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非洲月鱼(Gill 1863)在东大西洋的地方辐射:鲹科(硬骨鱼纲:鲹形目)的线粒体基因组特征与系统发育意义。

Endemic Radiation of African Moonfish, (Gill 1863), in the Eastern Atlantic: Mitogenomic Characterization and Phylogenetic Implications of Carangids (Teleostei: Carangiformes).

机构信息

Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea.

Fisheries Commission, Ministry of Fisheries and Aquaculture Development, Fisheries Scientific Survey Division, Tema P.O. Box BT 62, Ghana.

出版信息

Biomolecules. 2024 Sep 25;14(10):1208. doi: 10.3390/biom14101208.

DOI:10.3390/biom14101208
PMID:39456141
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11506752/
Abstract

This study offers an in-depth analysis of the mitochondrial genome of (Gill 1863), a species native to the Eastern Atlantic Ocean. The circular mitochondrial DNA molecule measures 16,541 base pairs and comprises 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a control region (CR). The nucleotide composition exhibits a notable adenine-thymine (AT) bias, accounting for 53.13%, which aligns with other species in the Carangidae family. Most PCGs initiate with the ATG codon, with the exception of Cytochrome C oxidase subunit I, which starts with GTG. Analysis of relative synonymous codon usage reveals that leucine and serine are the most prevalent amino acids in the mitochondrial genome of and its congeners ( and ). All tRNAs display the typical cloverleaf structure, though (S1) lacks a dihydrouracil arm. Pairwise comparisons of synonymous and nonsynonymous substitutions for all PCGs yielded values below '1', indicating strong purifying selection. The CR spans 847 bp, representing 5.12% of the mitochondrial genome, and is characterized by high AT content (62.81%). It is situated between (TGG) and (GAA). The CR contains conserved sequence blocks, with CSB-1 being the longest at 22 bp and CSB-D the shortest at 18 bp. Phylogenetic analysis, using Bayesian and Maximum-likelihood trees constructed from concatenated PCGs across 72 species, successfully differentiates from other carangids. This study also explores how ocean currents and gyres might influence lineage diversification and parapatric speciation of species between the Atlantic and Pacific Oceans. These results highlight the importance of the mitochondrial genome in elucidating the structural organization and evolutionary dynamics of and its relatives within marine ecosystems.

摘要

本研究深入分析了原产于东大西洋的(Gill 1863)的线粒体基因组。这个圆形的线粒体 DNA 分子长 16541 个碱基对,包含 13 个蛋白质编码基因(PCGs)、22 个转移 RNA(tRNA)基因、两个核糖体 RNA 基因和一个控制区(CR)。核苷酸组成表现出明显的腺嘌呤-胸腺嘧啶(AT)偏好性,占 53.13%,与其他 Carangidae 科的物种一致。大多数 PCGs 以 ATG 密码子起始,除了细胞色素 C 氧化酶亚基 I,它以 GTG 起始。相对同义密码子使用分析表明,亮氨酸和丝氨酸是线粒体基因组中最常见的氨基酸,和其同属物种(和)也是如此。所有 tRNA 都显示出典型的三叶草结构,尽管(S1)缺乏二氢尿嘧啶臂。所有 PCGs 的同义和非同义替换的成对比较产生的值均低于 '1',表明存在强烈的纯化选择。CR 跨度为 847 个碱基对,占线粒体基因组的 5.12%,其特点是高 AT 含量(62.81%)。它位于(TGG)和(GAA)之间。CR 包含保守序列块,其中 CSB-1 最长,为 22 个碱基对,CSB-D 最短,为 18 个碱基对。使用贝叶斯和最大似然树从 72 个物种的 PCGs 串联构建的系统发育分析成功地区分了与其他 Carangidae 鱼类的关系。本研究还探讨了洋流和漩涡如何影响大西洋和太平洋之间的鱼类谱系多样化和邻域物种形成。这些结果强调了线粒体基因组在阐明海洋生态系统中及其亲缘物种的结构组织和进化动态方面的重要性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/29f33c8f6ab6/biomolecules-14-01208-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/99e389e4778a/biomolecules-14-01208-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/0260c10ae2c7/biomolecules-14-01208-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/6dde00be7378/biomolecules-14-01208-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/29f33c8f6ab6/biomolecules-14-01208-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/99e389e4778a/biomolecules-14-01208-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/0260c10ae2c7/biomolecules-14-01208-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/6dde00be7378/biomolecules-14-01208-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4de7/11506752/29f33c8f6ab6/biomolecules-14-01208-g004.jpg

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