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

TY - JOUR

T1 - Pigs in sequence space

T2 - a 0.66X coverage pig genome survey based on shotgun sequencing

AU - Wernersson, Rasmus

AU - Schierup, Mikkel H.

AU - Jørgensen, Frank G.

AU - Gorodkin, Jan

AU - Panitz, Frank

AU - Stærfeldt, Hans-Henrik

AU - Christensen, Ole F.

AU - Mailund, Thomas

AU - Hornshøj, Henrik

AU - Klein, Ami

AU - Wang, Jun

AU - Liu, Bin

AU - Hu, Songnian

AU - Dong, Wei

AU - Li, Wei

AU - Wong, Gane K.S.

AU - Yu, Jun

AU - Wang, Jian

AU - Bendixen, Christian

AU - Fredholm, Merete

AU - Brunak, Søren

AU - Yang, Huanming

AU - Bolund, Lars

PY - 2005

Y1 - 2005

N2 - 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 sequence to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.

AB - 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 sequence to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.

U2 - 10.1186/1471-2164-6-70

DO - 10.1186/1471-2164-6-70

M3 - Journal article

C2 - 15885146

SN - 1471-2164

VL - 70

SP - 1

EP - 7

JO - BMC Genomics

JF - BMC Genomics

IS - 6

ER -