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

Skinner, Benjamin M, Sargent, Carole A, Churcher, Carol, Hunt, Toby, Herrero, Javier, Loveland, Jane E, Dunn, Matt, Louzada, Sandra, Fu, Beiyuan, Chow, William, and others. (2015) The pig X and Y Chromosomes: structure, sequence, and evolution. Genome Research, 26 (1). pp. 130-9. ISSN 1088-9051. (doi:10.1101/gr.188839.114) (KAR id:58281)

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http://dx.doi.org/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.

Item Type: Article
DOI/Identification number: 10.1101/gr.188839.114
Subjects: Q Science
Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: Peter Ellis
Date Deposited: 31 Oct 2016 12:21 UTC
Last Modified: 29 May 2019 18:06 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/58281 (The current URI for this page, for reference purposes)
Skinner, Benjamin M: https://orcid.org/0000-0002-7152-1167
Ellis, Peter J.I.: https://orcid.org/0000-0001-9709-7934
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