Characterization of complete mitochondrial genome of fives tripe wrasse (Thalassoma quinquevittatum, Lay & Bennett, 1839) and phylogenetic analysis

Kecheng Zhu; Na Wu; Xiaoxiao Sun; Huayang Guo; Nan Zhang; Shigui Jiang; Dianchang Zhang

doi:10.1016/j.gene.2016.10.042

Characterization of complete mitochondrial genome of fives tripe wrasse (Thalassoma quinquevittatum, Lay & Bennett, 1839) and phylogenetic analysis

Gene. 2017 Jan 20:598:71-78. doi: 10.1016/j.gene.2016.10.042. Epub 2016 Nov 2.

Authors

Kecheng Zhu¹, Na Wu¹, Xiaoxiao Sun¹, Huayang Guo¹, Nan Zhang¹, Shigui Jiang², Dianchang Zhang³

Affiliations

¹ Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Division of Aquaculture and Genetic Breeding, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou 510300, China.
² Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Division of Aquaculture and Genetic Breeding, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou 510300, China; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, China.
³ Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, Key Laboratory of Fishery Ecology & Environment, Guangdong Province, Division of Aquaculture and Genetic Breeding, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 231 Xingang Road West, Haizhu District, Guangzhou 510300, China. Electronic address: zhangdch@scsfri.ac.cn.

PMID: 27816474
DOI: 10.1016/j.gene.2016.10.042

Abstract

To further supplement the genome-level features in related species, T. quinquevittatum complete mtDNA was firstly sequenced and de novo assembled by next-generation sequencing. The full-length mtDNA of T. quinquevittatum was a 16,896bp fragment, which was atypical of Labridae, with 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region (D-loop region). Additionally, the mtDNA of T. quinquevittatum exhibited characteristics of A (27.1%), T (29.3%), G (17.8%), and C (25.8%) with a high A+T content (56.4%). Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Labridae species indicated a strong purifying selection within this group. Additionally, the phylogenetic analysis based on 13 concatenated PCGs nucleotide and amino acid datasets, showed high value support for the following sister clade among the four genera (T. quinquevittatum, Halichoeres trimaculatus, Halichoeres melanurus, Parajulis poecilepterus). The complete mtDNA of the T. quinquevittatum provided important information for the study in population genetics and evolutionary theory.

Keywords: Ka/Ks; Mitochondrial DNA; Phylogenetic analysis; Thalassoma quinquevittatum.

MeSH terms

Animals
Base Composition
Base Sequence
Codon
DNA, Mitochondrial / genetics
Evolution, Molecular
Fish Proteins / genetics
Genetics, Population
Genome, Mitochondrial*
Mitochondrial Proteins / genetics
Nucleic Acid Conformation
Perciformes / classification
Perciformes / genetics*
Phylogeny
RNA, Ribosomal / genetics
RNA, Transfer / chemistry
RNA, Transfer / genetics
Selection, Genetic

Substances

Codon
DNA, Mitochondrial
Fish Proteins
Mitochondrial Proteins
RNA, Ribosomal
RNA, Transfer