Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2019 Jul 12;4(2):2473–2474. doi: 10.1080/23802359.2019.1637287

Complete mitochondrial genome and phylogenic analysis of Rhinogobius cliffordpopei (Perciformes, Gobiidae)

Dan Wang a,b,c,*, Chaoxu Dai a,b,c,*, Qiang Li a,b,c, Yahong Li a,b,c, Zhizhi Liu a,b,c,✉
PMCID: PMC7687544  PMID: 33365588

Abstract

The Rhinogobius (Perciformes, Gobiidae), is a species-rich freshwater gobiid genus. In this article, the complete mitochondrial genome (mtDNA) of the Rhinogobius cliffordpopei was first determined. The mtDNA of R. cliffordpopei consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. In the phylogenetic tree, R. cliffordpopei firstly joined with R. brunneus, and next clustered with R. giurinus. Then, they constituted Gobiidae clade with the rest other six species. This relationship consists of taxonomic status. The results would provide basal molecular data for the future research of adaptive evolution in Rhinogobius.

Keywords: Rhinogobius cliffordpopei, mitochondrial genome, phylogenetic analysis

The Rhinogobius is a species-rich freshwater gobiid genus, extensively distributed in eastern Eurasia and some islands of the western Pacific. It is the largest genus of freshwater gobies in this area, involving more than 85 species and 39 genera distributed in China (Suzuki et al. 2004; Oijen et al. 2011). Rhinogobius cliffordpopei is a pint-size benthic fish, distributed in the Liao River, Yangtze River, and Qiantang River. Rhinogobius cliffordpopei is a small-sized fish and the body length of sexually matured individuals is normally 30 mm. Because of its high environmental adaptability and being lack of suitable predator R. cliffordpopei has bred a large population in many glasses of water now and threatened the growth and survival of native fish. Therefore, the fish has attracted more and more attention of ecologists and evolutionary biologists. It is time for people to take measures to control the fish’s reproduction. However, only a few kinds of research have studied on it (Wu and Zhong 2008; Kondo et al. 2013). So, we determined the mtDNA of R. cliffordpopei for the first time and compared with the mtDNA (GenBank: KP 892753) of Rhinogobius giurinus, which has highly similar phenotypes with the former. To do so, we wanted to find suitable molecular markers for the two species and provide useful basal information for the adaptive evolution research of Gobiidae in the future.

The sample was collected from the Qiantang River, Zhejiang province, China. The samples were stored in 75% ethanol at 4 °C in Fish Herbarium of Shanghai Ocean University. We used phenol/chloroform to extract the genomic DNA. Firstly, three PCR primers were initially obtained from similarity species, which were used to amplify the complete mitochondrial genome sequence. Secondly, the other six primers were designed according to obtained sequences to supplement residual gaps. DNA Baser V.3.5.4 (http://www.dnabaser.com/news/index.html) was used to assemble the complete sequence. The whole mitochondrial genome was annotated by MitoFish and Mitoannotator (Iwasaki et al. 2013) and then submitted to GenBank. All tRNA genes were recognized by tRNAsan-SE1.21 (Lowe and Eddy 1997), which was also used to characterize the anti-codons of all tRNAs. We used MEGA 7.0 to figure out the base composition. To further study the phylogenetic position of R. cliffordpopei, 16 similar species’ mtDNA were collected from GenBank. Firstly, the mitochondrial sequences were aligned using clustal W and the sequence adjusted manually. Secondly, Jmodel Test2 (Darriba et al. 2012) was employed to estimate the best DNA model, according to a smaller AIC date. Then, we used maximum-likelihood (ML) to reconstruct phylogenetic trees and the number of bootstrap replicates was 1000.

The complete mitochondrial genome of R. cliffordpopei was 16,525 bp in length (GenBank number: KT 357638). It was composed of 13 typical protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Besides ND6 and eight tRNA genes, other genes were encoded on the heavy strand. COI gene initiated with GTG, whereas the other protein-coding genes initiated with ATG. Two stop codons (TAA, TAG) and three incomplete stop codons (TAA, TA, T) were found in the protein-coding genes. The length of 22 tRNA genes ranged from 62–75 bp. The genes of 12s rRNAs and 16s rRNAs were separated by the tRNAphe, and tRNAleu. The control region was located between the tRNApro and tRNAphe. The content A + T (50.8%) was higher than the content G + C (49.2%), which was similar to other vertebrates (Li and Liu 2016). The upper mtDNA organization and structure of R. cliffordpopei is very similar to R. giurinus’. The two mtDNA had 2363 variation sites, accounting for 15%. Especially, there was a 10–22% variation in the protein-coding genes. The analysis showed that ND4 and ND5 genes had the most mutation loci and they would be useful molecular markers for identification of the two morphological similarity fish.

Altogether, 18 typical Gobies were used to construct a phylogenetic tree. In Figure 1, R. cliffordpopei firstly joined with R. brunneus, and next clustered with R. giurinus. Then, the nine species constituted Gobiidae clade. Finally, Gobiidae, Eleotridae, Rhyacichthyidae, and Odontobutidae formed sister groups. This relationship consists of taxonomic status (Wang et al. 2001; Thacker 2009; Agorreta and Rüber 2012; Tornabene et al. 2013).

Figure 1.

Figure 1.

Open in a new tab

The phylogenetic relationship for fish of the Gobiidei.

Acknowledgments

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

Disclosure statement

References

  1. Agorreta A, Rüber L. 2012. A standardized reanalysis of molecular phylogenetic hypotheses of Gobioidei. Syst Biodivers. 10:375–390. [Google Scholar]
  2. Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods. 9:772. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Iwasaki W, Fukunaga T, Isagozawa R, Yamaa K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol. 30:2531–2540. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Kondo M, Maeda K, Hirashima K, Tachihara K. 2013. Comparative larval development of three amphidromous Rhinogobius species, making reference to their habitat preferences and migration biology. Mar Freshwater Res. 64:249–266. [Google Scholar]
  5. Li Q, Liu ZZ. 2016. New complete mitochondrial genome of the Odontobutis potamophila (Perciformes, Odontobutidae): Genome description and phylogenetic performance. Mitochondrial DNA. 27:163–164. [DOI] [PubMed] [Google Scholar]
  6. Lowe TM, Eddy SR (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res. 25:955–964. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Oijen MJP, Suzuki T, Chen IS. 2011. On the earliest published species of Rhinogobius with a redescription of Gobius brunneus Temminck and Schlegel, 1845. J Natl Taiwan Mus. 64:1–17. [Google Scholar]
  8. Suzuki T, Shibukawa K, Yano K, Senou H (2004). A photographic guide to the gobioid fishes in Japan. Tokyo (Japan): Heibonsha. [Google Scholar]
  9. Thacker CE. 2009. Phylogeny of Gobioidei and placement within Acanthomorpha, with a new classification and investigation of diversification and character evolution. Copeia. 2009:93–104. [Google Scholar]
  10. Tornabene L, Chen Y, Pezold F. 2013. Gobies are deeply divided: phylogenetic evidence from nuclear DNA (Teleostei: Gobioidei: Gobiidae). Syst Biodivers. 11:345–361. [Google Scholar]
  11. Wang HY, Tsai MP, Dean J, Lee SC. 2001. Molecular phylogeny of gobioid fishes (Perciformes: Gobioidei) based on mitochondrial 12S rRNA sequences. Mol Phylogenet Evol. 20:390–408. [DOI] [PubMed] [Google Scholar]
  12. Wu HL, Zhong JS (2008). Taxonomic research of the Gobiopdei (Perciformes) in China. Beijing (China): Beijing Science Press; p. 150–153. [Google Scholar]

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

RESOURCES