title: The pig X and Y Chromosomes: structure, sequence, and evolution.
abstract: We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.
authors.affiliation: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Skinner
authors.affiliation: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
authors.forename: Carole A
authors.initials: CA
authors.lastname: Sargent
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Carol
authors.initials: C
authors.lastname: Churcher
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Toby
authors.initials: T
authors.lastname: Hunt
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom.
authors.forename: Javier
authors.initials: J
authors.lastname: Herrero
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Jane E
authors.initials: JE
authors.lastname: Loveland
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Matt
authors.initials: M
authors.lastname: Dunn
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Sandra
authors.initials: S
authors.lastname: Louzada
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Beiyuan
authors.initials: B
authors.lastname: Fu
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: William
authors.initials: W
authors.lastname: Chow
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: James
authors.initials: J
authors.lastname: Gilbert
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Siobhan
authors.initials: S
authors.lastname: Austin-Guest
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom;
authors.forename: Kathryn
authors.initials: K
authors.lastname: Beal
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom;
authors.forename: Denise
authors.initials: D
authors.lastname: Carvalho-Silva
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: William
authors.initials: W
authors.lastname: Cheng
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Daria
authors.initials: D
authors.lastname: Gordon
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Darren
authors.initials: D
authors.lastname: Grafham
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Matt
authors.initials: M
authors.lastname: Hardy
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Jo
authors.initials: J
authors.lastname: Harley
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Heidi
authors.initials: H
authors.lastname: Hauser
authors.affiliation: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Philip
authors.initials: P
authors.lastname: Howden
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Kerstin
authors.initials: K
authors.lastname: Howe
authors.affiliation: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
authors.forename: Kim
authors.initials: K
authors.lastname: Lachani
authors.affiliation: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
authors.forename: Peter J I
authors.initials: PJ
authors.lastname: Ellis
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Daniel
authors.initials: D
authors.lastname: Kelly
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Giselle
authors.initials: G
authors.lastname: Kerry
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: James
authors.initials: J
authors.lastname: Kerwin
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Bee Ling
authors.initials: BL
authors.lastname: Ng
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Glen
authors.initials: G
authors.lastname: Threadgold
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Thomas
authors.initials: T
authors.lastname: Wileman
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Jonathan M D
authors.initials: JM
authors.lastname: Wood
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Fengtang
authors.initials: F
authors.lastname: Yang
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Jen
authors.initials: J
authors.lastname: Harrow
authors.affiliation: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
authors.forename: Nabeel A
authors.initials: NA
authors.lastname: Affara
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
mesh_terms: D000818:Animals; D001483:Base Sequence; D002415:Cats / Q000235:genetics; D033481:Chromosomes, Mammalian / Q000235:genetics*; D004285:Dogs / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D005785:Gene Conversion; D015870:Gene Expression; D015723:Gene Library; D023061:Gene Order; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013552:Swine / Q000235:genetics*; D014960:X Chromosome / Q000235:genetics*; D014998:Y Chromosome / Q000235:genetics*