Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing
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Pigs in sequence space : a 0.66X coverage pig genome survey based on shotgun sequencing. / Wernersson, Rasmus; Schierup, Mikkel H.; Jørgensen, Frank G.; Gorodkin, Jan; Panitz, Frank; Stærfeldt, Hans-Henrik; Christensen, Ole F.; Mailund, Thomas; Hornshøj, Henrik; Klein, Ami; Wang, Jun; Liu, Bin; Hu, Songnian; Dong, Wei; Li, Wei; Wong, Gane K.S.; Yu, Jun; Wang, Jian; Bendixen, Christian; Fredholm, Merete; Brunak, Søren; Yang, Huanming; Bolund, Lars.
In: BMC Genomics, Vol. 70, No. 6, 2005, p. 1-7.Research output: Contribution to journal › Journal article › Research › peer-review
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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
VL - 70
SP - 1
EP - 7
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
IS - 6
ER -
ID: 8000305