@article{f644c1ff05854042bd07e08c46f6aa27,
title = "Pig genome sequence - analysis and publication strategy",
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.",
author = "Archibald, {Alan L.} and Lars Bolund and Carol Churcher and Merete Fredholm and Groenen, {Martien A.M.} and Barbara Harlizius and Lee, {Kyung Tai} and Denis Milan and Jane Rogers and Rothschild, {Max F.} and Hirohide Uenishi and Jun Wang and Schook, {Lawrence B.}",
note = "Funding Information: All authors are members of the Swine Genome Sequencing Consortium (SGSC) under whose auspices the pig genome is being sequenced. They are responsible for securing the funding for, and the management of, the pig genome sequencing project. ALA, DM, JR, MFR and LBS are members of the SGSC Steering Committee. ALA, MF, DM, JR, MFR, HU and LBS are members of the SGSC Technical Committee. LBS, CC, ALA, MAMG, DM, JR, MF, MFR comprise the SGSC Manuscript Steering Committee which is directing the SGSC{\textquoteright}s analysis and publication strategy. JR and CC led the sequencing team at the Wellcome Trust Sanger Institute which generated the BAC clone derived sequence data, during the initial and later stages of the project, respectively. LBS and JR were co-directors of the USDA grant which provided ca. 50% of the project funding. MAMG was work package leader for the EC-funded project to sequence chromosomes 7 and 14. BH and MAMG were project leaders for the IPG-funded project to sequence chromosome 4. ALA was the PI for the BBSRC grant on annotation and analysis. MFR secured US pig industry funding for the project and led a pilot project to generate finished sequence for part of chromosome 17. JW led the Beijing Genomics Institute effort to generate WGS data using Illumina next-gen sequencing technology partially funded by a grant of which LB was the PI. K-TL led the team at the Korean Livestock Research Institute that has contributed WGS data using Sanger capillary technology. HU leads the team at Japanese National Institute of Agrobiological Sciences which contributed full length cDNA sequence and some BAC clone sequence data. DM leads the team which is validating the sequence assembly against a high resolution radiation hybrid map. Finally, some of the leadership roles of the authors in the analysis of the sequence data are highlighted in Table 1. All authors have read and approved the manuscript. Funding Information: The Swine Genome Sequencing Consortium is grateful to the following for funding support for the pig genome sequencing project: the USDA National Institute of Food and Agriculture, formerly the Cooperative State Research, Education and Extension Service; the Agence Nationale de la Recherche; European Union SABRE; the Institute for Pig Genetics, Netherlands; INRA Genescope, France; Iowa Pork Producers Association; Iowa State University; Korean National Livestock Research Institute; National Institute of Agrobiological Sciences, Japan; National Pork Board, U.S.; North Carolina Pork Council; North Carolina Agricultural Research Service; North Carolina State University; the University of Illinois; the “Pigs and Health” programme of the Danish Advanced Technology Foundation, Denmark; the Wellcome Trust Sanger Institute; The Roslin Institute, University of Edinburgh and Biotechnology and Biological Sciences Research Council, U.K.; the University of Illinois Livestock Genome Sequencing Initiative.",
year = "2010",
month = jul,
day = "19",
doi = "10.1186/1471-2164-11-438",
language = "English (US)",
volume = "11",
journal = "BMC genomics",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",
number = "1",
}