Swine Genome Sequencing Project

The genome of the pig (Sus scrofa) comprises 18 autosomes, with X and Y sex chromosomes. The genome size is similar to that of human at around 2.7Gb.

The pig is a member of the artiodactyls, (cloven-hoofed mammal), which are an evolutionary clade distinct from the primates and rodents; there is extensive conserved homology between the pig genome and the human genome. The pig is therefore an important model for human health particularly for understanding complex traits such as obesity and cardiovascular disease. The funding for the clone based sequencing project at the Wellcome Sanger Institute ran from January 2006 to December 2009.

Clone mapping and sequencing

A physical map of the swine genome was generated by an international collaboration of four laboratories. Both high-throughput fingerprinting and BAC end sequencing were used to provide the template for an integrated physical map of the whole pig genome.

A bacterial clone physical map of the genome was constructed using restriction enzyme fingerprinting (Marra et al., 1997). Fingerprints were generated by digesting clones with HindIII. Following electrophoresis on agarose gels and data collection using a fluorimager, raw images were entered using the software, IMAGE. This produced an output of normalised band values and gel traces. Analysis of data took place in WebFPC, a version of which can be found here: WebFPC. Clones were contiguated on the basis of shared bands. Coverage across the 2.7Gb genome was generated at 15.3x.

The total number of fingerprints was 267884, which were assembled into 524 contigs. These data represent the output of a stringent automated assembly, resulting in contigs of highly overlapping sets of clones, followed by initial manual editing.

Fingerprinted clones breakdown by library
Library Fingerprinted clones Clones average insert (kb)
CHORI-242 103758 173
RPCI-44 61281 165
PigE 73866 150
INRA 28467 135
KNP 361 -
Unknown 151 -
Total 267884 -

The contigs were then merged by relaxing the stringency required for overlap, as well as interrogating all other available data, such as contig localisation to the human genome via BAC end sequences, RH and genetic maps. The map, created by Sean Humphray and his team, provided a template for clone tile path selection. For further information about the fingerprint map, follow this link:
http://genomebiology.com/2007/8/7/R139

End sequencing

Over 600,000 BAC end sequences (BES) were generated from four libraries in three laboratories. The BES are available from the NCBI trace archive.

Using WuBLASTn set for cross-species comparison, the non-repetitive BAC ends were searched against the human reference sequence. This anchoring acted as a framework in the construction of the porcine map and along with reduced stringency fingerprint matches, enabled accelerated merging through the whole genome.

The BAC end sequencing was funded by BBSRC/DEFRA/Roslin Institute, INRA/Genoscope and the United States Department of Agriculture.

Data Availability
  • NCBI Trace Archive - raw sequence data in the form of traces
  • EMBL - access clone sequences via public nucleotide database
  • FTP - download clone sequences via FTP
  • Blast - search for clone sequences

Collaborators and Funding

Funding

The mapping and BES projects were funded by:

  • USDA Cooperative State Research, Education and Extension Service (CSREES) administered the grant through the National Research Initiative
  • National Pork Board
  • Iowa Pork Board
  • Iowa State University
  • North Carolina Pork Council
  • North Carolina State University
  • Biotechnology and Biological Sciences Research Council (BBSRC)
  • Department for Environment, Food and Rural Affairs (DEFRA)
  • EU
Swine Genome Sequencing Consortium

The Sanger Institute is a member of the Swine Genome Sequencing Consortium (SGSC), a partnership of institutes involved in sequencing and genomics. The aim of the SGSC was to accelerate, facilitate and coordinate global swine genomic sequencing efforts.

Participating Centres
  • Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
  • Department of Animal Sciences, University of Illinois, Urbana, IL, USA
  • The Wellcome Sanger Institute, Hinxton, UK
  • Roslin Institute, Edinburgh, UK
  • INRA-CEA, Jouy-en-Josas, France
  • INRA-Toulouse, France
  • Agricultural Research Service, Clay Center, NE, USA
  • The Alliance for Animal Genomics, Bethesda, MD, USA
  • University of Nevada, Reno
  • Iowa State University, USA

Swine libraries

CHORI-242 BAC library
Strain
Duroc
Source
Female white blood cells
Vector
pTARBAC1.3
Host strain
E. coli DH10B
No. of Clones
196457
Av insert size
173 kb
Redundancy
11.4x
Originators
P. de Jong
BACPAC Resources
Distribution
P. de Jong
BACPAC Resources
Library no: CHORI-242
RPCI-44 BAC Library
Strain
37.5% Yorkshire, 37.5% Landrace, 25% Meishan
Source
Male white blood cells
Vector
pTARBAC2
Host strain
E. coli DH10B
No. of Clones
185389
Av insert size
165 kb
Redundancy
10.2x
Originators
P. de Jong
BACPAC Resources
Distribution
P. de Jong
BACPAC Resources
Library no: RPCI-44
PigE BAC Library
Strain
Large White x Meishan F1
Source
Male blood cells
Vector
pBeloBAC11
Host strain
E. coli DH10B
No. of Clones
97000
Av insert size
150 kb
Redundancy
4.7x
Originators
Susan Anderson and Alan Archibald
Distribution
ARK-Genomics
Library no: PigE BAC
References

  • A large-fragment porcine genomic library resource in a BAC vector.

    Anderson SI, Lopez-Corrales NL, Gorick B and Archibald AL

    Mammalian genome : official journal of the International Mammalian Genome Society 2000;11;9;811-4

    PUBMED: 10967147; DOI: 10.1007/s003350010155

INRA Porcine BAC library
Strain
Homozygous for the SLA H01 haplotype
Source
Male skin fibroblasts
Vector
pBeloBACII
Host strain
E. coli DH10B
No. of Clones
107520
Av insert size
135 kb
Redundancy
5x
Originators
Laboratoire de Radiobiologie et d'Etude du Génome (LREG)
Distribution
Francois Piumi
INRA BAC-YAC RESOURCE CENTER
Library no: Porcine BAC
KNP BAC library

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