Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile)

Zhu, Ke-Cheng; Liang, Yan; Wu, Na; Guo, Hua-Yang; Zhang, Nan; Jiang, Shigui

doi:10.1038/s41598-017-15702-0

Cited by 24 publications

(18 citation statements)

References 69 publications

(55 reference statements)

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“…The comparison of synonymous (Ks) and nonsynonymous (Ka) substitution rates in PCGs, evidenced for darwinian selection and adaptive molecular evolution in vertebrates 62 – 64 . The ratio of Ka/Ks was generally known as an indicator of selective pressure and evolutionary relations at molecular level among the homogenous or heterogeneous species 65 . It is reported that, for positive selection Ka/Ks > 1, for neutrality Ka/Ks = 1, and for negative selection Ka/Ks < 1 66 .…”

Section: Resultsmentioning

confidence: 99%

Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae

Kundu

Kumar

Tyagi

et al. 2018

Sci Rep

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The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in the CR. Further, the conserved motif 5′-GACATA-3′ and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.

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Section: Resultsmentioning

confidence: 99%

Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae

Kundu

Kumar

Tyagi

et al. 2018

Sci Rep

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“…ND1, ND2, and ND6 genes might have high evolutionary rates among the three species, while COXI-III and Cytb were low. The value of nonsynonymous substitution (Ka)/synonymous substitution (Ks) is a common indicator to assess selective pressure and evolutionary relationships of species in molecular studies [52]. Ka/Ks < 1, Ka/Ks = 1, and Ka/Ks > 1 were represented purifying selection, neutral mutation and positive selection, respectively [53].…”

Section: Variations Genetic Distance and Evolution Rates Of Pcgsmentioning

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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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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“…The genomic DNA extracts from standard phenol/chloroform method (Sambrook and Russel 2000). The method for preparing and sequencing the DNA library is referred to Zhu, Liang, et al (2017). For mtDNA sequence assemble, annotation and analysis are referred to .…”

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confidence: 99%

The complete mitochondrial genome of false trevally Lactarius Lactarius (Bloch and Schneider, 1801)

Yang

Qin

et al. 2019

Mitochondrial DNA Part B

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In the present study, the complete mitochondrial DNA sequence of the milkfish Lactarius lactarius is determined. The full-length of the mitochondrial genome consists of a 16,552 bp fragment, with the base composition of A (28.24%), C (29.82%), G (15.96%), and T (25.98%) with a high A þ T content (54.22%). The base compositions present clearly the AT skew, which is most obvious in the control region and protein-coding genes. It includes 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and a major non-coding control region (D-loop region). Furthermore, the composition and order of these genes are identical to most of other vertebrates. All the protein initiation codons are ATG, except that COX1 and ATP6 begin with GTG. All the protein termination codons are TAA, except ND3 and ND6 end with TAG, and COXII, ND4, Cytb finish only with incomplete T. Furthermore, the phylogenetic analysis base on 13 concatenated PCGs amino acid datasets among the 14 species, suggesting that high value support for the following sister clade with Toxotes chatareus. Our findings provide useful information for phylogenetic and evolutionary research of Perciformes species.

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Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile)

Cited by 24 publications

References 69 publications

Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae

Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae

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

The complete mitochondrial genome of false trevally Lactarius Lactarius (Bloch and Schneider, 1801)

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