Abstract
The complete mitochondrial genome sequence of Benthosema pterotum is first described in this article. The total length of mitogenome is 18,052 bp. It contains 13 protein-coding genes, 22 tRNA genes, and two ribosomal RNA genes. The overall base composition of H-strand is 27.83% A, 30.88% C, 25.61% T, and 15.69% G, with an A＋T bias of 53.43%. The phylogenetic analysis result showed that the B. pterotum and Electrona carlsbergi were close relationship.
Keywords: Benthosema pterotum, mitochondrial genomem, Myctophidae
The skinnycheek lantern fish Benthosema pterotum (Alcock), of the family Myctophidae, is widely distributed in the subtropical-tropical waters including East China Sea (Sassa et al. 2010). They are small in size ranging from 2 to 30 mm (Homaei et al. 2013). Benthosema pterotum feed on a variety of zooplankton, including copepods as the most important food item (Dalpadado and Gjøsaeter 1988; Valinassab et al. 2007).
The complete mitochondrial genome of B. pterotum first determined in this paper was expected to provide help on population genetics of B. pterotum and further molecular phylogenetic studies. The sample of B. pterotum in this article was collected from the East China Sea (121°56′E, 30°52′N) and stored in the East Sea Fisheries Research Institute Fish Specimen Room (Accession number: MBp201904100172). Its DNA was frozen at −80 °C in the Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture, China. According to genes from B. pterotum, 12S ribosomal RNA gene (Accession: LC146182), 16S ribosomal RNA gene (Accession: KR231720), cytochrome c oxidase subunit I (COI) gene (Accession: JX133773), cytochrome b (Cytb) gene (Accession: JX133771) primers were designed, and PCR amplification and sequencing were conducted.
The whole length of B. pterotum mitogenome was 18,052 bp and submitted in GenBank (Accession No. MN266306). The nucleotide composition of the heavy strand was 27.83% for A, 30.88% for C, 25.61% for T, and 15.69% for G, with a high A＋T bias of 53.43%. It contains 13 protein-coding genes, 22 tRNAs, and two rRNAs. Most genes were located on the heavy strand, but ND6 and 8 tRNA genes (tRNAGln, RNAAla, tRNAAsn, tRNATyr, tRNACys, tRNASer, tRNAGlu, tRNAPro) were encoded on the light strand. Most protein-coding genes initiated with ATG except for COI starting with GTG. Four types of protein-coding genes ended with typical termination codons TAA (ND1, ATPase 8, ATPase 6, COIII, ND4L), TAG (ND3, ND5, ND6), AGA (COI), and T–– (ND2, COII, ND4, Cytb). The length of 12S (located between tRNAGlu and tRNAMet) and 16S (located between tRNAPhe and tRNAPro) rRNA genes were 952 bp and 1683 bp, respectively.
To investigate the phylogenetic relationship, we downloaded the mitochondrial genome sequences of 17 currently available species. The concatenated sequences of 13 protein-coding genes, two rRNAs genes, and 22 tRNAs genes were aligned with the ClustalW program (Larkin et al. 2007). Using the Maximum-Likelihood (ML) method (Stamatakis 2006), the phylogenetic tree was constructed (Figure 1) using MEGA6 (Tamura et al. 2013). The best-fitting model (GTR + I + G) was obtained as the optimization model using jModelTest (Posada 2008). The result indicating that the B. pterotum and Electrona carlsbergi were close relationship (Figure 1).
Figure 1.
The phylogenetic tree based on the 13 protein-coding genes, two rRNAs genes, and 22 tRNAs genes of Arothron hispidus, Auxis rochei, Beryx splendens, Caesio cuning, Electrona carlsbergi, Hucho hucho, Kyphosus cinerascens, Lampadena atlantica, Lutjanus peru, Neoscopelus macrolepidotus, Pterocaesio tile, Salmo salar, Sargocentron rubrum, Scopelengys tristis, Setipinna taty, Triodon macropterus, and an outgroup Protopterus annectens. The bootstrap supports for Maximum-Likelihood (ML) method was indicated at each branch.
Funding Statement
This study was supported by Fund of Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, P. R. China [FREU2019-04].
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References
- Dalpadado P, Gjøsaeter J. 1988. Feeding ecology of the lanternfish Benthosema pterotum from the Indian Ocean. Mar Biol. 99(4):555–567. [Google Scholar]
- Homaei AA, Mymandi AB, Sariri R, Kamrani E, Stevanato R, Etezad SM, Khajeh K. 2013. Purification and characterization of a novel thermostable luciferase from Benthosema pterotum. J Photochem Photobiol B. 125:131–136. [DOI] [PubMed] [Google Scholar]
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics. 23(21):2947–2948. [DOI] [PubMed] [Google Scholar]
- Posada D. 2008. jModelTest: phylogenetic model averaging. Mol Biol Evol. 25(7):1253–1256. [DOI] [PubMed] [Google Scholar]
- Sassa C, Tsukamoto Y, Yamamoto K, Tokimura M. 2010. Spatio-temporal distribution and biomass of Benthosema pterotum (Pisces: Myctophidae) in the shelf region of the East China Sea. Mar Ecol Prog Ser. 407:227–241. [Google Scholar]
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690. [DOI] [PubMed] [Google Scholar]
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 30(12):2725–2729. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Valinassab T, Pierce G.J, Johannesson K. 2007. Lantern fish (Benthosema pterotum) resources as a target for commercial exploitation in the Oman Sea. J Appl Ichthyol. 23(5):573–577. [Google Scholar]