Complete mitochondrial genome of the Hydrophis melanocephalus slender-necked sea snake (Squamata, Elapidae)

Abstract

We here report the complete mitochondrial genome of the Hydrophis melanocephalus slender-necked sea snake from Okinawa, Japan. Its length is 17,182 bp, consisting of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and three non-coding regions, providing the basis for further phylogenetic and evolutionary studies of sea snakes.

Keywords:

• Slender-necked sea snake
• Hydrophis melanocephalus
• mitochondrial genome
• Elapidae

Hydrophis melanocephalus, a rarely studied slender-necked sea snake, has been often confused with other snakes, such as H. coggeri in the Australian region (Kharin 1984), Emydocephalus ijimae in Japan (Yi et al. 2019), and H. platurus and Laticauda semifasciata in Korea (Kim et al. 2018; Kim et al. 2020). Hydrophis melanocephalus is known to be distributed in Vietnam, China, Taiwan, Japan, and Philippines (David and Ineich 1999; Kharin and Czeblukov 2006). Several sightings of the snake have been recorded in Korean coastal regions (Shannon 1956; Won 1971; Kang and Yoon 1975), but no scientific records, such as specimens, photographs, or morphological measurements, exist. In this study, we reported the complete mitochondrial sequence of H. melanocephalus from Okinawa, Japan.

The specimen was captured in Toguchi, Motobu, Kunigami District, Okinawa, Japan (26°39′44.12″ N and 127°53′18.42″ E), and preserved in 70% ethanol at the National Marine Biodiversity Institute of Korea (Voucher No. MABIK AR00000052). Whole genomic DNA was extracted from the muscle tissue using the PCI (Phenol-Chloroform Isoamyl Alcohol) method with DNA extraction solution from Asahida et al. (1996), and proteinase K (Bioneer, Daejeon, South Korea). The whole mitochondrial DNA was sequenced using the Sanger method in a 3730xl DNA analyzer (Applied Biosystems, CA, USA). Sequencing was performed at Macrogen Inc. (Seoul, South Korea). To assemble and annotate the obtained mitochondrial DNA sequences, we used Geneious 9.0.4 (Biomatters Ltd, Auckland, New Zealand), tRNA Scan-SE1.21 software (http://lowelab.ucsc.edu/tRNAScan-SE/) (Lowe and Eddy 1997), and Dual Organellar GenoMe Annotator (DOGMA) (Wyman et al. 2004). The phylogenetic tree of H. malenocephalus was constructed with PAUP* v4.0b10 (Swofford 2003) using the complete mitogenomic sequences, obtained here, as well as from GenBank (Figure 1). The Bayesian inference and maximum-likelihood method were applied to construct the tree with 1000 bootstrap replicates.

Figure 1. Bayesian inference (BI) tree of Hydrophis melanocephalus based on its 13 mitochondrial protein-coding genes. Both Viperidae species were used as outgroup. The accession number of mitogenomes obtained from GenBank, are indicated after the scientific name of each species. Analyzed values (ML bootstrap value/Bayesian posterior probabilities) are denoted on each branch.

The total length of the H. melanochepalus mitochondrial genome was revealed to be 17,182 bp (GenBank Accession No. MK775532), with a base composition of 33.2% A, 27.3% T, 13.1% G, and 26.4% C, showing an A–T rich (60.5%) feature. The mitogenome contained 13 protein-coding genes (PCGs), two rRNA genes (12S and 16S rRNA), 22 tRNA genes, and three non-coding regions comprised of two control regions, and an L-strand replication origin (OL). Its arrangement pattern and transcribing directions were identical to those of other elapid snakes (Laticauda semifasciata and Emydocephalus ijimae; Kim et al. 2018; Yi et al. 2019).

The phylogenetic tree revealed that H. melanochepalus formed a sister group with H. platurus, another species of the Hydrophis genus, and showed close relationship with species from the Hydrophinae subfamily, consistent with a previous phylogenetic study of elapid snakes by Lee et al. (2016).

Geolocation information

Toguchi, Motobu, Kunigami District, Okinawa, Japan (26°39′44.12″ N and 127°53′18.42″ E).

Disclosure statement

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

Additional information

Funding

This work was supported by the National Marine Biodiversity Institute of Korea under Grant number [2020M00400].