Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats
Abstract
:1. Introduction
2. Results
2.1. Characteristics of Amblyopinae Mitogenomes
2.2. Phylogenetic Analyses
2.3. Positive Selection Analyses
3. Discussion
4. Materials and Methods
4.1. DNA Samples and Sequence Determination
4.2. Sequence Analysis
4.3. Phylogenetic Construction
4.4. Analysis of Selective Pressures
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Sampling Locality | Mitogenome Size | Accession No. |
---|---|---|---|
Amblyotrypauchen arctocephalus Alcock, 1890 [17] | South China Sea; Yangjiang, Guangdong | 17,133 bp | MK541896 |
Ctenotrypauchen chinensis Steindachner, 1867 [18] | South China Sea; Guangzhou, Guangdong | 16,552 bp | MK541901 |
Paratrypauchen microcephalus Bleeker, 1860 [19] | Yellow Sea; Dandong, Liaoning | 17,086 bp | MK541897 |
Taenioides gracilis Cuvier, 1837 [20] | South China Sea; Haikou, Hainan | 16,710 bp | MK541898 |
Taenioides anguillaris Linnaeus, 1758 [21] | East China Sea; Wenling, Zhejiang | 16,973 bp | OL625024 |
Taenioides sp. Thailand Kurita, 2012 [10] | South China Sea; Haikou, Hainan | 16,718 bp | MW682859 |
Species | Starting Point * | Sequences of Perfect Repeat (Length) | Number of Repeats | Sequences of Imperfect Repeat | Number of Repeats |
---|---|---|---|---|---|
Amblyotrypauchen arctocephalus | 1157 | AAACAGGAAAGACTCGAGCTAGGAATTGCATGCCCCAAACTATGTGTATATACATTATTACCAATGATTTCCCTTTGTAATAAAGCGCACATCATTCATTCAACCCTAAATACTTCAACAATTTTATAGCAGAAGCCTATATCTAA (146 bp) | 4 | AAACAGGAAAGCTTCGAGCTAGAAATTGCATGCCCCAAACTATGTGTATATACATTATTACAATGATTTC | 1 |
Ctenotrypauchen chinensis | 1156 | GAAACAGGAAAGCCTCGAGCTAGGAACTACATGCCCCAAATTGCATGTATATACATTATTACAATAATACCAATACAACAAATTATTTTTTAAACCAACAACCCTAAAATCAGGAAACCTGTCAAATTTTTAAGACAGTTATGCCCCCCA (150 bp) | 1 | GAAACAGGAAAGCCTCGAGCTAAGAACTTCATGCCCCAAATTGCATGCATATACATTATTGCAATGATTCT | 1 |
Paratrypauchen microcephalus | 1157 | AAACAGGAAAGCCTCGAGCTAGGAATTAACATGCCCCAAACTGTGAATACACACATTATTACAGTAATTCTGTTTGTAAACAACACAATTCAAAAATTCAACCCTTAAAAGTTTGTTATATTTATAGCACACCTCTTTCATAAA (144 bp) | 4 | AAACAGGAAAACCTCGAGCTAGAAATTAACATACCCCAAACGTGAATATACACACTATTATAATAATTT | 1 |
Taenioides gracilis | 1157 | AAACAGGAAAGCCTCGAGCATTAAAATTAACTGCCCACAAATTACCACATATACATTATTGCAAAAATTGCTACATATACATTATTACAATAATTCTTTTACTTAAATAATATTTTATAAACATTCAACCCTCAAGCCCCTATCAACCCCTTCCCCCAAAAAG (163 bp) | 1 | AACAAAAAATCCTCGAGTATAAAAACCCACTGCCTACAAATTTCTACATATTCATCATTACAGACAG | 1 |
Taenioides anguillaris | 1156 | AAAACAGGATAAGCCTCGAGCATAGGGACCACACCCCAAATTGCAACATATACATTATTGCAATAATTCTTTTACCTAAGCAGCAAACTATAGGCACCCCACCCTTAAAACTTCTATCAGCTTCTTTTACACTCTGACTTCACA (144 bp) | 3 | AAAACAGGATAAGCCTCGAGCATAGGGACCACACCCCAAATTGCAACATATACATTATTGCAAACAT | 1 |
Taenioides sp. Thailand | 1157 | AAACAGGAAAGCCTCGAGTATTAAAACTTACTACTCATAAATTGCTACATATACATTATTACAAAAATTGCTACATATATATTATTACAATAATTCTTTTACTTAAATAATAAAATATAAACACTCAACCCTAAAACTTCTAACACCTCTTTACACCCCTAA (162 bp) | 1 | AAACAAAAAAGCCTCGAGTATAGAAACTTGCACCTGCAAACTGCTAAATATATATTATTACAGACAG | 1 |
Trypauchen vagina | 1152 | CCCGGAAACAGGAAAGCCTCGAGTTAGGAATTATGTACCCCAAGTTACATACCTATACACTATTGCAATAATACCCACACAATAGACTATCTTTAAAAATTCAACCCTGAAAACAATATCAAATTTTTTATACATTTTAAA (141 bp) | 2 | CCCGGAAACAGGAAAGCCTCGAGTTAGGAATTATGTACCCCAAGTTACATACCTATACACTATTGCAATAATTCT | 1 |
Taenioides cirratus | 1156 | AAAACAGGATAAGTCTCGAGCATAGGGACCACGCCCCAAATTGCAACATATACATTATTGCAATAATTCTTTTACCTAAGCAGCAAACTATAGGCACCCCACCCTTAAAACTTCTATCAGCTTCTTTTACACTCTGACTTCAC (143 bp) | 3 | AAAACAGGATAAGTCTCGAGCATAGGGACCACGCCCCAAATTGCAACATATACATTATTGCAAACAT | 1 |
Trypauchenopsis sp. | 1157 | AAACAGGAAAGTCTCGAGCTAGGGACAAAACACCCCCAATTGCATAAATATACATTATTGCAATAATACTTTTATTGTTTTAATAATTCTATAATAGCGTGCCGTCAACTTACTATCATATTTTTTCCCCCGCCTAAAAGCCGTA (145 bp) | 1 | ATTTTTTATTGAAGAAAAGTAAAAATTCTTCAAGTGAACCTGCACCCCCACTTAACTCTTAAACATTATAATATAACTAA | 1 |
Odontamblyopus lacepedii | 1298 | TGAAATCAAAGATTTCCAAGTTATATGTACACATTATTACAATAATTCACTTTTTTATAATTTAAAACAACTAATAAGCCCGTCAAAACAATCTTAAAGCAACCCCGATAAAACTTTATA (120 bp) | 5 | TGAAATCAAAGATTTCCAAGTTATATGTACACATTATTACAATAATTCACTT | 1 |
Odontamblyopus sp. | 1306 | AAATCAAAGATTTCCAAGTTATATGTACACATTATTACAATAATTCATTTTTTTATAATTTAAAACAACTAACAAGCCCGTCCAAACAATCTTAAAGCGACCCCGATAAAACTTTATATG (120 bp) | 3 | AAATCAAAGATTTCCAAGTTATATGTACACATTATTACAATGATTCACTT | 1 |
Odontamblyopus rebecca | 1306 | ATGTTAAAGATTTACAAGTTATATGCACACATTATTACAATAATTCACTTTTTTTATGATTTAAAACAATCAACAAGCCCGTCCAAATAGTCTTAAAGTAACCCAGATAAAACTTTATATA (121 bp) | 3 | ATGTTAAAGATTTACAAGTTATATGCACACATTATTACAATAATTCACTT | 1 |
Boleophthalmus pectinirostris | 1159 | ACAGGAAAGTCTCGAGCAAGGGCCACATGCCCAAAGTTGTGTCAAATATATTACAATAATTCACTTATTAATATACAAAATAAAAGCACCCAACCCTTACTTAGCCCTAACACATCTCACCCTTTCCTAG (130 bp) | 5 | ACAGGAAAGTCTCGAGCAAGGGCCACATGCCCAGAGTTGTGTCAAATATATTATTATGATACTTACT | 1 |
Boleophthalmus sp. | 1159 | ACAGGAAAGCCTCGAGTGAGGGCCAAAAACCCAAAGTTGTGTCAAAGATATTACAATAATTCACTTACTAATATACAAAATAAAAGACACCCAACCCCGACAGAGCCCTCACACATTTTATTGCTCCAACC (131 bp) | 5 | ACAGGAAAGCCTCGAGTGAGGGCCAAAAACCCAAAGTTGTGTCAAAGATACTATTATGATATTTTCT | 1 |
Boleophthalmus boddarti | 1152 | CCCGGAAACAGGAAAGCCTCGAGCAAAGGGCACATACCCAAAGTTGTGTTAAACATATTACAATAATTCACTTGCTAATGTACAAAATAAGAGACACCCAACCCAGACTTAACCGTCACACACTTTTAATT (131 bp) | 2 | CCCGGAAACAGGAAAGCCTCGAGCAAAGGGCACATACCCAAAGTTGTGTTAAACATATTATTATGATTACTTTCT | 1 |
Scartelaos gigas | 1157 | AAACAGGAAAGCCTCGAGTTAGGGACCATGTGCTAAAAATGTACACATACACATTATTACAATAATTCACTTATCACACAAAATAAAGATAGAAACATTTAACCCAGCATTTTCTATCATCTTTTTAACCCCCCTCCTTCCAACCGTGGACTTTTATTCACCCGGAACCTT (171 bp) | 1 | AACAAAACCTAGTCTAAAGTTAGAAACCACATGCTCCAAAATGCGTGTATTTACATTATTGCAATAGTTCACTT | 1 |
Oxuderces dentatus | 1189 | ACCTCTCAAGTGTTTATGTACCAATTATTACAATAATTCATTTATTTGTACAAAAAATAATAAACCTCCGCCCTAAATAAACTAACAATTAAAAAATTACTATATAACTAATATCCCTCGATATAGATTTAACCAACACATGTAAATCGC (150 bp) | 4 | AGCT | 1 |
Parapocryptes serperaster | 1156 | GAAACAGGAAAGCCTCGAGCTAGAAATCATGCCCCCAAGTTGCATGCACAAATTATTACAATAATTCACTTATTAACTCACCCCACCCATCTCACCCCAACCGAAAAATCCCTGCCAACTTTGAATCCCCCGACCCCTAAACTCCTAGAGTAATATTCACCGTTAACCCAAACCCCAA (178 bp) | 4 | GAAACAGGAAAGCCTCGAGCTAGAAATCATGCCCCCAAGTTGCACGGCCCCCCACCT | 1 |
Periophthalmus argentilineatus | ----- | ----- | ----- | ----- | ----- |
Periophthalmus modestus | ----- | ----- | ----- | ----- | ----- |
Periophthalmus minutus | ----- | ----- | ----- | ----- | ----- |
Periophthalmus magnuspinnatus | ----- | ----- | ----- | ----- | ----- |
Periophthalmodon schlosseri | ----- | ----- | ----- | ----- | ----- |
Gene | Model | lnL | LRT | Parameter |
---|---|---|---|---|
atp6 | M0 | −12,288.396 | ω0 = 0.036 | |
M2 | −12,288.359 | 0.074 | ω0 = 0.035; ω1 = 0.040 | |
atp8 | M0 | −2884.378 | ω0 = 0.116 | |
M2 | −2884.367 | 0.021 | ω0 = 0.116; ω1 = 0.128 | |
cox1 | M0 | −21,414.251 | ω0 = 0.011 | |
M2 | −21,410.655 | 7.192 ** | ω0 = 0.011; ω1 = 0.055 | |
cox2 | M0 | −8871.766 | ω0 = 0.017 | |
M2 | −8871.123 | 1.285 | ω0 = 0.017; ω1 = 0.038 | |
cox3 | M0 | −10,794.094 | ω0 = 0.024 | |
M2 | −10,791.750 | 4.688 * | ω0 = 0.024; ω1 = 0.089 | |
cytb | M0 | −18,249.518 | ω0 = 0.021 | |
M2 | −18,248.658 | 1.719 | ω0 = 0.021; ω1 = 0.080 | |
nad1 | M0 | −15,830.249 | ω0 = 0.021 | |
M2 | −15,824.827 | 10.844 ** | ω0 = 0.021; ω1 = 0.338 | |
nad2 | M0 | −21,447.715 | ω0 = 0.053 | |
M2 | −21,437.677 | 20.076 ** | ω0 = 0.053; ω1 = 999.000 | |
nad3 | M0 | −6097.474 | ω0 = 0.041 | |
M2 | −6095.969 | 3.010 | ω0 = 0.040; ω1 = 999.000 | |
nad4 | M0 | −25,867.666 | ω0 = 0.041 | |
M2 | −25,862.873 | 9.585 ** | ω0 = 0.041; ω1 = 0.198 | |
nad4l | M0 | −4790.108 | ω0 = 0.032 | |
M2 | −4789.945 | 0.325 | ω0 = 0.031; ω1 = 999.000 | |
nad5 | M0 | −33,909.683 | ω0 = 0.044 | |
M2 | −33,907.749 | 3.867 * | ω0 = 0.043; ω1 = 0.095 | |
nad6 | M0 | −10,277.916 | ω0 = 0.043 | |
M2 | −10,275.634 | 4.564 * | ω0 = 0.043; ω1 = 0.912 |
Gene | Model | lnL | LRT | Parameter | Positive Selected Site |
---|---|---|---|---|---|
atp6 | Null model | −12,265.068 | P0 = 0.940; P1 = 0.030; P2a = 0.029; P2b = 0.001; ω0 = 0.032; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −12,264.833 | 0.471 | P0 = 0.955; P1 = 0.030; P2a = 0.015; P2b = 0.000; ω0 = 0.032; ω1 = 1.000; ω2a = 3.021; ω2b = 3.021 | ||
atp8 | Null model | −2874.537 | P0 = 0.842; P1 = 0.087; P2a = 0.064; P2b = 0.007; ω0 = 0.103; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −2874.010 | 1.053 | P0 = 0.860; P1 = 0.089; P2a = 0.046; P2b = 0.005; ω0 = 0.102; ω1 = 1.000; ω2a = 4.512; ω2b = 4.512 | ||
cox1 | Null model | −21,265.614 | P0 = 0.979; P1 = 0.008; P2a = 0.013; P2b = 0.000; ω0 = 0.008; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −21,265.614 | 0.000 | P0 = 0.979; P1 = 0.008; P2a = 0.013; P2b = 0.000; ω0 = 0.008; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
cox2 | Null model | −8871.244 | P0 = 0.975; P1 = 0.000; P2a = 0.025; P2b = 0.000; ω0 = 0.017; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −8871.244 | 0.000 | P0 = 0.975; P1 = 0.000; P2a = 0.025; P2b = 0.000; ω0 = 0.017; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
cox3 | Null model | −10,731.495 | P0 = 0.946; P1 = 0.028; P2a = 0.025; P2b = 0.001; ω0 = 0.018; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −10,728.961 | 5.067 * | P0 = 0.965; P1 = 0.029; P2a = 0.006; P2b = 0.000; ω0 = 0.018; ω1 = 1.000; ω2a = 31.441; ω2b = 31.441 | 162 (0.988) | |
cytb | Null model | −18,282.716 | P0 = 0.899; P1 = 0.014; P2a = 0.085; P2b = 0.001; ω0 = 0.019; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −18,282.716 | 0.000 | P0 = 0.899; P1 = 0.014; P2a = 0.085; P2b = 0.001; ω0 = 0.019; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
nad1 | Null model | −15,810.905 | P0 = 0.662; P1 = 0.004; P2a = 0.331; P2b = 0.002; ω0 = 0.020; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −15,810.905 | 0.000 | P0 = 0.662; P1 = 0.004; P2a = 0.331; P2b = 0.002; ω0 = 0.020; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
nad2 | Null model | −21,254.298 | P0 = 0.327; P1 = 0.018; P2a = 0.620; P2b = 0.035; ω0 = 0.045; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −21,248.610 | 11.376 ** | P0 = 0.900; P1 = 0.050 P2a = 0.047; P2b = 0.003; ω0 = 0.045; ω1 = 1.000; ω2a = 999.0; ω2b = 999.0 | 87(0.966); 123 (0.987); 213(0.984); 220 (0.989); 296 (0.986); 303 (0.960); 312 (0.975) | |
nad3 | Null model | −5981.539 | P0 = 0.000; P1 = 0.000 P2a = 0.915; P2b = 0.085; ω0 = 0.023; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −5981.466 | 0.146 | P0 = 0.000; P1 = 0.000 P2a = 0.915; P2b = 0.085; ω0 = 0.023; ω1 = 1.000; ω2a = 64.038; ω2b = 64.038 | ||
nad4 | Null model | −25,655.501 | P0 = 0.877; P1 = 0.057; P2a = 0.062; P2b = 0.004; ω0 = 0.030; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −25,653.475 | 4.053 * | P0 = 0.928; P1 = 0.060; P2a = 0.012; P2b = 0.001; ω0 = 0.030; ω1 = 1.000; ω2a = 11.628; ω2b = 11.628 | 44 (0.991); 384 (0.988) | |
nad4l | Null model | −4771.271 | P0 = 0.885; P1 = 0.028; P2a = 0.084; P2b = 0.003; ω0 = 0.028; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −4771.271 | 0.000 | P0 = 0.969; P1 = 0.031; P2a = 0.000; P2b = 0.000; ω0 = 0.028; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
nad5 | Null model | −33,633.451 | P0 = 0.916; P1 = 0.052; P2a = 0.030; P2b = 0.002; ω0 = 0.033; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −33,633.451 | 0.000 | P0 = 0.916; P1 = 0.052; P2a = 0.030; P2b = 0.002; ω0 = 0.033; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
nad6 | Null model | −10,198.030 | P0 = 0.785; P1 = 0.074; P2a = 0.129; P2b = 0.012; ω0 = 0.033; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000 | ||
Model A | −10,195.755 | 4.550 * | P0 = 0.866; P1 = 0.082; P2a = 0.047; P2b = 0.004; ω0 = 0.033; ω1 = 1.000; ω2a = 999.0; ω2b = 999.0 | 78 (0.951) |
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Lü, Z.; Liu, Y.; Zhao, S.; Fang, J.; Zhu, K.; Liu, J.; Gong, L.; Liu, L.; Liu, B. Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats. Int. J. Mol. Sci. 2023, 24, 4362. https://doi.org/10.3390/ijms24054362
Lü Z, Liu Y, Zhao S, Fang J, Zhu K, Liu J, Gong L, Liu L, Liu B. Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats. International Journal of Molecular Sciences. 2023; 24(5):4362. https://doi.org/10.3390/ijms24054362
Chicago/Turabian StyleLü, Zhenming, Yantao Liu, Shijie Zhao, Jiaqi Fang, Kehua Zhu, Jing Liu, Li Gong, Liqin Liu, and Bingjian Liu. 2023. "Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats" International Journal of Molecular Sciences 24, no. 5: 4362. https://doi.org/10.3390/ijms24054362