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

Skinner, Benjamin M and Sargent, Carole A and Churcher, Carol and Hunt, Toby and Herrero, Javier and Loveland, Jane E and Dunn, Matt and Louzada, Sandra and Fu, Beiyuan and Chow, William and Gilbert, James and Austin-Guest, Siobhan and Beal, Kathryn and Carvalho-Silva, Denise and Cheng, William and Gordon, Daria and Grafham, Darren and Hardy, Matt and Harley, Jo and Hauser, Heidi and Howden, Philip and Howe, Kerstin and Lachani, Kim and Ellis, Peter JI and Kelly, Daniel and Kerry, Giselle and Kerwin, James and Ng, Bee Ling and Threadgold, Glen and Wileman, Thomas and Wood, Jonathan MD and Yang, Fengtang and Harrow, Jen and Affara, Nabeel A and Tyler-Smith, Chris (2016) 'The pig X and Y Chromosomes: structure, sequence, and evolution.' Genome Research, 26 (1). pp. 130-139. ISSN 1054-9803

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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
Uncontrolled Keywords: Chromosomes, Mammalian; X Chromosome; Y Chromosome; Animals; Swine; Dogs; Cats; Humans; Sequence Alignment; Sequence Analysis, DNA; Evolution, Molecular; Gene Expression; Gene Conversion; Base Sequence; Gene Order; Gene Library; Molecular Sequence Data; Female; Male
Divisions: Faculty of Science and Health
Faculty of Science and Health > Life Sciences, School of
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 13 Jan 2020 10:59
Last Modified: 18 Aug 2022 12:29

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