Liang Xinjie, Sun Yuman, Chen Jian, Li Jiji, Ye Yingying
National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
Biochem Genet. 2024 Oct 29. doi: 10.1007/s10528-024-10948-6.
The systematic phylogeny of Pleocyemata species, particularly within the family Nephropidae, remains incomplete. In order to enhance the taxonomy and systematics of Nephropidae within the evolutionary context of Pleocyemata, we embarked upon a comprehensive study aiming to elucidate the phylogenetic position of Nephropsis grandis. Consequently, we determined the complete mitochondrial DNA sequence for N. grandis. The circular genome spans a length of 15,344 bp and exhibits a gene composition analogous to that observed in other metazoans, encompassing a comprehensive set of 37 genes. Additionally, the genome features an AT-rich region. The rRNAs exhibited the highest AT content among the 37 genes (70.41%), followed by tRNAs (67.42%) and protein-coding genes (PCGs) (62.76%). The absence of a dihydrouracil arm in trnS1 prevented the formation of the canonical cloverleaf secondary structure. Selective pressure analysis indicated that the PCGs underwent purifying selection. The Ka/Ks ratios for cox1, cox2, cox3, and cob were considerably lower compared to other PCGs, implying strong purifying selection acting upon these particular genes. The mitochondrial gene order in N. grandis was consistent with the reported order in ancestral Pleocyemata. Phylogenetic revealed that N. grandis forms a cluster with the genus Metanephrops, and this cluster further groups with Homarus and the genus Nephrops within the Nephropidae family. These findings provide robust support for N. grandis as an ancestral member of the Nephropidae family. This study highlights the significance of employing complete mitochondrial genomes in phylogenetic analysis and deepens our understanding of the evolution of the Nephropidae family.
十足目物种的系统发育，尤其是龙虾科内部的系统发育，仍然不完整。为了在十足目的进化背景下加强龙虾科的分类学和系统学研究，我们开展了一项全面研究，旨在阐明大新对虾的系统发育位置。因此，我们测定了大新对虾的完整线粒体DNA序列。这个环状基因组长度为15344碱基对，其基因组成与其他后生动物中观察到的类似，包含一套完整的37个基因。此外，该基因组有一个富含AT的区域。在这37个基因中，rRNA的AT含量最高（70.41%），其次是tRNA（67.42%）和蛋白质编码基因（PCG）（62.76%）。trnS1中缺乏二氢尿嘧啶臂，阻止了典型三叶草二级结构的形成。选择压力分析表明，PCG经历了纯化选择。与其他PCG相比，cox1、cox2、cox3和cob的Ka/Ks比值要低得多，这意味着这些特定基因受到了强烈的纯化选择。大新对虾的线粒体基因顺序与已报道的原始十足目的顺序一致。系统发育分析表明，大新对虾与新对虾属形成一个聚类，并且这个聚类在龙虾科内进一步与螯龙虾属和龙虾属归为一组。这些发现为大新对虾作为龙虾科的原始成员提供了有力支持。这项研究强调了在系统发育分析中使用完整线粒体基因组的重要性，并加深了我们对龙虾科进化的理解。
