Characterization of the complete mitochondrial genome of Periophthalmus modestus (Gobiiformes, Oxudercidae) and phylogenetic analysis

Abstract

The complete mitochondrial genome was determined for the shuttles hoppfish Periophthalmus modestus belonging to the family Oxudercidae. The length of the complete mitochondrial genome is 16,510 bp 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 15 species showed that P. modestus formed a well-supported monophyletic group with genus Periophthalmus species and rooted with other Oxudercidae species.

Keywords:

• Mitochondrial genome
• Gobiiformes
• Oxudercidae
• Periophthalmus modestus

The shuttles hoppfish Periophthalmus modestus (Gobiiformes, Oxudercidae) is distributed throughout the marginal seas of the northwestern Pacific, including China, Japan and Korea (Murdy 1989). Its belonging family Oxudercidae, mudskippers, are amphibious fish that inhabit mudflats, muddy creeks and lagoons and mangrove forests mostly in the tropics and subtropics (Baeck et al. 2008). Although previous molecular phylogenetic studies indicated the family Gobiidae is divided into two major clades, the families Oxudercidae and Gobiidae (Thacker and Roje 2011; Chakrabarty et al. 2012; Thacker 2013), the members of these two families remains controversial because both the Oxudercidae and Gobiidae are highly diverse, with many genera and potentially many subgroups. In the current study, we first determined the complete mitochondrial DNA sequence of P. modestus, and analyzed the phylogenetic relationship of this species with members of Oxudercidae and Gobiidae.

The P. modestus specimen used in this study was collected at Seocheon, Korea (36.01N, 126.39E) in June 2018. 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 TI00002734). The mitogenome was sequenced and assembled using Illumina Hiseq 4000 sequencing platform (Illumina, San Diego, CA) and SOAP denovo assembler at Macrogen Inc. (Seoul, 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. modestus (GenBank accession no. AP019406) is 16,510 bp long, 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 28.29% A, 27.85% C, 16.02% G, and 27.84% 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 65 to 76 bp. The 12S rRNA (956 bp) and 16S rRNA genes (1691 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, ND4L, ND5, and ND6; TAG in ATP8; and T in the remaining six genes. The control region (840 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 14 complete mitochondrial genome sequences downloaded from the National Center for Biotechnology Information. We confirmed that P. modestus formed a monophyletic group with other Oxudercidae members with high statistical support (Figure 1).

Figure 1. Phylogenetic position of Periophthalmus modestus based on a comparison with the complete mitochondrial genome sequences of 14 species. The analysis was performed using MEGA 7.0 software. The accession number for each species is indicated after the scientific name.

Acknowledgements

This work was supported by grant from the National Marine Biodiversity Institute Research Program [2019M00600] and the Marine Biotechnology Program [20170488] funded by the Ministry of Oceans and Fisheries, Korea.

Disclosure statement

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