Source: UNIVERSITY OF ILLINOIS submitted to
SWINE GENOME SEQUENCING CONSORTIUM (SGSC): PIG GENOME ASSEMBLY AND ANNOTATION CONFERENCE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0219087
Grant No.
2009-65205-05642
Project No.
ILLU-538-640
Proposal No.
2009-03340
Multistate No.
(N/A)
Program Code
92120
Project Start Date
Sep 1, 2009
Project End Date
Aug 31, 2010
Grant Year
2009
Project Director
Schook, L. B.
Recipient Organization
UNIVERSITY OF ILLINOIS
2001 S. Lincoln Ave.
URBANA,IL 61801
Performing Department
Animal Sciences
Non Technical Summary
This workshop is designed to meet the following goals: 1. To review the latest genome assembly (Sscrofa9) and the automated (Ensembl) annotation; 2. To organize workshop sessions to support the development of a summary manuscript of the pig genome and for related companion papers; 3. To provide training in the manual annotation of the pig genome to ensure the highest quality product; and 4. To provide an opportunity to recognize the global partners who have supported and conducted the pig genome sequencing project and transition the SGSC activities into full utilization of the pig genome sequence information. In order to achieve the defined outcomes and deliverables, the conference has been organized to provide significant discussion among the participants. The workshop will be held at the Wellcome Trust Genome campus which is one of the world's great centers for genomics and bioinformatics. The Genome Centre Conference Center provides the Francis Crick Auditorium and numerous smaller meeting rooms for breakout topical sessions. In addition, there are a limited number of residential rooms (approximately 60) on campus with additional housing available in the village of Hinxton (within walking distance) and in Cambridge (serviced by dedicated Sanger employee buses). The Conference Centre staff host numerous courses and workshops throughout the year and are well positioned to support the SGSC Workshop.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033510108025%
3033599108025%
3043510108025%
3043599108025%
Knowledge Area
303 - Genetic Improvement of Animals; 304 - Animal Genome;

Subject Of Investigation
3510 - Swine, live animal; 3599 - Swine, general/other;

Field Of Science
1080 - Genetics;
Goals / Objectives
This Animal Genome, Genetics, and Breeding proposal addresses the Conventional Breeding and Translational Animal Genomics priority of the program. The proposed Swine Genome Sequencing Consortium (SGSC) Conference will convene global researchers to participate in the assembly and annotation of the pig genome. The sequencing effort will provide 4X coverage of the CHORI-242 BAC minimal tiling path and directed improvement will provide an equivalent quality of 6X genomic coverage. Genome sequence data have been previously assembled and annotated with automated tools and published through the Pre-Ensembl genome browser, currently the Sscrofa8 (http://pre.ensembl.org/Sus_scrofa/Info/Index). The latest assembly (Sscrofa9, April 2009) is currently being annotated through the Ensembl automated pipeline and is scheduled for release in late 2009. This annotated sequence will be used in developing a manuscript describing the pig genome sequence as well as related companion manuscripts. The SGSC workshop was organized to meet several goals. First, this meeting will provide an essential opportunity to convene the broader pig genomics community as well as end-users to ensure rapid and full deployment of sequence information. Second, the workshop topics were identified with respect to topical areas that will be used in the development of a summary manuscript of the pig genome and for related companion papers. Third, participants will be trained in performing manual annotation of the pig genome. It will also serve to recognize the global partners (researchers, funders, industrial supporters, and staff) who have supported and conducted the pig genome-sequencing project.
Project Methods
This workshop provides recognition that the sequencing required to establish a draft sequence of the pig genome is complete as well as creating a timetable for completing the assembly and annotation activities required to support development of manuscripts. The SGSC Workshop will provide an opportunity for the international community to join together and recognize this historic achievement and for the funding agencies to assist in creating the next steps. For example, we will invite funders, producers and pork industry representatives from the United States, Asia, and Europe to participate. The historical relevance is significant. The SGSC workshop has been scheduled to precede the Pig Genome III meeting organized by the European Network for Pig Genomics (PigNet). This coordination of the meetings will permit broad international participation. The juxtaposition of the two meetings also symbolically represents a handoff from researchers active in genomic sequencing to those active in the application of genomic sequencing to address health and production issues.

Progress 09/01/09 to 08/31/10

Outputs
OUTPUTS: The Pig Genome III Conference held November 2-4, 2009 brought together researchers from the pig community to celebrate the completion of sequencing. This meeting provided an essential opportunity to convene the broader pig genomics community as well as end-users to ensure rapid and full deployment of the sequence information. Key speakers included: Allan Bradley, Lawrence Schook, Richard Clark, Carol Churcher, Chris Ponting, Alan Archibald, Jan Gorodkin, Alfonso Valencia, Leif Andersson, Soren Brunak, Greger Larson, Martien Groenen, Jan Merks, and Nico Katsanis. Session topics included: Physical Mapping and Sequencing; Sequence Assembly and Annotation; Biodiversity and Evolution; Genome Regulation; Comparative Genomics; Industrial Applications; and Biological and Biomedical Insights. PARTICIPANTS: The Pig Genome III meeting was funded in part by COST Action 861: European Network for Pig Genomics (PigNet) and two industry sponsors, Illumina and Pig Improvement Company (PIC). TARGET AUDIENCES: The Pig Genome III conference also served to stimulate interactions between researchers who have focused on creating the sequencing platform and conducting the sequencing with those investigators who are dedicated to using this information. Prior to the meeting, these have in part been separate research communities and the conference will provided a forum for introductions and to engage the broader community to participate in the analysis of the genome sequence. Finally, the conference was designed to create international guidelines to ensure the broadest dissemination and utilization of genomic information. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
The Pig Genome III conference was a great success, bringing together 125 researchers from the pig community to make plans for the continuing enhancement of the swine genome. The plans for analysis of the pig genome sequence, the application, and the results were made available through publication. The three-day workshop also taught participants how to use the annotation software so they can begin to annotate their regions of interest. Sanger will continue to provide support after the workshop to enable participants to work remotely to finish their annotation. The pig genome assembly version 10 (Build 10) has been officially released and placed on the Genome Analysis Centre (TGAC)'s FTP site: ftp://ftp.tgac.bbsrc.ac.uk It is also available for blast on NAGRP Bioinformatics site: http://www.animalgenome.org/blast/.

Publications

  • Archibald, A.L., Bolund, L., Churcher, C., Fredholm, M., Groenen, M.A.M., Harlizius, B., Lee, K.-T., Milan, D., Rogers, J., Rothschild, M.F., Uenishi, H., Wang, J. and Schook, L.B. 2010. The Swine Genome Sequencing Consortium: Pig genome sequence analysis and publication strategy. Genomics 2010, 11:438.http://www.biomedcentral.com/1471-2164/11/438.