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. 2005 May 10:6:70.
doi: 10.1186/1471-2164-6-70.

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

Rasmus Wernersson  1 , Mikkel H Schierup, Frank G Jørgensen, Jan Gorodkin, Frank Panitz, Hans-Henrik Staerfeldt, Ole F Christensen, Thomas Mailund, Henrik Hornshøj, Ami Klein, Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane K S Wong, Jun Yu, Jian Wang, Christian Bendixen, Merete Fredholm, Søren Brunak, Huanming Yang, Lars Bolund
Affiliations

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

Rasmus Wernersson et al. BMC Genomics. .

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 approximately 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.

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Figures

Figure 1
Figure 1
Evolutionary distances between mouse, pig and human for conserved sequences divided into functional classes using the annotation of the human genome. Branch lengths are estimated using the HKY substitution model with gamma correction [12].
Figure 2
Figure 2
The distribution of GC content in exons for human, pig and mouse. Only alignments with more than 40 base pairs of exon sequence were used.
See this image and copyright information in PMC

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