Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes

Lü, Zhen-Ming; Zhu, Kehua; Jiang, Hui; Lu, Xinting; Liu, Bingjian; Ye, Yingying; Jiang, Lihua; Liu, Liqin; Gong, Li

doi:10.1016/j.ijbiomac.2019.05.139

Cited by 25 publications

(16 citation statements)

References 80 publications

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“…Here, the absolute value of GC-skew was indeed larger than AT-skew, which conformed to conventional preferences that GC-skew was more obvious. The lowest AT-skew and highest GC-skew value were all found in ND6, and it was the only gene displayed positive value in the GC-skew curve, which was consistent with other studies [33,43,44]. Nucleotide skew might be attributed to the equilibrium between mutation pressure and selection pressure during replication and transcription, providing a potential direction for gene replication [27,45].…”

Section: Protein Coding Genes (Pcgs)supporting

confidence: 89%

“…In DNA sequences, AT-skew and GC-skew was considered as a potential indicator to measure strand asymmetry and the patterns of nucleotide composition [43]. The majority of the AT-skew values and GC-skew values of the 13 PCGs among the three species were negative, demonstrating base T and C were more plentiful than A and G ( Figure 3).…”

Section: Protein Coding Genes (Pcgs)mentioning

confidence: 99%

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Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

Ruan¹,

Li³

et al. 2020

IJMS

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Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.

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Section: Protein Coding Genes (Pcgs)supporting

confidence: 89%

Section: Protein Coding Genes (Pcgs)mentioning

confidence: 99%

Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

Ruan¹,

Li³

et al. 2020

IJMS

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“…The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating that bases T and C were more plentiful than A and G ( Figure 2). The lowest AT-skew and highest GC-skew values were all found in the ND6 gene, which is unusual but similar to other observations of strand asymmetry [21][22][23]. The AT-skews for the concatenated sequence of the PCGs in all 32 species were negative, completely different from those of the entire genome.…”

Section: Protein-coding Genes (Pcgs)supporting

confidence: 86%

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

Li¹,

et al. 2020

IJMS

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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.

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“…Seven PCGs (ND1, COI, ATP8, ATP6, COIII, ND4L, and ND5) were terminated with a stop codon TAA, three (ND2, ND3, and ND6) were terminated with TAG, and one (Cyt b) was terminated with AGA, in addition, ND4 And COII terminate with an incomplete nucleotide T-(Table 2). This result was very similar to that of Lu et al 13 . Whether in invertebrate or vertebrate mitochondrial genes, the presence of incomplete stop codons is a common phenomenon [51][52][53] .…”

supporting

confidence: 92%

“…So it was called "power house". The length of vertebrate mitochondria was 16-20 kb, which was usually a typical circular structure, containing 13 protein coding genes (PCGs), 22 tRNA genes (tRNA) and two rRNA genes (rRNA) 12,13 . The order of these genes was initially considered conservative because the mammalian complete mitochondrial genome and the African clawed frog have the same genetic order [14][15][16] .…”

mentioning

confidence: 99%

Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

Zhang

Zhu

Liu

et al. 2021

Sci Rep

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The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

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Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes

Cited by 25 publications

References 80 publications

Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

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

Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

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