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


CONCLUSIONS
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.
Wernersson
Rasmus
R
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark. raz@cbs.dtu.dk
Schierup
Mikkel H
MH
Jørgensen
Frank G
FG
Gorodkin
Jan
J
Panitz
Frank
F
Staerfeldt
Hans-Henrik
HH
Christensen
Ole F
OF
Mailund
Thomas
T
Hornshøj
Henrik
H
Klein
Ami
A
Wang
Jun
J
Liu
Bin
B
Hu
Songnian
S
Dong
Wei
W
Li
Wei
W
Wong
Gane K S
GK
Yu
Jun
J
Wang
Jian
J
Bendixen
Christian
C
Fredholm
Merete
M
Brunak
Søren
S
Yang
Huanming
H
Bolund
Lars
L
D000818:Animals; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005091:Exons; D016678:Genome; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D010802:Phylogeny; D012333:RNA, Messenger / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity; D013552:Swine
D012333:RNA, Messenger