Complete Mitochondrial Genome of Pseudocaranx dentex (Carangidae, Perciformes) Provides Insight into Phylogenetic and Evolutionary Relationship among Carangidae Family.

Busu Li,Shufang Liu,Huan Wang,Zhimeng Zhuang,Long Yang

doi:10.3390/genes12081234

Abstract

Pseudocaranx dentex (white trevally) which belongs to the Carangidae family, is an important commercial fishery and aquaculture resource in Asia. However, its evolution and population genetics have received little attention which was limited by the mitogenome information absence. Here, we sequenced and annotated the complete mitochondrial genome of P. dentex which was 16,569 bp in length, containing twenty-two tRNAs (transfer RNAs), thirteen PCGs (protein-coding genes), two rRNAs (ribosomal RNAs), and one non-coding region with conservative gene arrangement. The Ka/Ks ratio analysis among Carangidae fishes indicated the PCGs were suffering purify selection and the values were related to the taxonomic status and further influenced by their living habits. Phylogenetic analysis based on the PCGs sequences of mitogenomes among 36 species presented three major clades in Carangidae. According to the phylogenetic tree, we further analyzed the taxonomic confusion of Carangoides equula which was on the same branch with P. dentex but a different branch with Carangoides spp. We inferred Kaiwarinus equula should be the accepted name and belong to the independent Kaiwarinus genus which was the sister genus of Pseudocaranx. This work provides mitochondrial genetic information and verifies the taxonomic status of P. dentex, and further helps to recognize the phylogenetic relationship and evolutionary history of Carangidae.

Highlights

Mitochondria, the main place that accounts for the energy support of various life activities [1], contains their own store of genetic information, which is the mitochondrial genome
The mitochondrial species-specific DNA fragments, such as cytochrome c oxidase I (COI), cytochrome b (CYTB), and ribosomal RNA (12S and 16S) are molecular markers usually used for species identification and phylogenetic analysis in fishes [2,3,4]
The circular mitogenome of P. dentex was 16,569 bp in length consists of thirteen protein-coding genes (PCGs), twenty-two transfer RNAs, two ribosomal RNAs, and one non-coding region (Figure 1 and Table 2)

Summary

Introduction

Mitochondria, the main place that accounts for the energy support of various life activities [1], contains their own store of genetic information, which is the mitochondrial genome. The mitochondrial species-specific DNA fragments, such as cytochrome c oxidase I (COI), cytochrome b (CYTB), and ribosomal RNA (12S and 16S) are molecular markers usually used for species identification and phylogenetic analysis in fishes [2,3,4]. The mitochondrial genome which contains greater sequence and additional informative sites has been regarded as a powerful molecular marker to identify phylogenetic relationships and explore population genetics and taxonomic diagnosis because of its high conservation, maternal inheritance, compact gene arrangement, and easy detection [5]. Previous studies have examined the learning behavior [11] and physiological features [12] of P. dentex, but not its genetic characteristics and evolutionary patterns which are limited by the absence of mitogenome information

Methods

Results

Discussion

Conclusion