Abstract
The first complete mitochondrial genome of Metasepia tullbergi has been characterized in this study. The circular mitogenome is 16182 bp in length and comprises 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The organization of these genes is highly consistent with that of other Sepiidae. The overall base composition of mitogenome is 39.20% A, 36.07% T, 8.98% G, and 15.75% C, with 75.27% AT. Phylogenetic analysis further suggests that M. tullbergi is placed within the Sepiidae and is closely related to Sepia latimanus and S. apama.
Keywords: Cuttlefish, phylogenetic analysis, mitogenome, next-generation sequencing
The paintpot cuttlefish (Metasepia tullbergi) is a small cuttlefish belonging to the Sepiidae family. It is a neritic demersal species that inhabits the sandy and muddy continental shelf with a water depth of 20–100 m. M. tullbergi commonly appears in the Indo-Pacific region, including Japan, Korea, China, Hong Kong, Taiwan, the Philippines, and the Gulf of Thailand (Reid et al. 2005). As a member of the Metasepia genus, M. tullbergi has a small and thick, diamond-shaped cuttlebone and exhibits a unique body coloration (Thomas and MacDonald 2016). In this study, we aim to report the first complete mitochondrial genome of M. tullbergi and further analyze its phylogenetic relationship within the family Sepiidae.
The specimen of M. tullbergi was collected from the coastal water off northeastern Taiwan (121.9°E, 25.1°N) in May of 2020 and stored at National Taiwan Ocean University with a specimen number (NTOU-MT-01-2020). The total genomic DNA was prepared and then followed by the pair-end sequencing (2 × 150 bp) with Novaseq (Illumina, San Diego, CA). The de novo assembly of the complete mitochondrial genome of M. tullbergi was performed using Geneious Prime 2020.2 (Kearse et al. 2012). The identification and annotation of protein-coding genes (PCGs) were conducted using ORFfinder (https://www.ncbi.nlm.nih.gov/orfnder). Additionally, the transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were identified and annotated using MITOS Web Server (Bernt et al. 2013).
The complete mitochondrial genome of M. tullbergi was a closed-circular molecule with 16,182 bp in length (GenBank accession number: MT974497). It contains 13 PCGs, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (12S rRNA and 16S rRNA). The overall base composition of mitochondrial genome is biased toward A + T content at 75.27% (A = 39.20%, T = 36.07%, G = 8.98%, and C = 15.75%). The length of 13 PGCs ranges from 156 to 1749 bp. All PCGs initiate with ATG. 9 PCGs terminate with TAA while 4 PCGs (ATP6, NAD1, CYTB, and NAD6) terminate with TAG. The length of the 22 tRNA genes ranges from 60 to 73 bp. All tRNA genes possess a typical cloverleaf-shaped secondary structure. The 16S rRNA with a length of 1061 bp is located between trnL and trnV. The 12S rRNA with a length of 891 bp is located between trnV and trnC.
The phylogenetic position of M. tullbergi was further examined based on a maximum-likelihood phylogenetic tree constructed by 13 PCGs in the complete mitochondrial genomes of M. tullbergi and other closely related species using MEGA X (Kumar et al. 2018). The result indicated that M. tullbergi clustered within the Sepiidae and was closely related to Sepia latimanus and S. apama (Figure 1).
Figure 1.
Maximum-likelihood phylogenetic tree constructed by 13 PCGs in the mitochondrial genome of Metasepia tullbergi and the other nine Sepiidae species. Semirossia patagonica is used as the outgroup. Numbers beside each node represent percentages of 1000 bootstrap values.
Funding Statement
This study was supported by Taiwan Ocean Conservation and Fisheries Sustainability Foundation [109toffrest001].
Disclosure statement
No potential conflict of interest was reported by the author(s).
Data availability statement
The data that support the findings of this study are publicly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, Accession number: MT974497. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA679401, SRX9530327, SAMN16832771.
References
- Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF.. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319. [DOI] [PubMed] [Google Scholar]
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Reid A, Jereb P, Roper CFE.. 2005. Cuttlefishes. In: Jereb P, Roper CFE, editors. Cephalopods of the world. An annotated and illustrated catalogue of cephalopod species known to date. Vol. 1, Chambered nautiluses and sepioids (Nautilidae, Sepiidae, Sepiadariidae, Idiosepiidae and Spirulidae). Rome (Italy): Food and Agriculture Organization of the United Nations (FAO); p. 56–62. [Google Scholar]
- Thomas A, MacDonald C.. 2016. Investigating body patterning in aquarium-raised flamboyant cuttlefish (Metasepia pfefferi). PeerJ. 4:e2035. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The data that support the findings of this study are publicly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, Accession number: MT974497. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA679401, SRX9530327, SAMN16832771.