Pig genome sequence ready for analysis. The Swine Genome Sequencing Consortium (SGSC, http://piggenome.org is pleased to announce that the sequence data and assembly on which the draft pig genome sequence publications will be based are now available for analysis. This draft pig genome sequence (Sscrofa10.2) has been released by the International Swine Genome Sequencing Consortium under the terms of the Toronto Statement (Nature 2009, 461: 168). Sscrofa10.2 replaces the previous assembly, Sscrofa10, which had assembly errors. The International Swine Genome Sequencing Consortium is coordinating genome-wide analyses, as described in BMC Genomics 2010 11:438. Funders of the pig genome project are acknowledged in this marker paper. The sequence data, from which this assembly was constructed, comprise hierarchical shotgun sequence data providing 4-6x genome coverage from BAC clones representing a minimal tile path across the genome plus >30x genome coverage in whole genome shotgun sequence (WGS) Illumina reads. All the WGS data and most of the BAC data are derived from blood cells of a single Duroc female pig (Duroc 2-14; CHORI-242 BAC library) but also includes some data from other BAC libraries from other breeds. The Consortium is grateful to Mario Caccamo and his colleagues at The Genome Analysis Centre, Norwich, UK for their work in finalizing the assembly. We are also grateful for the efforts of Martien Groenen and colleagues, Wageningen and Bertrand Servin and colleagues, INRA, Toulouse for their contributions to checking the quality of the multiple iterations of the assembly over the summer. The sequence data and assembly have been posted on the NCBI ftp site at: ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Sus_scrofa/Sscrofa10.2/ All those who wish to analyze or use the sequence data are strongly encouraged to access the data from this NCBI ftp site in order to ensure that everyone is working with an identical primary dataset. Annotation of this draft pig genome sequence (Sscrofa10.2) has been initiated by the Ensembl team and the genome team at NCBI will also start their annotation effort soon. The annotation currently visible in the Ensembl and NCBI genome browsers should be used with caution - Ensembl is currently displaying the 2009 assembly (Sscrofa9) and the information displayed in the NCBI Map Viewer is based on the flawed assembly 10. The Consortium is holding a series of regular Skype conference calls to discuss and coordinate the analysis and annotation activities and to develop the main and companion papers describing the genome sequence and its use. We are aiming to produce substantive draft manuscripts before the end of the year. If you wish to join these discussions then please contact Larry Schook: email@example.com or Alan Archibald: firstname.lastname@example.org://www.intlpag.org/web/. This year another great meeting is planned. The swine workshop will be Saturday January 14 and chaired by Daniel Ciobanu. Students wishing to apply for travel funding should go to http://www.intlpag.org/web/index.php/attend/travel-grants http://www.animalgenome.org/QTLdb/). 2) Another change is that QTL data submission to the Animal QTLdb is now required by several journals prior to the publication of your paper. We encourage you to submit your QTL data directly to the database through the curator web portal http://www.animalgenome.org/QTLdb/app.html to speed up the review of your paper. 3) Good news for AnGenMap listserv users - the File Share Platform can now be used as an alternative to share non-plain-text files that are normally not allowed as email attachments on the AnGenMap listserv (e.g. .PDF, .doc, .xls, .ppt, .xlm, etc.) http://www.animalgenome.org/community/angenmap/faq.php#11. 4) An experimental pig genome database is under development. A number of new functions and utilities are under development http://www.animalgenome.org/pig/genome/db/ . If you have any new ideas for the pig genome database to better serve your purpose, please feel free to send your suggestions, note "pig genome database" in the "subject:" line, to email@example.com. 5) A local copy of the Biomart has been installed on AnimalGenome.ORG to serve the livestock research community. Currently, queries against the pig, cattle, chicken and horse genomes are supported. More species will be added upon the availability of the data. See: http://www.animalgenome.org:8181/. 6) The Blast Extension Analysis Program (BEAP) has been modified to assist users for easier setup. See the updated manual for details. http://www.animalgenome.org/tools/beap/. 7) The NAGRP data repository has been expanded to host supplementary data for publications. If you are looking for an online host for additional data to your publication, feel free to contact us at firstname.lastname@example.org http://www.animalgenome.org/repository/pub/. 8) The new pig genome assembly has been actively improved during the summer. The most recent build 10.2 has been submitted to NCBI and is available for blast analysis on the NAGRP blast server http://www.animalgenome.org/blast/.
As always, suggestions from the livestock community are always welcome. We are here to serve to community. You can either call Jim Reecy at +1-515-294-9269 or send them a note at email@example.com@nifa.usda.gov or by phone at 202-401-1766. http://www.animalgenome.org/pigs/community/meetings.html)
Items for Pig Genome Update 110 can be sent to me by no later than December 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 firstname.lastname@example.org http://www.animalgenome.org/pig/
cc: Muquarrab Qureshi, NAGRP Director, National Animal Genome Research Program, NIFA
© US Pig Genome Coordination Program