Chen Jiajie, Wang Xiaodong, Zeng Sheng, Tian Wei, Yang Deyuan, Ye Jinqing, Zhong Junsheng, Jiang Chaopeng
Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, 201306, Shanghai, China.
East China Sea Fisheries Research Institute, Fisheries Science of Chinese Academy, 200090, Shanghai, China.
Zookeys. 2024 Dec 4;1219:249-270. doi: 10.3897/zookeys.1219.130546. eCollection 2024.
The complete mitochondrial genome and phylogenetic analysis for from the South China Sea was performed using shallow genome skimming. For accurate species identification and redescription, morphometric and meristic characters were examined and compared with previous descriptions. To facilitate the identification of species and to enable comparison with the mitochondrial genome phylogeny, molecular comparisons were conducted using three mitochondrial genes: large ribosomal RNA ( rRNA), cytochrome c oxidase subunit 1 (), and NADH dehydrogenase (). The mitogenome (16 398 bp) comprised 38 mitochondrial genes, similar to most bony fishes: 13 protein-coding genes (PCGs), 2 rRNA and 22 transfer RNA genes, and 1 non-coding region. The complete mitogenome comprised 30.7% A, 24.2% T, 15.0% G, and 30.1% C. The A+T content (54.9%) was higher than the G+C content (45.1%). All PCGs started with the typical ATG codon, except , which started with GTG. Seven PCGs ended with incomplete stop codons (TA or T). The Ka/Ks ratios of all PCGs were < 1, indicating purifying selection. The phylogenies of Leiognathidae, both based on the amino acid sequences of the 13 PCGs and the single genes RNA and , were monophyletic with high nodal support (> 75%). (NC 026232) is believed to be a species, whereas (NC 057225) is not classified under in the NCBI database. The phylogenetic trees divided the Leiognathidae family into three clades. The mitogenome phylogeny suggested that the Leiognathidae and Chaetodontidae clades are sister groups. These findings provide important genetic data for population genetics research and a phylogenetic analysis of Leiognathidae.
利用浅层基因组重测序技术对来自中国南海的[具体物种名称未给出]进行了完整线粒体基因组测序及系统发育分析。为了进行准确的物种鉴定和重新描述，对形态测量和可数性状进行了检查，并与之前的描述进行了比较。为便于物种鉴定并与线粒体基因组系统发育进行比较，使用三个线粒体基因进行了分子比较：大核糖体RNA（rRNA）、细胞色素c氧化酶亚基1（[具体基因名称未给出]）和NADH脱氢酶（[具体基因名称未给出]）。线粒体基因组（16398 bp）包含38个线粒体基因，与大多数硬骨鱼类相似：13个蛋白质编码基因（PCGs）、2个rRNA和22个转移RNA基因，以及1个非编码区。完整的线粒体基因组中，A占30.7%，T占24.2%，G占15.0%，C占30.1%。A+T含量（54.9%）高于G+C含量（45.1%）。除了[具体基因名称未给出]以GTG起始外，所有PCGs均以典型的ATG密码子起始。7个PCGs以不完全终止密码子（TA或T）结束。所有PCGs的Ka/Ks比值均<1，表明存在纯化选择。基于13个PCGs以及单个基因rRNA和[具体基因名称未给出]的氨基酸序列构建的银鲈科系统发育树均为单系，且节点支持率较高（>75%）。[具体物种名称未给出1]（NC 026232）被认为是一个[具体物种名称未给出1]物种，而[具体物种名称未给出2]（NC 057225）在NCBI数据库中未被归类在[具体物种名称未给出1]之下。系统发育树将银鲈科分为三个分支。线粒体基因组系统发育分析表明，银鲈科和蝴蝶鱼科分支是姐妹群。这些发现为银鲈科的群体遗传学研究和系统发育分析提供了重要的遗传数据。
