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.
摘要：
越来越多的理解是代表个体的参考基因组不能捕获物种的所有基因库。这里,我们使用来自534个个体的全基因组测序数据,对中国家猪进行了群体规模的缺失序列检测.我们鉴定了132.41Mb在参考装配中不存在的序列，包括八个新基因。特别是,与其他品种相比，在中国高海拔地区传播的品种在启动子中出现新序列的频率显着不同。此外，我们剖析了非编码变体的作用，并鉴定了插入FMO3基因的3UTR中的新序列，这可能与肌内脂肪表型有关。这种新序列可能是肉质的候选标记。我们的研究提供了中国家猪缺失序列的全面概述，并表明该数据集是了解猪的多样性和生物学的宝贵资源。
