Complete mitochondrial genome and phylogenetic analysis of black-fin stream jewel goby Stiphodon percnopterygionus (Gobiiformes: Gobiidae) from Taiwan

Abstract

The complete mitochondrial genome of the black-fin stream jewel goby Stiphodon percnopterygionus has been amplified and sequenced. The whole mitochondrial genome is 16,502 base pairs (bp) in total length and consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region (CR). The overall base composition is 28.1% for A, 17.1% for G, 28.7% for C and 26.0% for T with AT comprising 54.1%. A phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) sequence data for 34 related taxa of the order Gobiiformes showed that S. percnopterygionus is closely related to S. tuivi. These findings will contribute for phylogenetic, phylogeography and further genetic studies in genus Stiphodon and related gobiid fishes.

Keywords:

• Mitogenome
• Gobiidae
• phylogenetic analysis
• Stiphodon percnopterygionus

The genus Stiphodon of the subfamily Sicydiinae comprises 37 valid species that are widely distributed in tropical and subtropical freshwater streams in Indo-Pacific islands (Maeda and Palla 2015; Fricke and Pauly 2021). Stiphodon percnopterygionus (Watson and Chen 1998), also known as the black-fin stream jewel goby, is a small amphidromous goby that inhabits rocky shallow streams in various part of southern Japan, and Taiwan (Watson and Chen 1998; Chen and Fang 1999; Nakabo 2013). Life history and population genetic structure of this species have been reported (Chen and Fang 1999; Yamasaki and Tachihara 2006; Yamasaki and Maeda 2007; Lord et al. 2015). Despite the fact that Stiphodon is the most speciose genus of Sicydiinae, complete mitochondrial genomes from only 3 species have been determined to date namely, S. alcedo (Maeda et al. 2011) from the Ryukyu Island of Japan, S. pelewensis (Herre 1936) and S. tuivi (Watson 1995) from Western Pacific (Lord et al. 2019). Herein, we report and describe for the first time the complete mitogenome of S. percnopterygionus and also present a metagenome-based-phylogenetic analysis to describe the position of S. percnopterygionus among other members of Gobiiformes.

Fish sample for sequencing was collected from Nanya Brook, New Taipei City, Taiwan (geographic location: 25°06′55″N 121°53″36.3″E) and deposited at National Taiwan Ocean University (http://imb.ntou.edu.tw/, I-Shiung Chen, [email protected]) with voucher number NTOUP-2019-08-751. DNA extraction from fin tissue was obtained using the commercial kit (GeneMark, Taichung, Taiwan). The entire mitogenome was amplified using the long polymerase chain reaction (PCR) technique (Miya and Nishida 1999) with 12 pairs of primers designed based on alignments of gobiid fish mitochondrial genome sequences dowloaded from GenBank (Chiang et al. 2013, 2015; Chen and Wen 2016) Amplified PCR products were sequenced on an ABI 3730XL DNA Analyzer at Academia Sinica (Nangang, Taiwan). All tRNA was scanned by tRNAscan-SE v.2.0 (Lowe and Chan 2016) and base composition was calculated using Mega X (Kumar et al. 2018).

The complete mitochondrial of S. percnopterygionus was amplified and sequenced to be 16,502 bp in length and contained 13 typical vertebrate protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 1 light-strand replication origin (O_L) and 1 control region (D-loop). The genes arrangement and structure were similar to those of most other vertebrate mitogenomes (Chiang et al. 2013, 2015; Huang et al. 2015a, 2015b; Chen and Wen 2016; Huang et al. 2016a, 2016b, 2016c; Wen and Chen 2016). Most of the genes were encoded on the heavy-strand (H-strand), except for one protein coding gene (ND6) and seven transfer RNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Tyr, tRNA-Ser1, tRNA-Glu, and tRNA Pro) which were encoded on the light-strand (L-strand). The overall base composition is 28.1% for A, 17.1% for G, 28.7% for C and 26.0% for T, with a slight majority of AT content (54.1%). Twelve PCGs began with an ATG start codon while just one, for COI started with GTG. Three PCGs ended with an incomplete stop codon T– (COII, ND4, and Cyt b), two PCGs ended with stop codon TA- (ATPase6, COIII), and two other PCGs with stop codon TAG (ND3 and ND6), and the remainder shared the same stop codon TAA (ND1, ND2, COI, ATPase 8, ND4L, ND5). Among PCGs, ND5 found to be the longest (1839 bp) while ATPase 8 was the shortest (165 bp). Two rRNA genes (12S rRNA and 16S rRNA) were 950 bp and 1690 bp in length, respectively, being located between tRNA-Phe and tRNA-Leu, and separated by the tRNA-Val gene. The control region (D-loop) was 841 bp in length, located between the tRNA-pro and tRNA-Phe genes.

Phylogenetic analysis of Stiphodon percnopterygionus and its relatives was performed using maximum likelihood (ML) and Bayesian inference (BI) methods based on the sequences of 13 mitochondrial PCGs from 34 taxa of the order Gobiiformes retrieved from GeneBank. ML and BI analysis were conducted using standard RAxML (Stamatakis 2014) and MrBayes (Ronquist et al. 2012), respectively. ML was performed with 1000 bootstrap replicates and BI was performed as follow: Markov chains were run for 5,000,000 generations with trees being sampled every 500 generations, four chains and a burn-in step for the first 500 generations. GTR + G + I was used as the substitution model based on Akaike Information Criterion (AIC) estimated by MrModeltest (Nylander 2004). The phylogenetic tree (Figure 1) confirms that the 28 taxa were found within Gobiidae clade and remains constituted Eleotridae clade, Odontobutidae clade, and Rhyacichthyidae clade which is concordant with the result previous classifications of Order Gobiiformes (Pezold 1993; Gill and Mooi 2012; Agorreta et al. 2013; Fricke et al. 2022). The tree also demonstrated that, S. percnopterygionus is most closely related to S. tuivi. The further phylogenetic approach of the congeners would be in process to facilitate the detailed phylogenetic perspectives of Stiphodon.

Figure 1. Phylogenetic tree of selected species of Order Gobiiformes based on maximum likelihood (ML) and Bayesian inference (BI) using 13 protein-coding genes. Bootstrap value and posterior probability shown on the branches. The number after each species name is the corresponding GenBank accession number.

Ethic approval

Collection of fish sample was approved under the project grant No. 1050707 issued by Yangmingshan National Park, Taipei, Taiwan.

Author contributions

Tonisman Harefa: Conception and design, PCR experiments, analysis and interpretation of the data, drafting of manuscript, revising manuscript, final approval of the version to be published. I-Shiung Chen: Conception and design, analysis and interpretation of the data, revising manuscript, final approval of the version to be published. All authors agree to be accountable for all aspects of the work.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

Mitochondrial genome sequence can be accessed via accession number MW548257 in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/nuccore/MW548257. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA786405, SRR19216410, and SAMN23671125, respectively.

Additional information

Funding

This work was supported by Forestry Bureau Fund, Agriculture Council, Taipei and also partial support from Yangmingshan National Park, Taipei, Taiwan. The authors are responsible for the content and writing of this paper.