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苗菁, 李继姬, 叶莹莹, 郭宝英, 徐开达. 陆川小笠贝线粒体全基因组测序及笠贝科系统发育分析[J]. 水生生物学报, 2023, 47(8): 1248-1260. DOI: 10.7541/2023.2022.0316
引用本文: 苗菁, 李继姬, 叶莹莹, 郭宝英, 徐开达. 陆川小笠贝线粒体全基因组测序及笠贝科系统发育分析[J]. 水生生物学报, 2023, 47(8): 1248-1260. DOI: 10.7541/2023.2022.0316
MIAO Jing, LI Ji-Ji, YE Ying-Ying, GUO Bao-Ying, XU Kai-Da. COMPLETE MITOCHONDRIAL GENOME SEQUENCING OF LOTTIA LUCHUANA AND PHYLOGENTIC ANALYSIS OF THE FAMILY LOTTIIDAE[J]. ACTA HYDROBIOLOGICA SINICA, 2023, 47(8): 1248-1260. DOI: 10.7541/2023.2022.0316
Citation: MIAO Jing, LI Ji-Ji, YE Ying-Ying, GUO Bao-Ying, XU Kai-Da. COMPLETE MITOCHONDRIAL GENOME SEQUENCING OF LOTTIA LUCHUANA AND PHYLOGENTIC ANALYSIS OF THE FAMILY LOTTIIDAE[J]. ACTA HYDROBIOLOGICA SINICA, 2023, 47(8): 1248-1260. DOI: 10.7541/2023.2022.0316

陆川小笠贝线粒体全基因组测序及笠贝科系统发育分析

COMPLETE MITOCHONDRIAL GENOME SEQUENCING OF LOTTIA LUCHUANA AND PHYLOGENTIC ANALYSIS OF THE FAMILY LOTTIIDAE

  • 摘要: 为对笠贝科进行系统发育分析, 研究通过二代测序技术得到了陆川小笠贝(Lottia luchuana)的线粒体全基因组, 对基因组基本结构特点做了分析, 发现共含有38个基因, 包含13个蛋白质编码基因(PCGs), 2个RNA, 23个tRNA。对碱基含量分析发现T碱基含量最高为32.34%, C碱基最低为14.99%, 选择笠贝科13个物种的线粒体基因组进行选择压力分析发现所有PCGs都受到纯化选择。另外通过结合腹足纲下6个亚纲的线粒体基因组的13个PCGs构建了系统发育树, 发现笠贝科为单系群, 与帽贝科Patellidae具有较近的亲缘关系。对笠形腹足亚纲的线粒体基因重排进行比较发现笠贝科在笠形腹足亚纲中表现出最广泛的不规律的重排。从重建的笠形腹足亚纲的分歧时间的年代图谱, 得到笠贝的分化最早发生在中生代侏罗纪时期, 在新生代物种大量分化。研究结果有助于理解不同笠贝物种的亲缘关系, 以及腹足纲内各亚纲之间的进化地位与关系。

     

    Abstract: The family Lottiidae (Gray 1840) is one of the most primitive gastropods in existence, and the mitochondrial gene (mitogenome) have been used to analyze the phylogenetic relationship in Patellogastropoda, but the complete mitogenome of some species in Lottiidae have not been mentioned. In this study, we obtained the complete mitogenome of Lottia luchuana by next-generation sequencing technology, and analyzed the basic characteristics of its genome, and we found that it contains 38 genes, including 13 protein-coding genes (PCGs), two RNAs, 23 tRNAs, one more trnM than most Gastropoda species. The base content analysis showed that T base content was the highest at 32.34%, and C base content was the lowest at 14.99%. Gly, Phe, Ser and Val were the four most commonly used amino acids, UUA (Leu2), UUU (Phe), CCU (Pro) and AGA (Ser2) are the four most commonly used codons. We selected the mitogenomes of Lottiidae 13 species for selection pressure analysis and all PCGs had a Ka/Ks ratio below 1 and were subjected to purification selection. In addition, a phylogenetic tree was constructed by combining the 13 PCGs of the mitogenomes of six subclass under Gastropoda, and the Lottiidae is a monophyletic group, and has a relatively close relationship with Patellidae, but the results of this analysis are still affected by the attraction of long branches, so that the branch of Patellogastropoda is divided into two parts, but with the increase of species richness, it may gradually resist the attraction of long branches. A linear sequence comparison of the mitogenomes of all species of Patellogastropoda showed that Lottiidae showed the most extensive irregular rearrangement in Patellogastropoda, and also changed in the number of tRNAs. From the reconstructed chronological map of the divergence time of Patellogastropoda, it is concluded that the differentiation of limpet first occurred in the Jurassic period of the Mesozoic, and a large number of species diverged rapidly in the Cenozoic. These results will help people better understand the phylogenetic relationship between limpet, as well as the evolutionary relationship and evolutionary status of each subclass within the Gastropoda, provide more reference for species classification.

     

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