School of Life Sciences, Xiamen University, Xiamen 361102, China.
CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
Int J Mol Sci. 2023 May 15;24(10):8756. doi: 10.3390/ijms24108756.
Lampriform fishes (Lampriformes), which primarily inhabit deep-sea environments, are large marine fishes varying from the whole-body endothermic opah to the world's longest bony fish-giant oarfish, with species morphologies varying from long and thin to deep and compressed, making them an ideal model for studying the adaptive radiation of teleost fishes. Moreover, this group is important from a phylogenetic perspective owing to their ancient origins among teleosts. However, knowledge about the group is limited, which is, at least partially, due to the dearth of recorded molecular data. This study is the first to analyze the mitochondrial genomes of three lampriform species ( and ) and infer a time-calibrated phylogeny, including 68 species among 29 orders. Our phylomitogenomic analyses support the classification of Lampriformes as monophyletic and sister to Acanthopterygii; hence, addressing the longstanding controversy regarding the phylogenetic status of Lampriformes among teleosts. Comparative mitogenomic analyses indicate that tRNA losses existed in at least five Lampriformes species, which may reveal the mitogenomic structure variation associated with adaptive radiation. However, codon usage in Lampriformes did not change significantly, and it is hypothesized that the nucleus transported the corresponding tRNA, which led to function substitutions. The positive selection analysis revealed that and were positively selected in opah, which might have co-evolved with the endothermic trait. This study provides important insights into the systematic taxonomy and adaptive evolution studies of Lampriformes species.
灯笼鱼目鱼类（Lampriformes）主要栖息在深海环境中，是从全身温血的月鱼到世界上最长的硬骨鱼——皇带鱼的大型海洋鱼类，其物种形态从长而细到深而压缩不等，是研究硬骨鱼类适应性辐射的理想模型。此外，由于它们在硬骨鱼中的古老起源，这个群体从系统发育的角度来看也很重要。然而，由于记录的分子数据匮乏，人们对该群体的了解有限。本研究首次分析了三种灯笼鱼目物种（ 和 ）的线粒体基因组，并推断出一个时间校准的系统发育关系，包括 29 个目中的 68 个种。我们的系统发生线粒体基因组分析支持将灯笼鱼目作为单系群与棘鳍鱼亚纲并列的分类地位；从而解决了关于硬骨鱼中灯笼鱼目系统发育地位的长期争议。比较线粒体基因组分析表明，至少有五种灯笼鱼目物种存在 tRNA 丢失，这可能揭示了与适应性辐射相关的线粒体基因组结构变异。然而，灯笼鱼目的密码子使用没有发生显著变化，据推测，核将相应的 tRNA 运输到细胞核，从而导致功能替代。阳性选择分析表明，月鱼中的 和 受到正选择，这可能与温血特性共同进化。本研究为灯笼鱼目物种的系统分类学和适应性进化研究提供了重要的见解。
