Tan Suxu, Wang Wenwen, Li Jinjiang, Sha Zhenxia
Institute of Aquatic Biotechnology, College of Life Sciences, Qingdao University, Qingdao, Shandong, 266071, China.
Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China.
BMC Genomics. 2025 Jan 20;26(1):50. doi: 10.1186/s12864-025-11204-w.
Pleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species.
Our analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices.
This study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations.
鲽形目鱼类，也被称为比目鱼，是重要的模式动物和经济动物。然而，对其重要细胞器线粒体进行全面的基因组研究却很有限。因此，我们旨在分析111种比目鱼线粒体基因组的结构、密码子偏好、核苷酸多样性、选择压力和重复序列，并重建系统发育关系。
我们的分析揭示了蛋白质编码基因和rRNA基因的基因含量保守，但不同物种的tRNA基因和控制区数量不同。在比目鱼物种中发现了各种基因重排，特别是在牙鲆科中nad5-nad6-cytb基因块的重排、鲾鲼科中nad6和cytb基因的交换重排，以及舌鳎亚科中控制区易位和tRNA-Gln基因倒位，这表明它们独特的进化历史和/或功能优势。密码子使用表现出明显的偏好，腺嘌呤是第三密码子位置最常见的核苷酸。核苷酸多样性和选择压力分析表明，不同的蛋白质编码基因经历了不同程度的进化压力，cytb和cox基因是最保守的。使用整个线粒体基因组信息和串联独立比对的蛋白质编码基因进行的系统发育分析在很大程度上反映了物种的分类，但显示出不同的系统发育关系。简单序列重复和各种长重复序列的鉴定增加了基因组组织的复杂性，并为进化研究和育种实践提供了标记。
本研究在我们对比目鱼线粒体基因组的理解方面迈出了重要一步，为比目鱼线粒体基因组的结构、保守性和变异提供了有价值的见解，对理解它们的进化历史、功能基因组学和渔业管理具有重要意义。未来的研究可以更深入地探讨保护生物学、进化生物学和变异的功能用途。
