Pig Genome Update No. 105
November 1, 2010
New White Paper on swine genome progress and future directions was.
recently prepared in response to a request by the USDA and other agencies
to benchmark progress in livestock genomes. The white paper received
inputs from swine genome researchers around the globe including
researchers from the International Swine Genome Sequencing Consortium
(SGSC). The white paper can be seen at
http://www.animalgenome.org/pigs/community/WhitePaper/. Your thoughts are
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A data repository was set up by the NRSP-8 Bioinformatics Team for the pig.
genome research community to share data. It can be seen at
Currently available data sets are the Illumina 60K SNP locations for build
10 contributed by Martien Groenen. Those who wish to share data, please
contact the Swine Genome Coordinators Max Rothschild
firstname.lastname@example.org), or Bioinformatics Coordinator Jim Reecy
email@example.com), or send an email directly to the NAGRP
Bioinformatics Team firstname.lastname@example.org .
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Build 10 for the Sus scrofa reference genome sequence was recently.
released thanks to the efforts of many people and great collaboration
across the world. The sequence and accompanying information will be in a
final version and released from TGAC's ftp (FTP site: ftp.tgac.bbsrc.ac.uk
; User: pig10 ; Password: Sscrofa10 ). This final version was based on the
latest freeze of the physical map. The assembly is the result of the
integration of all the sequenced clones and contigs produced by SOAPdenovo
and Cortex whole genome shotgun (WGS) assemblies. These WGS assemblies
were generated using Illumina reads sequenced at BGI and the Sanger
Institute (~40X coverage). As part of the release AGP files with
information about the source of every contig were provided. The WGS
contigs will be submitted to EMBL/Genbank, and after that the WGS contigs
will be renamed in the AGP with the corresponding accession numbers. This
assembly provides an almost complete coverage of the pig genome.
Additional details will be presented in the future. (kindly provided by
Mario Caccamo (TGAC) and the International Swine Genome Sequencing
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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
email@example.com] or Alan Archibald [firstname.lastname@example.org] .
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New publishing format for Pig Genome Update coming soon. Starting January
1, 2011 the Pig Genome Update will be published 4 times a year. Your input
and ideas are always welcome. Please contribute.
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PAG 2011 Swine Workshop and other PAG happenings. This year at the NRSP-8
Swine Sub-Committee Workshop on January 15, 2011, we will celebrate the
"end of the beginning"- the completion of the draft pig genome sequence.
We have a great joint session planned with the Cattle/Sheep group in the
morning, as this was very successful last year. At this joint session, we
will hear from both academia and the industry regarding the nature of the
genome (A. Archibald) and the use of it to understand traits of interest
(B. Harzilius). In the afternoon, we will have several talks on
annotating (J. Loveland) and analyzing the genome (M. Groenen, H.-J.
Megens, O. Madsen). We will finish with a talk on GWAS in reproduction
and disease (D. Ciobanu). Hope to see you all there! (kindly submitted by
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The Sunday the NRSP8 workshop will feature Professor Morris Soller giving.
the NRSP8 Distinguished Lecture. The PAG plenary talks and other
activities at PAG XIX promise to deliver a quality meeting. Now is the
time to register. Please note: NRSP-8 coordination funding will be
available to partially support travel or registration for committee
members or members of their labs. If interested, please contact
email@example.com prior to December 1.
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Upcoming meetings (see:
National Swine Improvement Federation Annual Meeting and Genetic
Symposium, Kansas City, Missouri, December 2 -3, 2010, for details please
- Plant and Animal Genome XIX Conference, January 15-19, 2011, San Diego CA.
For details seehttp://www.intl-pag.org/
- Gordon Research Conference in Quantitative Genetics & Genomics, Feb.
20-25, 2011, Hotel Galvez, Galveston, TX. See
- Swine in Biomedical Research, July 17-19, 2011, Chicago IL, for details
contact Larry Schook at firstname.lastname@example.org
Items for Pig Genome Update 106 can be sent to me by no later than December 15
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
cc: Muquarrab Qureshi, NAGRP Director, National Animal Genome Research Program, NIFA
© US Pig Genome Coordination Program