The Mitochondrial Genome of Ylistrum japonicum (Bivalvia, Pectinidae) and Its Phylogenetic Analysis
Abstract
:1. Introduction
2. Results
2.1. Mitochondrial Genome Composition
2.2. Protein-Coding Genes
2.3. rRNA and tRNA Genes
2.4. Control Region
2.5. Gene Order
2.6. Gene Collinearity
2.7. Phylogenetic Analysis
2.8. Systematic Descriptions
3. Discussion
4. Materials and Methods
4.1. Sample Collection
4.2. DNA Extraction, Library Preparation, and Next Generation Sequence
4.3. Sequence Assembly and Annotation
4.4. Gene Collinearity
4.5. Phylogenetic Analysis with Mitochondrial Genome
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene | Sequence Location | Size (bp) | Start Codon | Stop Codon | Intergenic Nucleotide (bp) |
---|---|---|---|---|---|
rrnL | 18–1509 | 1492 | 17 | ||
cox1 | 1527–3158 | 1632 | ATG | TAA | 17 |
trnS | 3219–3286 | 68 | 60 | ||
nad4 | 3334–4581 | 1248 | GTG | TAG | 47 |
trnH | 4588–4652 | 65 | 6 | ||
trnD | 4690–4757 | 68 | 37 | ||
nad4L | 4769–5089 | 321 | ATG | TAA | 11 |
cox3 | 5094–5939 | 846 | GTG | TAG | 4 |
nad2 | 5942–6904 | 963 | GTG | TAA | 2 |
nad3 | 6904–7275 | 372 | ATC | TAA | −1 |
trnA | 7291–7356 | 66 | 15 | ||
nad6 | 7431–7958 | 528 | GTG | TAA | 74 |
trnL | 7960–8024 | 65 | 1 | ||
cytb | 8028–9402 | 1375 | TTG | T | 3 |
trnW | 9403–9471 | 69 | 0 | ||
trnP | 9522–9586 | 65 | 50 | ||
nad5 | 9594–11,381 | 1788 | TTG | TAG | 7 |
cox2 | 11,532–12,524 | 993 | ATG | TAG | 150 |
trnR | 13,380–13,447 | 68 | 855 | ||
atp6 | 13,498–14,211 | 714 | ATG | TAG | 50 |
trnM | 14,216–14,280 | 65 | 4 | ||
atp8 | 14,284–14,439 | 156 | GTG | TAG | 3 |
trnQ | 14,451–14,521 | 71 | 11 | ||
trnI | 14,542–14,612 | 71 | 20 | ||
trnL | 14,638–14,706 | 69 | 25 | ||
trnM | 14,713–14,784 | 72 | 6 | ||
trnE | 14,788–14,853 | 66 | 3 | ||
trnC | 15,053–15,118 | 66 | 199 | ||
trnS | 15,129–15,195 | 67 | 10 | ||
trnY | 15,205–15,271 | 68 | 9 | ||
trnT | 15,283–15,350 | 68 | 11 | ||
trnG | 15,372–15,437 | 66 | 21 | ||
rrnS | 15,459–16,415 | 957 | 21 | ||
rrnL | 16,453–17,939 | 1486 | 37 | ||
trnK | 18,145–18,216 | 72 | 205 | ||
trnN | 18,301–18,367 | 67 | 84 | ||
trnF | 18,381–18,445 | 65 | 13 | ||
trnV | 18,459–18,525 | 67 | 13 | ||
nad1 | 18,528–19,475 | 948 | GTG | TAG | 2 |
Subfamily | Tribe in This Research | Previous Tribe | Species | Genbank Accession Numbers | Genetic Compartments |
---|---|---|---|---|---|
Ingroup | |||||
Aequipectinini | Aequipectinini | Argopecten irradians irradians | DQ665851 | mitogenome | |
Aequipectinini | Aequipectinini | Argopecten purpuratus | KT161260 | mitogenome | |
Aequipectinini | Aequipectinini | Argopecten ventricosus | KT161261 | mitogenome | |
Pectininae | Amusiini | Amusiini | Amusium pleuronectes | MT419374 | mitogenome |
Amusiini | Amusiini | Amusium pleuronectes | AJ571616 | 16S rRNA | |
Amusiini | Amusiini | Amusium pleuronectes | HM630497 | 16S rRNA | |
Decatopectinini | Amusiini | Ylistrum japonicum | PP571649 | mitogenome | |
Decatopectinini | Amusiini | Ylistrum japonicum | KF982785 | 16S rRNA | |
Decatopectinini | Amusiini | Ylistrum japonicum | HM622707 | 16S rRNA | |
Decatopectinini | Amusiini | Ylistrum balloti | HM540095 | 16S rRNA | |
Decatopectinini | Amusiini | Ylistrum balloti | JF339127 | 16S rRNA | |
Decatopectinini | Decatopectinini | Anguipecten picturatus | HM630511 | 16S rRNA | |
Decatopectinini | Decatopectinini | Antillipecten antillarum | HMS35657 | 16S rRNA | |
Pectinini | Pectinini | Pecten maximus | KP900975 | mitogenome | |
Pectinini | Pectinini | Pecten maximus | KF982791 | 16S rRNA | |
Pectinini | Pectinini | Pecten albicans | KP900974 | mitogenome | |
Pectinini | Pectinini | Pecten maximus | JN896624 | 16S rRNA | |
Palliolinae | Palliolini | Palliolini | Placopecten magellanicus | DQ088274 | mitogenome |
Chlamydini | Chlamydini | Chlamy farreri | EF473269 | mitogenome | |
Chlamydinae | Fortipectinini | Fortipectinini | Mizuhopecten yessoensis | FJ595959 | mitogenome |
Mimachlamydini | Mimachlamydini | Mimachlamys varia | MZ520326 | mitogenome | |
Outgroup | |||||
Crassostreinae | Magallana bilineata | MT985154 | mitogenome | ||
Magallana gigas | MZ497416 | mitogenome | |||
Mytilinae | Mytilus galloprovincialis | DQ399833 | mitogenome | ||
Mytilus trossulus | AY823625 | mitogenome |
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Han, Y.; Xie, Y.; Hao, Z.; Mao, J.; Wang, X.; Chang, Y.; Tian, Y. The Mitochondrial Genome of Ylistrum japonicum (Bivalvia, Pectinidae) and Its Phylogenetic Analysis. Int. J. Mol. Sci. 2024, 25, 8755. https://doi.org/10.3390/ijms25168755
Han Y, Xie Y, Hao Z, Mao J, Wang X, Chang Y, Tian Y. The Mitochondrial Genome of Ylistrum japonicum (Bivalvia, Pectinidae) and Its Phylogenetic Analysis. International Journal of Molecular Sciences. 2024; 25(16):8755. https://doi.org/10.3390/ijms25168755
Chicago/Turabian StyleHan, Yida, Yaoyu Xie, Zhenlin Hao, Junxia Mao, Xubo Wang, Yaqing Chang, and Ying Tian. 2024. "The Mitochondrial Genome of Ylistrum japonicum (Bivalvia, Pectinidae) and Its Phylogenetic Analysis" International Journal of Molecular Sciences 25, no. 16: 8755. https://doi.org/10.3390/ijms25168755