Complete mitochondrial genome of cocktail wrasse Pteragogus flagellifer

Abstract

We determined the complete mitochondrial (mt) sequence of the Cocktail wrasse, Pteragogus flagellifer. The mt genome is 16,807 bp long and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions. All its mt protein-coding genes begin with an ATG start codon except for CO1, which begins with GTG. The order of the mt genes is largely identical to that of typical vertebrates, although the position of the TMF-regulated nuclear protein (trnP) is unique among known Labridae gene arrangements. The phylogenetic tree of Labridae showed that P. flagellifer is relatively close to Pseudolabrus.

Keywords:

• Cocktail wrasse
• gene rearrangement
• mitochondrial genome

Pteragogus is a genus of wrasses native to the Indo-West Pacific, the Red Sea to South, Papua New Guinea, northern to southern Japan, the shores of the Korean Peninsula, and south to Australia. Cocktail wrasse, Pteragogus flagellifer, is found among coral or rocky reefs and weedy marine bottoms. Jeju Island is rich in coral and rocky reefs and, therefore, is the habitat of numerous wrasses including P. flagellifer.

Pteragogus flagellifer was caught in a coastal reef off Jeju Island, South Korea (geospatial coordinates: 33°31'59"N, 126°35'23"E). The total DNA was extracted and stored in deep freezer in Jeju Biodiversity Research Institute. The complete mitochondrial (mt) genome was sequenced (GenBank accession num. EF409976). The mt genome was 16,807 bp long, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and two noncoding regions.

The A/C/G/T base composition of the 13 PCGs was 22.3/30.8/18.0/28.9. The PCG proportion of G at the third position in a codon is relatively low, and pyrimidines are overrepresented in the second codon position (68.0%), as previously reported for other vertebrate mt genomes, owing to the hydrophobic character of the proteins (Naylor et al. 1995). Among 22 tRNAs, trnS^AGY has no discernible dihydrouridine (DHU) stem, similar to that in the lamprey (Lee and Kocher 1995), bichir (Noack et al. 1996), ayu (Ishiguro et al. 2001), and rock bream (Oh et al. 2007).

The P. flagellifer mt gene arrangement is identical to that of typical vertebrates, although the trnP position relative to the control region is unique among known Labridae gene arrangements.

The major control region of the P. flagellifer mt genome spans 893 bp, consistent with those of other vertebrates (Lee et al. 1995). The control region is located between the trnT and trnP genes while other typical bony fishes have their control region located between the trnP and trnF genes. Many mt genome studies have revealed numerous independently evolved gene rearrangements (Kumazawa et al. 1996; Macey et al. 1997), and mt gene rearrangements related to the control region have been studied in various animals (Ishikawa et al. 2000; Sumida et al. 2001; Kumazawa and Endo 2004; Dong and Kumazawa 2005; Peng et al. 2006; Su et al. 2007; Jühling et al. 2012). This discovery might provide meaningful insights for studying the speciation and evolutionary process of Labridae.

The mt genome of P. flagellifer has an additional presumably redundant, non-coding region located between trnP and trnF. The non-coding region is 232 bp long and contains several palindromic sequences.

To examine P. flagellifer in the molecular phylogeny of Labridae, we constructed a maximum-likelihood (ML) tree using the nucleotide sequences of 13 PGGs from all Labridae mt genomes registered in GenBank (Figure 1). In the ML tree, P. flagellifer was a sister taxon to Pseudolabrus. The tree topology was not consistent with that of previous studies (Cowman et al. 2009).

Figure 1. Molecular phylogenetic analysis of mitochondrial (mt) 13 protein-coding genes (PCGs) in 19 species of Labridae. The phylogenetic tree was constructed using maximum-likelihood (ML) method based on the GTR + G + I (Nei and Kumar2000) as the best nucleotide substitution model based on Akaike information criterion (AIC) (Akaike1974). The rate variation model allowed for some sites to be evolutionarily invariable. Percentages of trees where associated taxa were clustered together were shown next to branches. Evolutionary analyses were conducted using the MEGA7 (Kumar et al.2016).

Disclosure statement

The authors declare that they have no competing interests.