Complete mitochondrial genome of Pristicon trimaculatus (Kurtiformes, apogonidae): mitogenome characterization and phylogenetic analysis

Abstract

Pristicon trimaculatus is a tropical reef-associated marine fish belonging to the family Apogonidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of P. trimaculatus. The complete mitochondrial genome is 16,512 bp length and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of nine species showed that P. trimaculatus formed a monophyletic group with other Apogonidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues of the Kurtiformes.

Keywords:

• Mitochondrial genome
• kurtiformes
• apogonidae
• Pristicon trimaculatus

The three-spot cardinalfish, Pristicon trimaculatus (Kurtiformes, Apogonidae), is a tropical marine fish which inhabits inshore coral reefs of the western Pacific ocean, from Ryukyu Islands to Western Australia and the southern Great Barrier Reef, east to Samoa and the Marshall Islands (Randall and Fraser 1999). Its belonging family Apogonidae, the cardinalfishes, are distinguished by their large mouths and the division of the dorsal fin into two separate fins (Johnson et al. 1998). This species is also known to broods its eggs inside the mouth (Thresher 1984). In numerous molecular studies, Apogonidae, Gobiodei and Kurtus formed monophyletic group (Li et al. 2009; Thacker 2009; Near et al. 2012; Near and Keck 2013; Betancur-R et al. 2014), but not strongly supported in the bootstrap analysis (Thacker et al. 2015). This is the first study to determine the complete mitochondrial genome of P. trimaculatus, and to analyze the phylogenetic relationship of this species with members of Apogonidae.

The P. trimaculatus specimen was collected from Chuuk ST 1, Micronesia (7.27N, 151.54E). Total genomic DNA was extracted from tissue of the specimen, which has been deposited in the National Marine Biodiversity Institute of Korea (Voucher No. MABIK 0000642). The mitogenome was sequenced and assembled using Illumina Hiseq 4000 sequencing platform (Illumina, San Diego, CA) and SOAPdenovo assembler at Macrogen Inc. (Korea), respectively. The complete mitochondrial genome was annotated using MacClade ver. 4.08 (Maddison and Maddison 2005) and DNASIS ver 3.2 (Hitachi Software Engineering, Tokyo, Japan).

The complete mitochondrial genome of P. trimaculatus (GenBank accession no. AP018928) is 16,512 bp length, and includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. The ND6 gene and eight tRNA genes are encoded on the light strand. The overall base composition of the heavy strand is 27.68% A, 29.19% C, 16.57% G, and 26.56% T. Similar to the mitogenomes of other vertebrates, the AT content is higher than the GC content (Saccone et al. 1999). All tRNA genes can fold into a typical cloverleaf structure, with lengths ranging from 66 to 74 bp. The 12S rRNA (957 bp) and 16S rRNA genes (1685 bp) are located between tRNA^Phe and tRNA^Val and between tRNA^Val and tRNA^Leu(UUR), respectively. Of the 13 protein-coding genes, 12 begin with an ATG start codon; the exception being the COI gene, which start with GTG. The stop codon of the protein-coding genes is TAA in ND1, ND2, COI, ATP8, ND4L and ND5; TA in ATP6 and COIII; AGA in ND6; and T in the remaining four genes. The control region (844 bp) is located between tRNA^Pro and tRNA^Phe.

Phylogenetic trees were constructed by the maximum-likelihood method using MEGA 7.0 software (Kumar et al. 2016) for the newly sequenced genome and a further nine complete mitochondrial genome sequences downloaded from the National Center for Biotechnology Information. We confirmed that P. trimaculatus formed a monophyletic group with other Apogonidae species with high statistical support (Figure 1). This mitochondrial genome provides important resources for addressing taxonomic issues and studying molecular evolution.

Figure 1. Phylogenetic position of Pristicon trimaculatus based on a comparison with the complete mitochondrial genome sequences of 9 species. The analysis was performed using MEGA 7.0 software. The accession number for each species is indicated after the scientific name.

Disclosure statement

The authors report no conflict of interests. The authors alone are responsible for the content and writing of the paper.

Additional information

Funding

This work was supported by grant from the National Marine Biodiversity Institute Research Program (2018M00900) and the Marine Biotechnology Program (20170488) funded by the Ministry of Oceans and Fisheries, Korea.