Corresponding author: Joong-Ki Park (
Academic editor: Andrew David
The family
Lee Y, Park J-K (2022) Complete mitochondrial genome of
The genus
The implementation of new sequencing technologies (e.g., next-generation sequencing; NGS) and various bioinformatics tools has allowed mitochondrial genome sequencing to be markedly easier, cost-effective, and widely used for studying phylogeny in various metazoan groups, including
Whole-genome sequencing libraries were prepared using the MGIEasy DNA library prep kit (BGI, Shenzhen, China) according to the manufacturer’s instructions and quantified using the QuantiFluor ssDNA System (Promega Corporation, Madison, WI, USA). Sequencing was conducted on the MGISEQ-2000 system with 150 base-pair reads. A total of 48,608,637 raw reads were obtained, and adapter-trimmed using a skewer program (
To determine the relationship between
Complete mitochondrial genomes used for phylogenetic analysis in this study.
Family | Species | Diet | GenBank | Reference |
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Molluscivorous | — |
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Molluscivorous |
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— | |
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Molluscivorous |
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Molluscivorous | — |
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Molluscivorous | — |
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Molluscivorous |
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Piscivorous |
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Piscivorous |
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Piscivorous |
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Piscivorous |
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Vermivorous | — |
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Vermivorous | — |
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Vermivorous | — |
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Vermivorous |
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Vermivorous | — |
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Vermivorous | — |
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Vermivorous | — |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous |
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Vermivorous | — |
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Vermivorous |
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Vermivorous |
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This study | |
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Vermivorous | — |
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Vermivorous |
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Vermivorous | — |
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Vermivorous |
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Vermivorous | — |
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Vermivorous |
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Vermivorous |
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All |
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Vermivorous |
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— |
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Gene regions in the mitochondrial genome of
Gene | Start | Stop | Strand direction | Length (bp) | Codon (start) | Codon (stop) | Overlapping regions | Intergenic spacers |
---|---|---|---|---|---|---|---|---|
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1 | 1,548 | H | 1,548 | ATG | TAA | 1 | 166 |
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1,715 | 2,401 | H | 687 | ATG | TAA | — | — |
tRNA-Asp ( |
2,402 | 2,468 | H | 67 | — | — | ||
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2,469 | 2,630 | H | 162 | ATG | TAA | — | 6 |
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2,637 | 3,359 | H | 723 | ATG | TAA | — | 11 |
tRNA-Met ( |
3,371 | 3,438 | L | 68 | — | 12 | ||
tRNA-Tyr ( |
3,451 | 3,516 | L | 66 | — | 1 | ||
tRNA-Cys ( |
3,518 | 3,582 | L | 65 | — | — | ||
tRNA-Trp ( |
3,583 | 3,648 | L | 66 | — | — | ||
tRNA-Gln ( |
3,646 | 3,711 | L | 66 | 3 | 24 | ||
tRNA-Gly ( |
3,736 | 3,802 | L | 67 | — | 35 | ||
tRNA-Glu ( |
3,838 | 3,902 | L | 65 | — | — | ||
small subunit |
3,903 | 4,854 | H | 952 | — | — | ||
tRNA-Val ( |
4,855 | 4,921 | H | 67 | — | — | ||
large subunit |
4,922 | 6,296 | H | 1,375 | — | — | ||
tRNA-Leu1 ( |
6,297 | 6,366 | H | 70 | — | 6 | ||
tRNA-Leu2 ( |
6,373 | 6,441 | H | 69 | — | — | ||
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6,442 | 7,383 | H | 942 | ATG | TAG | — | 16 |
tRNA-Pro ( |
7,400 | 7,468 | H | 69 | — | — | ||
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7,469 | 7,975 | H | 507 | ATG | TAA | — | 13 |
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7,989 | 9,128 | H | 1,140 | ATG | TAA | — | 11 |
tRNA-Ser2 ( |
9,140 | 9,204 | H | 65 | — | 16 | ||
tRNA-Thr (trnT) (tgt) | 9,221 | 9,289 | L | 69 | — | 22 | ||
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9,312 | 9,608 | H | 297 | ATG | TAG | — | — |
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9,602 | 10,984 | H | 1,383 | ATG | TAG | 7 | — |
tRNA-His ( |
10,984 | 11,049 | H | 66 | 1 | — | ||
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11,050 | 12,765 | H | 1,716 | ATG | TAA | — | — |
tRNA-Phe ( |
12,765 | 12,829 | H | 65 | 1 | — | ||
D-loop | 12,830 | 13,415 | H | 586 | — | — | ||
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13,416 | 14,195 | H | 780 | ATG | TAA | — | 34 |
tRNA-Lys ( |
14,230 | 14,298 | H | 69 | — | 9 | ||
tRNA-Ala ( |
14,308 | 14,374 | H | 67 | — | 22 | ||
tRNA-Arg ( |
14,397 | 14,465 | H | 69 | — | 11 | ||
tRNA-Asn ( |
14,477 | 14,545 | H | 69 | — | 12 | ||
tRNA-Ile ( |
14,558 | 14,626 | H | 69 | — | 5 | ||
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14,632 | 14,985 | H | 354 | ATG | TAA | — | 15 |
tRNA-Ser1 ( |
15,001 | 15,068 | H | 68 | — | — | ||
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15,069 | 1 | H | 1,053 | ATG | TAA | — | — |
Mitochondrial genome structure of
The lengths of 13
Nucleotide composition of the mitochondrial genome of
Nucleotide sequence | Length (bp) | A (%) | C (%) | G (%) | T (%) | A+T (%) | G+C (%) |
---|---|---|---|---|---|---|---|
Entire sequence | 16,120 | 29.0 | 16.3 | 17.6 | 37.1 | 66.1 | 33.9 |
Protein coding sequence | 11,292 | 26.3 | 17.0 | 17.5 | 39.2 | 65.5 | 34.5 |
Codon position* | |||||||
1st | 3,751 | 26.9 | 17.2 | 24.7 | 31.2 | 58.1 | 41.9 |
2nd | 3,751 | 18.3 | 20.9 | 16.6 | 44.2 | 62.5 | 37.5 |
3rd | 3,751 | 33.4 | 13.1 | 11.4 | 42.1 | 75.5 | 24.5 |
Ribosomal RNA gene sequence | 2,327 | 35.5 | 14.4 | 18.4 | 31.6 | 67.2 | 32.8 |
Transfer RNA gene sequence | 1,481 | 34.0 | 16.2 | 17.7 | 32.1 | 66.1 | 33.9 |
D-loop region sequence | 586 | 31.1 | 15.4 | 17.6 | 35.8 | 67.1 | 32.9 |
*Termination codons were not included.
The relative synonymous codon usage (
Twenty-two tRNA genes were found in the mitochondrial genome of
Predicted tRNA structures of
Phylogenetic analysis using
Phylogenetic relationships of the genus
This work was supported by National Marine Biodiversity Institute of Korea (2022M01100) and the Basic Science Research Program of the National Research Foundation of Korea (NRF) funded by the Ministry of Education (no. 2020R1I1A1A01074213; 2020R1A2C2005393).