variation
Christian Bendixen (christian.bendixen@agrsci.dk)
- Repetitive DNA, transposable elements
Geoff Faulkner (geoff.faulkner@roslin.ed.ac.uk)
- Speciation, wild and related suids and selection
Lawrence Schook (schook@uiuc.edu)
- Evolution
Leif Andersson (Leif.andersson@imbim.uu.se)
- Comparative genomicas
Martien Groenen (Martien.groenen@wur.nl)
- Imprinting
Ole Madsen (Ole.madsen@wur.nl)
- SNP
Martien Groenen (martien.groenen@wur.nl)
- ncRNA
Jan Gorodkin (gorodkin@genome.ku.dk)
- Gene builds
Steve Searle (Searle@sanger.ac.uk)
- Protein interactions
Soren Brunak (brunak@cbs.dtu.dk)
- Immune genes
Chris Tuggle (cktuggle@iastate.edu)
- Reproduction
Max Rothschild (mfrothsc@iastate.edu)
- Obesity
Max Rothschild (mfrothsc@iastate.edu)
- Olfaction, neuropeptide and prohormone
Sandra Rodriguez-Zas (rodrgzzs@illinois.edu)
- Manual annotation
Jim Reecy (jreecy@iastate.edu)
- Biomedical Models
Lawrence Schook (schook@illinois.edu)
o o o o o o o o o o o
Companion Manuscripts. The Steering Committee encourages topic groups as
well as others to develop companion manuscripts. The Steering Committee
would request that groups forward their intent to develop a companion
manuscript (including a tentative title) to their attention (either
Larry Schook or Alan Archibald) in order to coordinate data exchange and
to ensure no overlaps or competing efforts. Also, developing a list of
potential companion manuscripts will permit the Steering Committee to
negotiate with journals for a dedicated issue focused on the pig genome
project. Also, please forward your ideas as to potential journal(s) for
the Steering Committee to contact. Submission of companion manuscripts
has a target date of September 1, 2010.
o o o o o o o o o o o
SGSC Genome Manuscript Steering Committee
Alan Archibald, Roslin Institute, UK (alan.archibald@roslin.ed.ac.uk)
Mario Caccamo, The Genome Analysis Center (TGAC), UK
(mario.caccamo@bbsrc.ac.uk)
Carol Churcher, Wellcome Trust Sanger Institute, UK (carol@sanger.ac.uk)
Merete Fredholm, U Copenhagen, Denmark (mf@life.ku.dk)
Martien Groenen, Wageningen U, Netherlands (Martien.Groenen@wur.nl)
Kyung-Tae Lee, Korean National Institute of Animal Science
(ktlee2@gmail.com)
Denis Milan, INRA, France (denis.milan@toulouse.inra.fr)
Jane Rogers, The Genome Analysis Center (TGAC), UK
(jane.rogers@bbsrc.ac.uk)
Max Rothschild, Iowa State U, USA (mfrothsc@iastate.edu)
Lawrence Schook, U of Illinois, USA (Chair) (schook@illinois.edu)
Jun Wang, BGI, China (wangjun30@gmail.com)
Hirohide Uenishi, (huenishi@affrc.go.jp)
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 URL: http://www.animalgenome.org/QTLdb/app.html. (2) In addition to
the previously released QTLdb results in GFF3 format, the same data is
now 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/. (3) 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/ . (4) 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.
(5) 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. 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)
Animal Genomics for Animal Health International Symposium, 31 May - 2
June 2010, at the Maison de la Chimie, Paris France, See
https://colloque.inra.fr/agah2010/ for more info.
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.
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Items for Pig Genome Update 103 can be sent to me by no later than July 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 |
+-----------------------------------+--------------------------------------
