College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China.
PLoS One. 2019 Nov 8;14(11):e0224677. doi: 10.1371/journal.pone.0224677. eCollection 2019.
Chicken mitochondrial DNA is a circular molecule comprising ~16.8 kb. In this study, we used next-generation sequencing to investigate mitochondrial heteroplasmy in the whole chicken mitochondrial genome. Based on heteroplasmic detection thresholds at the 0.5% level, 178 cases of heteroplasmy were identified in the chicken mitochondrial genome, where 83% were due to nucleotide transitions. D-loop regionwas hot spot region for mtDNA heteroplasmy in the chicken since 130 cases of heteroplasmy were located in these regions. Heteroplasmy varied among intraindividual tissues with allele-specific, position-specific, and tissue-specific features. Skeletal muscle had the highest abundance of heteroplasmy. Cases of heteroplasmy at mt.G8682A and mt.G16121A were validated by PCR-restriction fragment length polymorphism analysis, which showed that both had low ratios of heteroplasmy occurrence in five natural breeds. Polymorphic sites were easy to distinguish. Based on NGS data for crureus tissues, mitochondrial mutation/heteroplasmy exhibited clear maternal inheritance features at the whole mitochondrial genomic level. Further investigations of the heterogeneity of the mt.A5694T and mt.T5718G transitions between generations using pyrosequencing based on pedigree information indicated that the degree of heteroplasmy and the occurrence ratio of heteroplasmy decreased greatly from the F0 to F1 generations in the mt.A5694T and mt.T5718G site. Thus, the intergenerational transmission of heteroplasmy in chicken mtDNA exhibited a rapid shift toward homoplasmy within a single generation. Our findings indicate that heteroplasmy is a widespread phenomenon in chicken mitochondrial genome, in which most sites exhibit low heteroplasmy and the allele frequency at heteroplasmic sites changes significantly during transmission events. It suggests that heteroplasmy may be under negative selection to some degree in the chicken.
鸡线粒体 DNA 是一种圆形分子，大小约为 16.8kb。在本研究中，我们使用下一代测序技术研究了整个鸡线粒体基因组中的线粒体异质性。基于 0.5%水平的异质性检测阈值，在鸡线粒体基因组中发现了 178 个异质性病例，其中 83%是由于核苷酸转换引起的。D-环区域是鸡线粒体 DNA 异质性的热点区域，因为 130 个异质性病例位于这些区域。异质性在个体组织之间存在等位基因特异性、位置特异性和组织特异性。骨骼肌具有最高的异质性丰度。通过 PCR-限制性片段长度多态性分析验证了 mt.G8682A 和 mt.G16121A 的异质性病例，结果表明这两个位点在五个自然品种中的异质性发生率都较低。多态性位点易于区分。基于 crureus 组织的 NGS 数据，线粒体突变/异质性在整个线粒体基因组水平上表现出明显的母系遗传特征。进一步使用基于系谱信息的焦磷酸测序研究代际间 mt.A5694T 和 mt.T5718G 转换的异质性表明，在 mt.A5694T 和 mt.T5718G 位点，从 F0 到 F1 代，异质性的程度和异质性的发生率大大降低。因此，鸡 mtDNA 中异质性的代际传递在单个世代内迅速向同质性转变。我们的研究结果表明，异质性是鸡线粒体基因组中的一种普遍现象，其中大多数位点的异质性程度较低，在传递事件中异质性位点的等位基因频率变化显著。这表明异质性在某种程度上可能受到鸡的负选择。
