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

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.

Sex Determination Using RNA-Sequencing Analyses in Early Prenatal Pig Development

“…The LOC110255257, LOC100625207, LOC110255320, LOC110257894, and LOC396706 genes are located in the Y chromosome, however, they have not yet been fully characterized in Sus scrofa genome. According to Skinner et al [49], there are few data available on the porcine Y chromosome. Therefore, although these genes are located on this chromosome and have shown contribution to sex determination of pig conceptuses due to the discrepant reads CPM among samples, their functions will not be addressed in this study.…”

Spermatogenesis and the Evolution of Mammalian Sex Chromosomes

“…Sex-linked ampliconic gene families have been identified in several mammals, including mice [80], cattle [83], and humans [84]. Ampliconic gene regions vary dramatically in size and position, even among closely related mammals [3,4,81,85,86, Figure 2A]. In particular, ampliconic gene regions on the Y chromosome have been independently acquired and expanded multiple times in mammals (Table 1), with similar patterns of expression and high specificity to postmeiotic spermatogenesis [3,84].…”

“… A. Cladogram and Y chromosome sketches showing that the structure and size of the Y chromosome is highly variable even between closely related species, largely because of variation in the ampliconic regions [4,81,85,86,89]. Chromosome sketches for species marked with (*) show only the male specific region of the Y chromosome.…”

Did sex chromosome turnover promote divergence of the major mammal groups?

“…The Y chromosome is a relic of the X that degraded to different extents, leaving tiny overlapping sets of active genes 38. The male‐specific region of the human Y retains only 27 active genes, though some are present in multiple copies (mostly inactive); cat and pig Y chromosomes have slightly more 39 and mice fewer 40. Only two genes on the mouse Y are critical for a male phenotype and reproduction 41.…”