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Jan, 2016;26 (1): 130-9.

The pig X and Y Chromosomes: structure, sequence, and evolution.

Benjamin M Skinner, Carole A Sargent, Carol Churcher, Toby Hunt, Javier Herrero, Jane E Loveland, Matt Dunn, Sandra Louzada, Beiyuan Fu, William Chow, James Gilbert, Siobhan Austin-Guest, Kathryn Beal, Denise Carvalho-Silva, William Cheng, Daria Gordon, Darren Grafham, Matt Hardy, Jo Harley, Heidi Hauser, Philip Howden, Kerstin Howe, Kim Lachani, Peter J I Ellis, Daniel Kelly, Giselle Kerry, James Kerwin, Bee Ling Ng, Glen Threadgold, Thomas Wileman, Jonathan M D Wood, Fengtang Yang, Jen Harrow, Nabeel A Affara, Chris Tyler-Smith
Author Information
  1. Benjamin M Skinner: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
  2. Carole A Sargent: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
  3. Carol Churcher: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  4. Toby Hunt: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  5. Javier Herrero: 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.
  6. Jane E Loveland: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  7. Matt Dunn: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  8. Sandra Louzada: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  9. Beiyuan Fu: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  10. William Chow: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  11. James Gilbert: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  12. Siobhan Austin-Guest: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  13. Kathryn Beal: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom;
  14. Denise Carvalho-Silva: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom;
  15. William Cheng: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  16. Daria Gordon: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  17. Darren Grafham: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  18. Matt Hardy: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  19. Jo Harley: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  20. Heidi Hauser: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  21. Philip Howden: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  22. Kerstin Howe: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  23. Kim Lachani: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
  24. Peter J I Ellis: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
  25. Daniel Kelly: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  26. Giselle Kerry: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  27. James Kerwin: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  28. Bee Ling Ng: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  29. Glen Threadgold: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  30. Thomas Wileman: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  31. Jonathan M D Wood: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  32. Fengtang Yang: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  33. Jen Harrow: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  34. Nabeel A Affara: Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom;
  35. Chris Tyler-Smith: Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
PMID: 26560630 DOI: 10.1101/gr.188839.114

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.

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Grants

  1. BB/I025506/1/Biotechnology and Biological Sciences Research Council
  2. WT098051/Wellcome Trust
  3. U41 HG007234/NHGRI NIH HHS
  4. BB/F021372/1/Biotechnology and Biological Sciences Research Council
  5. 095908/Wellcome Trust
  6. /Wellcome Trust

MeSH Term

Animals
Base Sequence
Cats
Chromosomes, Mammalian
Dogs
Evolution, Molecular
Female
Gene Conversion
Gene Expression
Gene Library
Gene Order
Humans
Male
Molecular Sequence Data
Sequence Alignment
Sequence Analysis, DNA
Swine
X Chromosome
Y Chromosome
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 10

Word Cloud

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