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Open Access Highly Accessed Research article

Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

Rasmus Wernersson1, Mikkel H Schierup2, Frank G Jørgensen2, Jan Gorodkin3, Frank Panitz4, Hans-Henrik Stærfeldt1, Ole F Christensen2, Thomas Mailund2, Henrik Hornshøj4, Ami Klein3, Jun Wang56, Bin Liu6, Songnian Hu6, Wei Dong6, Wei Li6, Gane KS Wong6, Jun Yu6, Jian Wang6, Christian Bendixen4, Merete Fredholm3, Søren Brunak1, Huanming Yang6* and Lars Bolund56*

Author affiliations

1 Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

2 Bioinformatics Research Center, University of Aarhus, Aarhus, Denmark

3 Division of Genetics, The Royal Veterinary and Agricultural University, Copenhagen, Denmark

4 Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, Foulum, Denmark

5 Institute of Human Genetics, University of Aarhus, Aarhus, Denmark

6 Beijing Genomics Institute, Beijing, China

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Citation and License

BMC Genomics 2005, 6:70  doi:10.1186/1471-2164-6-70

Published: 10 May 2005

Abstract

Background

Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls.

Results

We have generated ~3.84 million shotgun sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis.

The non-repetitive fraction of the sequences was aligned to the UCSC human-mouse alignment and the resulting three-species alignments were annotated using the human genome annotation. Ultra-conserved elements and miRNAs were identified. The results show that for each of these types of orthologous data, pig is much closer to human than mouse is. Purifying selection has been more efficient in pig compared to human, but not as efficient as in mouse, and pig seems to have an isochore structure most similar to the structure in human.

Conclusion

The addition of the pig to the set of species sequenced at low coverage adds to the understanding of selective pressures that have acted on the human genome by bisecting the evolutionary branch between human and mouse with the mouse branch being approximately 3 times as long as the human branch. Additionally, the joint alignment of the shot-gun sequences to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.