基于家系基因组测序对骡基因组结构多样性分析

为分析马(Equus caballus)和驴(Equus asinus)杂交后两套结构和功能完善的独立基因组在骡基因组中整合后的结构多样性,本研究以马属动物三成员家系的全基因组序列为研究对象,分别以纯血马基因组和驴基因组为参考,识别驴、马和骡的InDel、SNP和CNV;通过生物信息分析,分析骡的de novo SNP及其突变频率、识别骡特异性CNV,并进行功能分析。结果显示:1)驴、马和骡分别获得100.01、103.78和114.36 Gb 的高质量Illumina基因组测序数据。2)以纯血马基因组为参考,识别的InDels、SNPs和CNVs分别为402 533~2 110 786、5 012 403~23 819 055和2 126~3 761;以驴基因组为参考,识别的InDels、SNPs和CNVs分别为527 351~2 279 875、3 212 499~23 549 224和3 572~7 812。3)骡de novo SNPs分别为555和419,其突变频率为1.72×10^-7~2.21×10^-7。4)获得骡特异性CNVs分别为396和859,总长度分别为2.15和3.77 Mb。5)变异相关基因主要和机体的免疫及癌症过程相关。综上,骡基因组发生了高频率的de novo SNPs和特异性CNVs,这些结构变异可能对马和驴异种杂交不相容以及骡的遗传适应性具有重要意义,为进一步开展马和驴异种杂交的遗传基础及其分子机制的研究提供候选遗传位点。

Structural diversity analysis of mule genome based on family genome sequencing

In order to analyze the structural diversity of the mule genome combining the two sets of perfectly functional and structurally well-characterized genetic programs after hybridization between horses(Equus caballus)and donkeys(Equus asinus), the study identified InDel, SNP, and CNV for the donkeys, horses, and mules, basing on the whole-genome sequences from an Equus parent-offspring trio and using the Thoroughbred genome and donkey genome as reference. Through bioinformatics analysis, the de novo SNP and its mutation frequency of mule were analyzed, the mule specific CNV was identified, and functional analysis was carried out. The results showed that: 1)for the donkey, horse and mule, 100. 01, 103. 78 and 114. 36 Gb high-quality Illumina genome sequencing data were generated, respectively. 2)Using the Thoroughbred genome as reference, the identified InDels, SNPs and CNVs were 402 533-2 110 786, 5 012 403-23 819 055 and 2 126-3 761, respectively. Using the donkey genome as reference, the identified InDels, SNPs and CNVs were 527 351-2 279 875, 3 212 499-23 549 224 and 3 572-7 812. 3)De novo SNPs of mule were 555 and 419, respectively, with a mutation frequency of 1. 72×10^-7 -2. 21×10^-7. 4)A total of 396 and 859 mule-specific CNVs were also identified, with a total length of 2. 15 and 3. 77 Mb, respectively. 5)The genes associated with the structural variation were mainly involved in immune processes and cancer processes. In summary, the genome of the mule exhibits high frequency of de novo SNPs and specific CNVs, which may be of great significance for the incompatibility of interspecific hybridization between horses and donkeys and the genetic adaptability of mules. These structural variations provides candidate genetic sites for further research on the genetic basis and molecular mechanisms of the crossing of horses and donkeys.