RT Journal Article SR Electronic T1 The pig X and Y chromosomes: structure, sequence and evolution JF bioRxiv FD Cold Spring Harbor Laboratory SP 012914 DO 10.1101/012914 A1 Benjamin M. Skinner A1 Carole A. Sargent A1 Carol Churcher A1 Toby Hunt A1 Javier Herrero A1 Jane Loveland A1 Matt Dunn A1 Sandra Louzada A1 Beiyuan Fu A1 William Chow A1 James Gilbert A1 Siobhan Austin-Guest A1 Kathryn Beal A1 Denise Carvalho-Silva A1 William Cheng A1 Daria Gordon A1 Darren Grafham A1 Matt Hardy A1 Jo Harley A1 Heidi Hauser A1 Philip Howden A1 Kerstin Howe A1 Kim Lachani A1 Peter J.I. Ellis A1 Daniel Kelly A1 Giselle Kerry A1 James Kerwin A1 Bee Ling Ng A1 Glen Threadgold A1 Thomas Wileman A1 Jonathan M D Wood A1 Fengtang Yang A1 Jen Harrow A1 Nabeel A. Affara A1 Chris Tyler-Smith YR 2014 UL http://biorxiv.org/content/early/2014/12/19/012914.abstract 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.