PT - JOURNAL ARTICLE AU - Benjamin M. Skinner AU - Carole A. Sargent AU - Carol Churcher AU - Toby Hunt AU - Javier Herrero AU - Jane Loveland AU - Matt Dunn AU - Sandra Louzada AU - Beiyuan Fu AU - William Chow AU - James Gilbert AU - Siobhan Austin-Guest AU - Kathryn Beal AU - Denise Carvalho-Silva AU - William Cheng AU - Daria Gordon AU - Darren Grafham AU - Matt Hardy AU - Jo Harley AU - Heidi Hauser AU - Philip Howden AU - Kerstin Howe AU - Kim Lachani AU - Peter J.I. Ellis AU - Daniel Kelly AU - Giselle Kerry AU - James Kerwin AU - Bee Ling Ng AU - Glen Threadgold AU - Thomas Wileman AU - Jonathan M D Wood AU - Fengtang Yang AU - Jen Harrow AU - Nabeel A. Affara AU - Chris Tyler-Smith TI - The pig X and Y chromosomes: structure, sequence and evolution AID - 10.1101/012914 DP - 2014 Jan 01 TA - bioRxiv PG - 012914 4099 - http://biorxiv.org/content/early/2014/12/19/012914.short 4100 - http://biorxiv.org/content/early/2014/12/19/012914.full AB - 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, and incorporating information from optical mapping and fibre-FISH. The X chromosome carries 1,014 annotated genes, 689 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 (e.g. the cancer/testis antigen family) or inactive (e.g. AWAT1), and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y chromosome assembly focussed on 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. The long arm of the chromosome is almost entirely repetitive, containing previously characterised sequences. 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, to compare the pig X and Y chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y chromosome evolution.