RT Journal
A1 Skinner, Benjamin M.
A1 Sargent, Carole A.
A1 Churcher, Carol
A1 Hunt, Toby
A1 Herrero, Javier
A1 Loveland, Jane E.
A1 Dunn, Matt
A1 Louzada, Sandra
A1 Fu, Beiyuan
A1 Chow, William
A1 Gilbert, James
A1 Austin-Guest, Siobhan
A1 Beal, Kathryn
A1 Carvalho-Silva, Denise
A1 Cheng, William
A1 Gordon, Daria
A1 Grafham, Darren
A1 Hardy, Matt
A1 Harley, Jo
A1 Hauser, Heidi
A1 Howden, Philip
A1 Howe, Kerstin
A1 Lachani, Kim
A1 Ellis, Peter J.I.
A1 Kelly, Daniel
A1 Kerry, Giselle
A1 Kerwin, James
A1 Ng, Bee Ling
A1 Threadgold, Glen
A1 Wileman, Thomas
A1 Wood, Jonathan M.D.
A1 Yang, Fengtang
A1 Harrow, Jen
A1 Affara, Nabeel A.
A1 Tyler-Smith, Chris
T1 The pig X and Y Chromosomes: structure, sequence, and evolution
JF Genome Research 
JO Genome Research 
YR 2016 
FD January 01 
VO 26 
IS 1 
SP 130 
OP 139 
DO 10.1101/gr.188839.114 
UL http://genome.cshlp.org/content/26/1/130.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 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.