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. 2019 Sep 17;4(2):3020–3021. doi: 10.1080/23802359.2019.1664949

Complete mitochondrial genome and phylogenetic analysis of Stonogobiops yasha (Perciformes, Gobiidae)

Hengtong Qiu a,b, Cuili Wang a,b,✉
PMCID: PMC7706908  PMID: 33365837

Abstract

The complete mitochondrial genome sequence of Stonogobiops yasha was first determined in this study. The circle genome was 16,566 bp long and consisted of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The mitochondrial gene arrangement of S. yasha is similar to those of most other gobies. The phylogenetic analysis using the neighbor-joining method showed that the kinship between Stonogobiops and Acentrogobius is closer than those between Stonogobiops and other selected genera. This is the first record of the complete mitogenome for the genus Stonogobiops.

Keywords: Stonogobiops yasha, mitogenome, Gobiidae, phylogenetic analysis

Stonogobiops yasha, which belongs to Gobiidae, Gobioidei, and Perciformes in taxonomy, is widely distributed in reefs across the western Pacific Ocean (Yoshino and Shimada 2001). Because of their white body with reddish-orange longitudinal stripes, S. yasha is one of the most attractive gobies available to marine aquarists (Chang et al. 2009). We expect the establishment of S. yasha mitogenome could provide help for phylogenetic assessment and population studies.

The samples of S. yasha were imported from Manado, North Sulawesi, Indonesia (1°30′ N, 124°58′ E) to Nanning Normal University, and their genomic DNA were extracted from muscle using the standard phenol/chloroform protocol (Sambrook and Russell 2001). We designed 10 pairs of primers for sequencing through the alignment of 80 Gobiidae mitogenomes sequenced in their entirety using the primer 5 software (Singh et al. 1998). The specimen of S. yasha is stored at Museum of Biology, Nanning Normal University with accession no. NNNU001812.

The complete mitochondrial genome sequence of S. yasha has been deposited in GenBank with accession no. MN067902. The circular genome (16,566 bp) comprised 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and 1 control region. The nucleotide composition of the heavy strand of S. yasha was 28.18% for A, 27.73% for C, 16.76% for G, and 27.33% for T, with a slight A + T bias of 55.51%. On one hand, all the protein-coding genes were initiated with ATG codon, except for the COI, which started with GTG. On the other hand, seven protein-coding genes (ND1, COXI, ATP8, ATP6, ND4L, ND5, and ND6) employed the typical termination codon TAA. ND2 and ND3 are terminated with TAG, and the remaining protein-coding genes (COXII, COXIII, ND4, and CYTB) used one incomplete stop codon (T-). The tRNA genes were identified by the online software tRNAScan-SE1.21 (Lowe and Eddy 1997), 22 tRNA genes were found, and the length of the 22 tRNA genes varied from 65 to 75 bp. Unlike other tRNA genes, distributed on the heavy strand, the eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu, and tRNAPro) were distributed on the light strand. The two ribosomal RNA genes, 12S rRNA gene (945 bp) and 16S rRNA gene (1684 bp), were located between tRNAPhe and tRNALeu and separated by tRNAVal. The control region was located between tRNAPro and tRNAPhe and consisted of 914 nucleotides.

The complete mitogenome sequences of 15 fishes and 3 mammals have been used to construct a phylogenetic tree (Figure 1) by neighbor-joining method (1000 bootstrap replicates, MEGA7 software) (Kumar et al. 2016). All the fishes were clustered into one group, while all the mammals formed the other group. The fishes in the suborder Gobioidei were grouped together while Danio rerio formed a side branch. In the Gobioidei, all the fishes were separated into two branches, one comprising the family Gobiidae and the other comprising the family Odontobutidae. Stonogobiops yasha was clustered into one clade with other two species from the genus Acentrogobius, which was then grouped with Glossogobius, Periophthalmus, Gillichthys, and Mugilogobius to form a cluster. This indicates that the kinship between Stonogobiops and Acentrogobius is closer than those between Stonogobiops and other selected genera.

Figure 1.

Figure 1.

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Phylogenetic analysis of 18 complete mitogenome sequences using MEGA 7 by the Neighbor-joining method and 1000 replications of bootstrap. The mitogenome sequence of S. yasha is highlighted within a box.

Disclosure statement

The authors report no conflicts of interest. The authors are responsible for the content and writing of the paper.

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