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Open AccessArticle

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations

by Zhenhai Li 1,†, Min Li 2,3,†, Shannan Xu 2, Li Liu 1, Zuozhi Chen 2,3,* and Keshu Zou 1,4,*
1
Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Science, South China Agriculture University, Guangzhou 510642, China
2
Key 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, China
3
Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
4
Guangdong Laboratory for Lingnan Modern Agriculture, South China Agriculture University, Guangzhou 510642, China
*
Authors to whom correspondence should be addressed.
These authors contribute equally to this work.
Int. J. Mol. Sci. 2020, 21(13), 4685; https://doi.org/10.3390/ijms21134685
Received: 5 June 2020 / Revised: 26 June 2020 / Accepted: 27 June 2020 / Published: 30 June 2020
(This article belongs to the Section Biochemistry)
Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) 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 (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (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 ATP8 showed the highest evolutionary rate and COXI/COXII 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. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene. View Full-Text
Keywords: Alectis indicus; Decapterus tabl; Alepes djedaba; comparative characterization; mitochondrial genome; phylogeneny Alectis indicus; Decapterus tabl; Alepes djedaba; comparative characterization; mitochondrial genome; phylogeneny
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Li, Z.; Li, M.; Xu, S.; Liu, L.; Chen, Z.; Zou, K. Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations. Int. J. Mol. Sci. 2020, 21, 4685.

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