title: Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.
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.
  
  
  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.
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark. raz@cbs.dtu.dk
authors.forename: Rasmus
authors.initials: R
authors.lastname: Wernersson
authors.forename: Mikkel H
authors.initials: MH
authors.lastname: Schierup
authors.forename: Frank G
authors.initials: FG
authors.lastname: Jørgensen
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
authors.forename: Frank
authors.initials: F
authors.lastname: Panitz
authors.forename: Hans-Henrik
authors.initials: HH
authors.lastname: Staerfeldt
authors.forename: Ole F
authors.initials: OF
authors.lastname: Christensen
authors.forename: Thomas
authors.initials: T
authors.lastname: Mailund
authors.forename: Henrik
authors.initials: H
authors.lastname: Hornshøj
authors.forename: Ami
authors.initials: A
authors.lastname: Klein
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Wei
authors.initials: W
authors.lastname: Dong
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Gane K S
authors.initials: GK
authors.lastname: Wong
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Christian
authors.initials: C
authors.lastname: Bendixen
authors.forename: Merete
authors.initials: M
authors.lastname: Fredholm
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.forename: Lars
authors.initials: L
authors.lastname: Bolund
mesh_terms: 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
chemical_list: D012333:RNA, Messenger