{Reference Type}: Review
{Title}: Assembly of novel sequences for Chinese domestic pigs reveals new genes and regulatory variants providing new insights into their diversity.
{Author}: Du H;Diao C;Zhuo Y;Zheng X;Hu Z;Lu S;Jin W;Zhou L;Liu JF;
{Journal}: Genomics
{Volume}: 116
{Issue}: 2
{Year}: 2024 03 3
{Factor}: 4.31
{DOI}: 10.1016/j.ygeno.2024.110782
{Abstract}: There is an increasing understanding that a reference genome representing an individual cannot capture all the gene repertoire of a species. Here, we conduct a population-scale missing sequences detection of Chinese domestic pigs using whole-genome sequencing data from 534 individuals. We identify 132.41 Mb of sequences absent in the reference assembly, including eight novel genes. In particular, the breeds spread in Chinese high-altitude regions perform significantly different frequencies of new sequences in promoters than other breeds. Furthermore, we dissect the role of non-coding variants and identify a novel sequence inserted in the 3'UTR of the FMO3 gene, which may be associated with the intramuscular fat phenotype. This novel sequence could be a candidate marker for meat quality. Our study provides a comprehensive overview of the missing sequences in Chinese domestic pigs and indicates that this dataset is a valuable resource for understanding the diversity and biology of pigs.