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The complete mitochondrial genome of Cynops cyanurus cyanurus (Caudata: Salamandridae) and its phylogenetics analysis.

ABSTRACT: The complete mitochondrial of Cynops cyanurus cyanurus was determined by using Sanger sequencing and the mitogenome size of C. c. cyanurus was 16,465 bp. It contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, 1 control region (D-loop) and a non-coding region (NC). In addition, the phylogenetic tree shows that C. c. cyanurus has the closest relationship with C. c. chuxiongensis. Hoping this study can improve our understanding of the species evolutionary relationship of Cynops.

SUBMITTER: Li H

PROVIDER: S-EPMC7748605 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNAIle has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)n stretch and several G(A)nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.

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The complete mitochondrial genome of Cynops cyanurus cyanurus (Caudata: Salamandridae) and its phylogenetics analysis.

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