Characterization of the complete mitochondrial genome of Sphaeramia orbicularis (Kurtiformes, Apogonidae)

Abstract

The complete mitochondrial genome was determined for the orbicular cardinalfish Sphaeramia orbicularis belonging to the family Apogonidae. The length of the complete mitochondrial genome is 16,458 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 9 species showed that S. orbicularis formed a well-supported monophyletic group with other Apogonidae species.

Keywords:

• Mitochondrial genome
• Kurtiformes
• Apogonidae
• Sphaeramia orbicularis

The orbiculate cardinalfish, Sphaeramia orbicularis (Kurtiformes: Apogonidae) is widespread throughout the meromictic marine lakes and lagoons of the Palau Islands, Micronesia (Gotoh et al. 2009). They mostly inhabit in shallow water of the reefs in the tropics but a few species belonging to the Apogonidae have been reported in temperate zone (Thacker and Roje 2009). This family is known for remarkable reproductive characteristic which is mouth brooding including oral incubation by males (Choi et al. 2012). In the current study, we first determined the complete mitochondrial DNA sequence of S. orbicularis, and to analyze the phylogenetic relationship of this species with members of Apogonidae.

The S. orbicularis specimen used in this study 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 0000633). The mitogenome was sequenced and assembled using Illumina Hiseq 4000 sequencing platform (Illumina, San Diego, CA) and SOAP denovo 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 S. orbicularis (GenBank accession no. AP018927) is 16,458 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 26.01% A, 30.25% C, 17.90% G, and 25.84% 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 66 to 74 bp. The 12S rRNA (959 bp) and 16S rRNA genes (1645 bp) are located between tRNA^Phe and tRNA^Val and between tRNA^Val and tRNA^Leu(UUR), respectively. Of the 13 protein-coding genes, 13 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 ND2, COI, ATP8, ND4L and ND5; TAG in ND1; AGA in ND6 and Cytb; TA in ATP6 and COIII; and T in the remaining three genes. The control region (824 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 eight complete mitochondrial genome sequences downloaded from the National Center for Biotechnology Information. We confirmed that S. orbicularis formed a monophyletic group with other Apogonidae species and the Apogonidae species formed a sister-group relationship with the family Gobiidae species with high statistical support (Figure 1).

Figure 1. Phylogenetic position of Sphaeramia orbicularis based on a comparison with the complete mitochondrial genome sequences of 8 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 2018M01000) and the Marine Biotechnology Program (20170488) funded by the Ministry of Oceans and Fisheries, Korea.