Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations
Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (<i>Alectis indicus</i>, <i>Decapterus tabl</i>, and <i>Alepes djedaba</i>) were sequenced, characterized, and compared with 29 other species o...
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MDPI AG
2020-06-01
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| Series: | International Journal of Molecular Sciences |
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| author | Zhenhai Li Min Li Shannan Xu Li Liu Zuozhi Chen Keshu Zou |
| author_facet | Zhenhai Li Min Li Shannan Xu Li Liu Zuozhi Chen Keshu Zou |
| author_sort | Zhenhai Li |
| collection | DOAJ |
| description | Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (<i>Alectis indicus</i>, <i>Decapterus tabl</i>, and <i>Alepes djedaba</i>) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (<i>12S rRNA</i> and <i>16S rRNA</i>), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only <i>tRNA-Ser</i> (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that <i>ATP8</i> showed the highest evolutionary rate and <i>COXI</i>/<i>COXII</i> were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. <i>A. indicus</i> began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while <i>D. tabl</i> (21.25 Mya) and <i>A. djedaba</i> (14.67 Mya) differentiated in the middle Oligocene. |
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| language | English |
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| spelling | doaj.art-b2342747474540ceb8597a76da6863422023-11-20T05:30:24ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-06-012113468510.3390/ijms21134685Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic ConsiderationsZhenhai Li0Min Li1Shannan Xu2Li Liu3Zuozhi Chen4Keshu Zou5Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, ChinaKey Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, ChinaKey Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, ChinaJoint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, ChinaKey Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, ChinaJoint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, ChinaCarangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (<i>Alectis indicus</i>, <i>Decapterus tabl</i>, and <i>Alepes djedaba</i>) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (<i>12S rRNA</i> and <i>16S rRNA</i>), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only <i>tRNA-Ser</i> (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that <i>ATP8</i> showed the highest evolutionary rate and <i>COXI</i>/<i>COXII</i> were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. <i>A. indicus</i> began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while <i>D. tabl</i> (21.25 Mya) and <i>A. djedaba</i> (14.67 Mya) differentiated in the middle Oligocene.https://www.mdpi.com/1422-0067/21/13/4685<i>Alectis indicus</i><i>Decapterus tabl</i><i>Alepes djedaba</i>comparative characterizationmitochondrial genomephylogeneny |
| spellingShingle | Zhenhai Li Min Li Shannan Xu Li Liu Zuozhi Chen Keshu Zou Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations International Journal of Molecular Sciences <i>Alectis indicus</i> <i>Decapterus tabl</i> <i>Alepes djedaba</i> comparative characterization mitochondrial genome phylogeneny |
| title | Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations |
| title_full | Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations |
| title_fullStr | Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations |
| title_full_unstemmed | Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations |
| title_short | Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations |
| title_sort | complete mitogenomes of three carangidae perciformes fishes genome description and phylogenetic considerations |
| topic | <i>Alectis indicus</i> <i>Decapterus tabl</i> <i>Alepes djedaba</i> comparative characterization mitochondrial genome phylogeneny |
| url | https://www.mdpi.com/1422-0067/21/13/4685 |
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