Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
Mol Biol Rep. 2022 Feb;49(2):943-950. doi: 10.1007/s11033-021-06913-w. Epub 2021 Nov 2.
The mitogenomic heteroplasmy is the presence of multiple haplotypes in the mitochondria, which could cause genetic diseases and is also associated with many critical biological functions. The topmouth culter (Culter alburnus Basilewsky, 1855) is one of the most important freshwater fish in the family of Cyprinidae in China. At present, there are no reports on the topmouth culter's mtDNA heteroplasmy and the existence of which is not known.
This study aimed to analyze the mitogenomic heteroplasmy in the topmouth culter by the next-generation sequencing of the fins' total DNA. The results confirmed the existence of the heteroplasmy and indicated the presence of the extensive heteroplasmy in the topmouth culter's mitogenome. There were 38 heteroplasmic variations in the protein-coding genes from the three specimens, with 33 non-synonymous substitutions accounting for 86.84% and five synonymous substitutions accounting for 13.16%. Among them, the ND6 had the most heteroplasmic variations but only one synonymous substitution. After removing the putative nuclear mitochondrial DNA fragments, the ratio of primary haplotype in the three specimens was 43.89%, 74.72%, and 32.76%, respectively. The three specimens contained 21, 7, and 21 haplotypes of the mitogenomes, respectively. Due to the extensive heteroplasmy, we reconstructed the phylogenetic tree of the topmouth culter using the RY-coding method, which improved the performance of the phylogenetic tree to some extent.
This study reported the mitogenomic heteroplasmy in the topmouth culter and enhanced the knowledge regarding the mitogenomic heteroplasmy in phylogenetic studies. As the topmouth culter is a commercial species, the mitogenomic heteroplasmy is crucial for the fisheries management of the topmouth culter.
线粒体异质性是指线粒体中存在多种单倍型，这可能导致遗传疾病，并且与许多关键的生物学功能有关。翘嘴红鲌（Culter alburnus Basilewsky, 1855）是中国鲤科鱼类中最重要的淡水鱼类之一。目前，尚无关于翘嘴红鲌 mtDNA 异质性的报道，其存在与否尚不清楚。
本研究旨在通过对鳍总 DNA 的下一代测序来分析翘嘴红鲌的线粒体异质性。结果证实了异质性的存在，并表明翘嘴红鲌线粒体基因组中存在广泛的异质性。从三个样本的蛋白质编码基因中发现了 38 个异质变异，其中 33 个是非同义替换，占 86.84%，5 个同义替换，占 13.16%。其中，ND6 异质性变异最多，但只有一个同义替换。去除可能的核线粒体 DNA 片段后，三个样本的主要单倍型比例分别为 43.89%、74.72%和 32.76%。三个样本的线粒体基因组分别包含 21、7 和 21 种单倍型。由于广泛的异质性，我们使用 RY 编码方法重建了翘嘴红鲌的系统发育树，这在一定程度上提高了系统发育树的性能。
本研究报道了翘嘴红鲌的线粒体异质性，增加了对系统发育研究中线粒体异质性的认识。由于翘嘴红鲌是一种商业物种，线粒体异质性对翘嘴红鲌的渔业管理至关重要。
