Am I repeating myself? Determining the repetitive landscape of the pig X chromosome

Mammalian sex chromosomes evolved from a homologous pair of autosomes via the acquisition of a major sex determining gene. This event led to the suppression of recombination between the chromosomes and consequently their independent evolution. Both X and Y have been observed to accumulate amplified gene families in mice and humans, but it remains unclear to what extent this is true in other mammalian species. The pig X chromosome was recently sequenced to a high quality and in this study, it was investigated to determine the presence and extent of potential amplicons. LASTZ was used to align the pig X sequence to itself and identify regions of similarity that could represent ampliconic sequences. Further analysis revealed many of the similarities to be interspersed along the chromosome, and in some cases particularly clustered around the centromere. This distribution of hits suggests many of the similarities to be the result of known repetitive elements which commonly cluster within centromeric and pericentromeric regions. There were also some regions showing segmental duplications and gene duplications. Further investigation of the hits through NCBI BLAST revealed them to be fragments of LINE-1 (Long Interspersed Nuclear Element 1) retrotransposons, orthologues of duplicated genes, and uncharacterised loci. Mammalian X chromosomes are often enriched with LINE-1s which are thought to play a role in X-inactivation and controlling gene expression. Some of the duplicated genes are of potential interest for further analysis as their function is unknown. At this stage, no independent amplicons have been found in the pig X chromosome, in contrast to what has been observed in humans and mice. However, the current assembly contains gaps between contigs and unmasked repeats which may obscure where potential amplicons might be found. The data from this study can be used to improve the current annotation of the pig X chromosome.