Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2022 Nov 11;7(11):1968–1970. doi: 10.1080/23802359.2022.2142070

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

Tonisman Harefa 1, I-Shiung Chen 1,✉
PMCID: PMC9662017  PMID: 36386025

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, iscfish@gmail.com) 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 (OL) 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.

Figure 1.

Open in a new tab

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.

Funding Statement

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.

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.

References

  1. Agorreta A, San Mauro D, Schliewen U, Van Tassell JL, Kovačić M, Zardoya R, Rüber L.. 2013. Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies. Mol Phylogenet Evol. 69(3):619–633. [DOI] [PubMed] [Google Scholar]
  2. Chen IS, Fang LS.. 1999. The freshwater and estuarine fishes of Taiwan. Pingtung: National Museum of Marine Biology and Aquarium Press; p. 1–287 (In Chinese). [Google Scholar]
  3. Chen IS, Wen ZH.. 2016. The complete mitochondrial genome of whiskered eel goby Taenioides cirratus (Perciformes, Gobioidei). Mitochondrial DNA A DNA Mapp Seq Anal. 27(2):1509–1511. [DOI] [PubMed] [Google Scholar]
  4. Chiang TY, Chen IS, Lin HD, Chang WB, Ju YM.. 2013. Complete mitochondrial genome of Sicyopterus japonicus (Perciformes, Gobiidae). Mitochondrial DNA A. 24(3):191–193. [DOI] [PubMed] [Google Scholar]
  5. Chiang T-Y, Chen I-S, Lin H-D, Hsiao S-T, Ju Y-M.. 2015. Complete mitochondrial genome of the amphidromous, red tailed goby Sicyopterus lagocephalus (Pallas) (Teleostei, Gobiidae). Mitochondrial DNA A. 26(5):670–671. [DOI] [PubMed] [Google Scholar]
  6. Fricke R, Eschmeyer WN, Van der Laan R.. 2022. Eschmeyer’s catalog of fishes: genera, species, references. http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp, version (12/09/2022).
  7. Fricke R, Pauly D.. 2021. Fish base. World Wide Electronic Publication. http://www.fishbase.org, version (10/08/2021). [Google Scholar]
  8. Gill AC, Mooi RD.. 2012. Thalasseleotrididae, new family of marine gobioid fishes from New Zealand and temperate Australia, with revised definition its sister taxon, the Gobiidae (Teleostei: Acanthomorpha). Zootaxa. 3266(1):41–52. [Google Scholar]
  9. Herre AWCT. 1936. Fishes in the zoological museum of Stanford University, III. New genera and species of gobies and blennies and a new Myxus, from the Pelew Islands and Celebes. Philipp J Sci. 59:275–287. [Google Scholar]
  10. Huang SP, Shen CN, Chen IS.. 2015a. The complete mitochondrial genome of the Abe’s mangrove goby Mugilogobius abei (Teleostei, Gobiidae). Mitochondrial DNA A. 26(1):143–144. [DOI] [PubMed] [Google Scholar]
  11. Huang SP, Shen CN, Chen IS.. 2015b. The complete mitochondrial genome of the Java fat-nose goby Pseudogobius javanicus (Teleostei, Gobiidae). Mitochondrial DNA A. 26(1):159–161. [DOI] [PubMed] [Google Scholar]
  12. Huang SP, Shen CN, Chen IS.. 2016a. The complete mitochondrial genome of the Redigoby Redigobius bikolanus (Perciformes, Gobiidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(1):525–526. [DOI] [PubMed] [Google Scholar]
  13. Huang SP, Chen IS, Jang-Liaw NH, Shao KT, Yung MMN.. 2016c. Complete mitochondrial reveals a new phylogenetic perspective on the brackish water goby Mugilogobius group (Teleostei: Gobiidae: Gobionellinae). Zoolog Sci. 33(5):566–574. [DOI] [PubMed] [Google Scholar]
  14. Huang SP, Chen IS, Shen CN.. 2016b. The complete mitochondrial genome of the small-scaled Wu’s goby Wuhanlinigobius polylepis. Mitochondrial DNA A DNA Mapp Seq Anal. 27(6):3823–3825. [DOI] [PubMed] [Google Scholar]
  15. Kumar S, Stecher G, Li M, Knyaz C, Tamura K.. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lord C, Bellec L, Dettaï A, Bonillo C, Keith P.. 2019. Does your lip stick? Evolutionary aspects of the mouth morphology of the Indo-Pacific clinging goby of the Sicyopterus genus (Teleostei: Gobiodei: Sicydiinae) based on mitogenome phylogeny. J Zool Syst Evol Res. 57(4):910–925. [Google Scholar]
  17. Lord C, Maeda K, Keith P, Watanabe S.. 2015. Population structure of the Asian amphidromous Sicydiinae goby, Stiphodon percnopterygionus, inferred from mitochondrial COI sequences, with comments on larval dispersal in the northwest Pacific Ocean. Vie Milieu Life Environ. 65(2):63–71. [Google Scholar]
  18. Lowe TM, Chan PP.. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44(W1):W54–W57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Maeda K, Mukai T, Tachihara K.. 2011. A new species of amphidromous goby, Stiphodon alcedo, from the Ryukyu Archipelago (Gobiidae: sicydiinae). Cybium. 35(4):285–298. [Google Scholar]
  20. Maeda K, Palla HP.. 2015. A new species of the genus Stiphodon from Palawan, Philippines (Gobiidae: Sicydiinae). Zootaxa. 4018(3):381–395. [DOI] [PubMed] [Google Scholar]
  21. Miya M, Nishida M.. 1999. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Mar Biotechnol. 1(5):416–0426. [DOI] [PubMed] [Google Scholar]
  22. Nakabo T. 2013. Fishes of Japan with pectorial keys to the species. 3rd ed. Hadano: Tokai University Press; p. 2428 (in Japanese). [Google Scholar]
  23. Nylander JAA. 2004. MrModeltest v2. Program distributed by the author. Uppsala: Evolutionary Biology Centre Uppsala University. [Google Scholar]
  24. Pezold F. 1993. Evidence for monophyletic Gobiinae. Copeia. 1993(3):634–643. [Google Scholar]
  25. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choiceacross a large model space. Syst Biol. 61(3):539–542. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Stamatakis A. 2014. RAxML Version 8: a tool for phylogenetic analysis and post analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Watson RE. 1995. Gobies of the genus Stiphodon from French Polynesia, with descriptions of two new species (Teleostei: Gobiidae: Sicydiinae. Ichthyol Explor Freshw. 6:33–48. [Google Scholar]
  28. Watson RE, Chen IS.. 1998. Freshwater gobies of the genus Stiphodon from Japan and Taiwan (Teleostei: Gobiidae: Sicydiini). Aqua J Ichthyol Aquat Biol. 3:55–68. [Google Scholar]
  29. Wen ZH, Chen IS.. 2016. The complete mitochondrial genome of spotted hidden-teeth goby Apocryptodon punctatus Tomiyama (Perciformes, Gobiidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(1):607–608. [DOI] [PubMed] [Google Scholar]
  30. Yamasaki N, Maeda K.. 2007. Pelagic larval duration and morphology at recruitment of Stiphodon percnopterygionus (Gobiidae: Sicydiinae). Raffles Bull Zool. 14:209–214. [Google Scholar]
  31. Yamasaki N, Tachihara K.. 2006. Reproductive biology and morphology of eggs and larvae of Stiphodon percnopterygionus (Gobiidae: Sicydiinae) collected from Okinawa Island. Ichthyol Res. 53(1):13–18. [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

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.

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES