The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement, Taxon Sampling, and DNA Extraction
2.2. PCR Amplification and Sequencing
2.3. Sequence Assembly, Annotation, and Analysis
2.4. Phylogenetic Analysis and Divergence Time Estimation
3. Results and Discussion
3.1. Sequencing Data and Genome Composition
3.2. PCGs and Codon Usage
3.3. Transfer RNAs and Control Region
3.4. Gene Rearrangement
3.5. Phylogenetic Analysis
3.6. Divergence Time Estimation
3.7. Genetic Divergence
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene | Direction | Location | Size (bp) | Anticodon | Start Codon | Stop Codon | Intergenic Nucleotides |
---|---|---|---|---|---|---|---|
trnF | + | 1–70 | 70 | GAA | 0 | ||
rrnS | + | 71–1028 | 958 | −1 | |||
trnV | + | 1028–1096 | 69 | TAC | 21 | ||
rrnL | + | 1118–2702 | 1585 | −1 | |||
trnL2 | + | 2702–2777 | 76 | TAA | 0 | ||
nad1 | + | 2778–3749 | 972 | ATG | TAG | −1 | |
trnI | + | 3749–3819 | 71 | GAT | 131 | ||
trnH (Ψ) | + | 3951–4017 | 67 | CTG | 0 | ||
trnS1 | + | 4018–4083 | 66 | GCT | −1 | ||
trnL1 | + | 4083–4154 | 72 | TAG | 1 | ||
nad5 | + | 4156–5976 | 1821 | ATG | TAA | 135 | |
trnT | + | 6112–6182 | 71 | TGT | 1 | ||
trnP | − | 6184–6253 | 70 | TGG | 15 | ||
CR2 | 6267–7553 | 1286 | −1 | ||||
trnQ | − | 7553–7623 | 71 | TTG | −1 | ||
trnM | + | 7623–7691 | 69 | CAT | 0 | ||
nad2 | + | 7692–8732 | 1041 | ATG | TAG | −2 | |
trnW | + | 8731–8809 | 79 | TCA | 1 | ||
trnA | − | 8811–8879 | 69 | TGC | 1 | ||
trnN | − | 8881–8954 | 74 | GTT | 3 | ||
OL | + | 8958–8984 | 27 | −2 | |||
trnC | − | 8983–9048 | 66 | GCA | 0 | ||
trnY | − | 9049–9119 | 71 | GTA | 1 | ||
cox1 | + | 9121–10,668 | 1548 | GTG | AGG | −9 | |
trnS2 | − | 10,660–10,730 | 71 | TGA | 3 | ||
trnD | + | 10,734–10,803 | 70 | GTC | 0 | ||
cox2 | + | 10,804–11,490 | 687 | ATG | TAG | 1 | |
trnK | + | 11,492–11,563 | 72 | TTT | 1 | ||
atp8 | + | 11,565–11,732 | 168 | ATG | TAA | −16 | |
atp6 | + | 11717–12,399 | 683 | ATG | TA(A) | 18 | |
cox3 | + | 12,418–13,202 | 785 | ATG | TA(A) | −1 | |
trnG | + | 13,202–13,271 | 70 | TCC | 0 | ||
nad3-a | + | 13,272–13,445 | 174 | ATG | --- | 1 | |
nad3-b | + | 13,447–13,621 | 175 | --- | T(AA) | 0 | |
trnR | + | 13,622–13,690 | 69 | TCG | 0 | ||
nad4l | + | 13,691–13,987 | 297 | ATG | TAA | −7 | |
nad4 | + | 13,981–15,358 | 1378 | ATG | T(AA) | 640 | |
nad6 | − | 15,999–16,523 | 525 | ATG | AGG | 0 | |
trnE | − | 16,524–16,591 | 68 | TTC | 4 | ||
cob | + | 16,596–17,762 | 1167 | ATG | TAA | 48 | |
trnP (Ψ) | − | 17,811–17,872 | 62 | --- | 17 | ||
CR1 | 17,890–19,093 | 1203 | 0 |
Species | Total Size (bp) | Complete Mitogenome | tRNAs | PCGs | rRNAs | CRs | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A + T% | AT-skew | GC-skew | A + T% | AT-skew | GC-skew | A + T% | AT-skew | GC-skew | A + T% | AT-skew | GC-skew | A + T% | AT-skew | GC-skew | ||
P. m. peguense | 19,093 | 61.2 | 0.106 | −0.335 | 61.9 | 0.040 | 0.031 | 59.9 | 0.034 | −0.313 | 60.2 | 0.236 | −0.149 | 66.3 | 0.011 | −0.344 |
P. m. megalorcephalum | 19,196 | 61.5 | 0.106 | −0.323 | 61.9 | 0.048 | 0.020 | 59.9 | 0.034 | −0.313 | 60.0 | 0.236 | −0.149 | 68.1 | −0.008 | −0.223 |
P. m. shiui | 19,043 | 61.4 | 0.107 | −0.329 | 62.3 | 0.071 | −0.053 | 59.7 | 0.033 | −0.311 | 60.3 | 0.237 | −0.147 | 66.9 | −0.006 | −0.256 |
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | P. m. peguense | |||||||||||||||||
2 | P. m. megalorcephalum | 0.068 | ||||||||||||||||
3 | P. m. shiui | 0.059 | 0.024 | |||||||||||||||
4 | M. annamensis | 0.257 | 0.266 | 0.255 | ||||||||||||||
5 | M. megalocephala | 0.268 | 0.271 | 0.259 | 0.094 | |||||||||||||
6 | M. mutica | 0.255 | 0.260 | 0.250 | 0.058 | 0.086 | ||||||||||||
7 | M. reevesii | 0.261 | 0.264 | 0.253 | 0.087 | 0.051 | 0.080 | |||||||||||
8 | M. nigricans | 0.260 | 0.265 | 0.253 | 0.089 | 0.049 | 0.081 | 0.040 | ||||||||||
9 | M. rivulata | 0.253 | 0.261 | 0.251 | 0.081 | 0.082 | 0.079 | 0.076 | 0.074 | |||||||||
10 | M. sinensis | 0.260 | 0.266 | 0.256 | 0.090 | 0.055 | 0.081 | 0.049 | 0.047 | 0.077 | ||||||||
11 | T. graeca | 0.245 | 0.253 | 0.242 | 0.198 | 0.198 | 0.194 | 0.194 | 0.193 | 0.190 | 0.195 | |||||||
12 | T. kleinmanni | 0.251 | 0.255 | 0.245 | 0.201 | 0.201 | 0.195 | 0.197 | 0.194 | 0.197 | 0.198 | 0.089 | ||||||
13 | T. marginata | 0.246 | 0.253 | 0.244 | 0.201 | 0.202 | 0.195 | 0.196 | 0.193 | 0.193 | 0.196 | 0.082 | 0.071 | |||||
14 | C. amboinensis | 0.259 | 0.266 | 0.256 | 0.118 | 0.121 | 0.114 | 0.115 | 0.114 | 0.113 | 0.114 | 0.194 | 0.198 | 0.194 | ||||
15 | C. aurocapitata | 0.277 | 0.286 | 0.276 | 0.127 | 0.123 | 0.126 | 0.119 | 0.122 | 0.121 | 0.121 | 0.218 | 0.222 | 0.219 | 0.116 | |||
16 | C. flavomarginata | 0.260 | 0.268 | 0.258 | 0.110 | 0.112 | 0.107 | 0.107 | 0.109 | 0.105 | 0.111 | 0.193 | 0.201 | 0.196 | 0.099 | 0.085 | ||
17 | C. galbinifrons | 0.257 | 0.262 | 0.251 | 0.106 | 0.110 | 0.106 | 0.105 | 0.105 | 0.102 | 0.105 | 0.192 | 0.194 | 0.195 | 0.092 | 0.096 | 0.083 |
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Luo, H.; Li, H.; Huang, A.; Ni, Q.; Yao, Y.; Xu, H.; Zeng, B.; Li, Y.; Wei, Z.; Yu, G.; et al. The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis. Genes 2019, 10, 487. https://doi.org/10.3390/genes10070487
Luo H, Li H, Huang A, Ni Q, Yao Y, Xu H, Zeng B, Li Y, Wei Z, Yu G, et al. The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis. Genes. 2019; 10(7):487. https://doi.org/10.3390/genes10070487
Chicago/Turabian StyleLuo, Hongdi, Haijun Li, An Huang, Qingyong Ni, Yongfang Yao, Huailiang Xu, Bo Zeng, Ying Li, Zhimin Wei, Guohua Yu, and et al. 2019. "The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis" Genes 10, no. 7: 487. https://doi.org/10.3390/genes10070487