College of Life Science and Technology, Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, China.
School of Life Sciences, Xiamen University, Xiamen 361102, China.
Genes (Basel). 2023 Jan 2;14(1):128. doi: 10.3390/genes14010128.
In the last decade, the phylogenetic relationships within the genus have become controversial, due to a lack of molecular data. The mitochondrial genome plays a vital role in the reconstruction of phylogenetic relationships and in revealing the molecular evolution of bony fishes. Herein, we obtained the complete mitogenome of via HiFi reads of the Pacbio Sequel II system and DNBSEQ short-reads. We compared all available mitogenomes of the genus and reconstructed the phylogeny of Nemacheilidae, based on the mitogenomes, using maximum likelihood (ML) methods. The results show that the complete mitogenome sequence of was circular and 16,568 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA), 2 ribosomal RNA (rRNA), and a typical control region (D-loop). The most common start codons were ATG, except for , and TAA/TAG were the stop codons for all PCGs. In total, 677 SNPs and 9 INDELs have been found by comparing the sequence divergence between this study and previous reports. Purity selection was found in all PCGs. Phylogeny was inferred by analyzing the 13 PCGs and the concatenated nucleotide sequences of 30 mitogenomes. The phylogenetic analyses based on the nucleotides of the 13 PCGs supported the assumption that the genus can be divided into 4 main clades and demonstrated that and are closely related species for the first time. This study laid the foundation for further study on the mitogenome and phylogeny of Nemacheilidae fishes.
在过去的十年中，由于缺乏分子数据，属内的系统发育关系变得备受争议。线粒体基因组在重建系统发育关系和揭示硬骨鱼类的分子进化方面发挥着重要作用。在此，我们通过 Pacbio Sequel II 系统的 HiFi 读取和 DNBSEQ 短读取获得了 通过 HiFi 读取和 DNBSEQ 短读取获得了 的完整线粒体基因组。我们比较了属内所有可用的线粒体基因组，并基于线粒体基因组，使用最大似然 (ML) 方法重建了 Nemacheilidae 的系统发育关系。结果表明， 的完整线粒体基因组序列为圆形，长度为 16568bp，包括 13 个蛋白编码基因 (PCGs)、22 个转移 RNA (tRNA)、2 个核糖体 RNA (rRNA) 和一个典型的控制区 (D-loop)。除了 之外，最常见的起始密码子是 ATG，所有 PCGs 的终止密码子都是 TAA/TAG。通过比较本研究与以往报道的序列差异，共发现 677 个 SNP 和 9 个 INDEL。所有 PCGs 都存在纯化选择。通过分析 13 个 PCGs 和 30 个线粒体基因组的核苷酸序列推断出系统发育关系。基于 13 个 PCGs 核苷酸的系统发育分析支持了属可以分为 4 个主要分支的假设，并首次证明 和 是密切相关的物种。本研究为进一步研究 Nemacheilidae 鱼类的线粒体基因组和系统发育关系奠定了基础。
