8种石首鱼类线粒体基因组特征及分子系统进化分析

Analysis of the mitochondrial genome characteristics and phylogenetic relationships of eight sciaenid fishes

为探讨石首鱼科(Sciaenidae)鱼类分子系统进化关系,采用生物信息学方法分析了黑鳃梅童鱼(Collichthys niveatus)、棘头梅童鱼(C.lucidus)、大黄鱼(Larimichthys crocea)、小黄鱼(L.polyactis)、鮸鱼(Miichthys miiuy)、白姑鱼(Pennahia argentata)、黄姑鱼(Nibea albiflora)和皮氏叫姑鱼(Johnius belangerii)共8种石首鱼类线粒体基因组全序列的基本特征。结果显示,除皮氏叫姑鱼外,其余7种石首鱼类编码的37个基因排列顺序与脊椎动物线粒体基因组相同。基因组碱基分布存在不均衡现象,A+T含量高于G+C含量。线粒体基因组的基因变异位点分析结果表明,ND4和ND5基因可作为COI基因的辅助分子标记,应用于石首鱼类群体遗传学的研究中。黄鱼亚科5种鱼类13个蛋白质编码基因的Ka/Ks比值远低于1,显示出较强的纯化选择。皮氏叫姑鱼与其他石首鱼间的遗传距离均较大且亲缘关系较远,暗示叫姑鱼属或为石首鱼类中较为原始的类群。基于线粒体基因组全序列构建NJ系统树支持黄鱼亚科和白姑鱼亚科亲缘关系较近的形态学结论。而基于去除控制区后序列和13个蛋白质编码基因序列构建的系统树则表明两亚科鱼类间的差别在非编码区更为明显。

To explore the phylogenetic relationships of sciaenid fishes, the basic characteristics of mitochondrial genomes in eight sciaenid fishes （Collichthys niveatus, C. lucidus, Larimichthys crocea, L. polyactis, Miichthys miiuy, Pennahia argentata, Nibea albiflora, and Johnius belangerii） were revealed by comprehensive bioinformatic analysis. The results showed that mitochondrial genomes contained 37 standard vertebrate genes, and the order was identical except for in J. belangerii. The base distribution was not balanced, and the content of A＋T was higher than that of G＋C. Genetic variation analysis of 13 protein-coding genes and 2 ribosomal RNA genes among sciaenid fishes showed that the ND4 and ND5 genes could be used as supplementary molecular markers to the COI gene and applied to research on population genetic diversity. The Ka/Ks ratios of 13 mitochondrial protein-coding genes in five Pseudosciaeninae fishes were much lower than 1, indicating strong purifying selection. The genetic distances between J. belangerii and other sciaenid fishes were high, and relationships were distant, which suggested that Johnius fishes might be the relatively primitive group. A neighbor-joining phylogenetic tree based on the complete mitochondrial genome supported the morphological conclusion that fishes of Pseudosciaeninae and Argyrosominae were closely related. Furthermore, phylogenetic trees based on sequences deleting the control region and 13 protein-coding genes showed that the differences between these two subfamilies were much more evident.