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Pig Genome Newsletter #101
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #101
Date: Thu, 04 Mar 2010 15:57:37 -0600
Pig Genome Update # 101:
- PDF version is available at
http://www.animalgenome.org/pigs/newsletter/pdf/No.101.pdf
- Web version is available at
http://www.animalgenome.org/pigs/newsletter/No.101.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. 101 **************
* *
* <angenmap@animalgenome.org> *
* March 1, 2010 *
***************************************
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1. Updates on the pig genome assembly and the publications
2. The SGSC Genome Manuscript Steering Committee was established
3. The Sscrofa10 Assembly nears completion
4. Guideline for Pig Genome Sequencing Manuscript Authorship
5. Companion Manuscripts
6. SGSC Genome Manuscript Steering Committee
7. Swine Genome Manual Annotation Training is planned for April
8. Many people are awaiting the release of the AFRI RFA later this month
9. Pig Genome Update Newsletters are distributed electronically
10. Help exists for Genetic Line Preservation and Use
11. Upcoming meetings ( 4 items )
===========================================================================
Updates on the pig genome assembly and the publications that are likely
to result are of primary importance. This newsletter is reprinting much
of the information recently published in the SGSC Pig Genome Manuscript
Newsletter provided kindly by Larry Schook, Cathy Tingley and the
committee. For more details and a full copy of all topics please
contact Cathy Tingley at tingley@ad.uiuc.edu.
o o o o o o o o o o o
The SGSC Genome Manuscript Steering Committee was established following
the Pig Genome III Conference to coordinate activities associated with
developing an assembly incorporating all sequence information to date
and to create a manuscript based on the assembled and annotated pig
genome. The Steering Committee is also providing coordination for
related companion manuscripts. With support from the USDA, the Steering
Committee is holding teleconferences every two weeks to discuss issues
related to developing manuscripts related to the pig genome project. It
is the intent of the Steering Committee to be fully inclusive and invite
full participation of the broader community. Due to the logistics and
costs of including every one of the calls, we do invite you to forward
questions and comments to our attention so they can be added to the
teleconference agenda. Please forward comments or questions to the
attention of either Alan Archibald or Larry Schook. Also, feel free to
contact any one on the Steering Committee regarding specific topical
issues.
o o o o o o o o o o o
The Sscrofa10 Assembly nears completion. The Sanger Institute and The
Genome Analysis Center (TGAC) are working on the release of the pig
genome assembly (Sscrofa10) that will provide the basis for the pig
genome and companion manuscripts. Their aim is to release an early
version of this assembly to the working groups for their analyses in
early April. They will distribute the files through an FTP site together
with information on those regions that changed with respect to the
current assembly (Sscrofa9). This early release will allow researchers
to incorporate corrections identified by the analyses of the working
groups before the submission of the assembly Sscrofa10 to the Ensembl
group for annotation. To request access via the FTP site please contact
Mario Caccamo (mario.caccamo@bbsrc.ac.uk).
o o o o o o o o o o o
Guideline for Pig Genome Sequencing Manuscript Authorship. Authorship is
provided to those individuals who intellectually contribute to the
analyses and development of the pig genome manuscript as defined by the
included topical areas. Manual annotation of pig genes submitted to
Ensembl is not in and of itself sufficient for inclusion as an author.
The SGSC Genome Manuscript Steering Committee is charged with the
responsibility to recognize scholarly contributions related to
authorship. Thus, all participants working with Topic Leaders will be
considered as co-authors. As for citation of authors, the SGSC Genome
Manuscript Steering Committee has made the following decision. The list
of authors will consist of the Steering Committee followed by authors
(alphabetically). Specific responsibilities of each author will be noted
(e.g. Leader of Manual Annotation, contribution to Genome Diversity).
Authorship for related companion manuscripts is at the discretion of the
collaborating individuals.
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
Swine Genome Manual Annotation Training is planned for and April.
Everyone is invited to attend a manual annotation training session,
which will be held in Ames, Iowa on April 1 (afternoon) and all day
April 2nd. Participants will be provided instruction on how to use the
Wellcome Trust Sanger Institute "Otterlace" program, which facilitates
structural annotation of sequenced genomes, in this case the swine
genome. Participants will need to provide their own Mac or Linux
computer as the "Otterlace" program needs to be loaded on to the
computer. Any one that is interested in attending the training session
is encouraged to contact James Reecy (jreecy@iastate.edu) for additional
details.
o o o o o o o o o o o
Many people are awaiting the release of the AFRI RFA later this month.
You can sign up for announcements regarding the AFRI RFAs on
Grants.gov. This saves you from having to keep checking our web page.
To receive notifications of all new announcements pertaining to AFRI
RFA, you can register via Grants.gov at
http://www.grants.gov/search/subscribeAdvanced.do. First enter the
e-mail address at which you would like to receive the announcements.
Then enter "10.310" for CFDA Number and finally select "Subscribe to
Mailing List". Other criteria may be selected; however, your e-mail
address and the CFDA number are the only data required to receive AFRI
announcements. You do not need to be a registered user of Grants.gov to
use this service. You may modify your subscriptions or unsubscribe at
any time.
o o o o o o o o o o o
Pig Genome Update Newsletters are distributed electronically through
AnGenMap (http://www.animalgenome.org/community/discuss). Previous
newsletters are at
http://www.animalgenome.org/pigs/newsletter/index.html. Coordinator
updates can also be found
http://www.animalgenome.org/pigs/community/NRSP8/. Please provide your
input as the Swine Genome Coordinator so that we can improve the
coordination effort.
o o o o o o o o o o o
Help exists for Genetic Line Preservation and Use. The USDA ARS
National Animal Germplasm Program (NAGP) can serve as a way to preserve
your research lines. NAGP has the ability to freeze semen, and other
tissues, and securely store it long term. These resources are available
to preserve research lines either to capture genetic variation at phases
during the project, freeze the foundation population as an example, or
to preserve material from lines that are being terminated. So, if you
are interested in preserving any of your genetic lines, contact either
Terry Stewart (tstewart@purdue.edu, 765-494-0138), chairman of the swine
species committee or Harvey Blackburn (Harvey.Blackburn@ars.usda.gov,
970/495-3268). For parties interested in maintaining ownership of the
material there is the option of establishing a material transfer
agreement with USDA/ARS. To learn more NAGP and the extensive material
already in the collection, visit the NAGP web site at
http://www.ars.usda.gov/Main/docs.htm?docid=16979 (kindly submitted by
Terry Stewart).
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 102 can be sent to me by no later than April 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 |
+-----------------------------------+--------------------------------------
