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Open Access Highly Accessed Correspondence

Pig genome sequence - analysis and publication strategy

Alan L Archibald1*, Lars Bolund23, Carol Churcher4, Merete Fredholm5, Martien AM Groenen6, Barbara Harlizius7, Kyung-Tai Lee8, Denis Milan9, Jane Rogers10, Max F Rothschild11, Hirohide Uenishi12, Jun Wang132, Lawrence B Schook14* and the Swine Genome Sequencing Consortium

Author Affiliations

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK

2 BGI-Shenzhen, Shenzhen 518083, China

3 Institute of Human Genetics, Aarhus University, DK-8000 Aarhus, Denmark

4 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

5 Copenhagen University, Copenhagen, Denmark

6 Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands

7 Institute for Pig Genetics, Beuningen, The Netherlands

8 Korean National Institute of Animal Science, Suwon, Kyunggi-do, Korea

9 INRA Toulouse, France

10 The Genome Analysis Centre, Norwich, UK

11 Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa 50011, USA

12 National Institute of Agrobiological Sciences, Japan

13 Department of Biology, University of Copenhagen, Copenhagen, Denmark

14 Institute of Genomic Biology, University of Illinois, Urbana, Illinois, USA

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BMC Genomics 2010, 11:438  doi:10.1186/1471-2164-11-438

Published: 19 July 2010

Abstract

Background

The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing.

Results

Assemblies of the BAC clone derived genome sequence have been annotated using the Pre-Ensembl and Ensembl automated pipelines and made accessible through the Pre-Ensembl/Ensembl browsers. The current annotated genome assembly (Sscrofa9) was released with Ensembl 56 in September 2009. A revised assembly (Sscrofa10) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30× genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication.

Conclusions

In this marker paper, the Swine Genome Sequencing Consortium (SGSC) sets outs its plans for analysis of the pig genome sequence, for the application and publication of the results.