Pig Genome Update No. 101angenmap@animalgenome.orgMarch 1, 2010 |
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.
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. 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). 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. 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. 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). Swine Genome Manual Annotation Training is planned for 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. 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. 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. 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). 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.
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
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