Terrestrial Adaptation in Chelonoidis vicina as Revealed Based on Analysis of the Complete Mitochondrial Genome
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Complete Mitogenome Data and Species Sample
2.2. Mitogenome Analyses
2.3. Comparative Mitochondrial Genome Analyses
2.4. Phylogenetic Construction
2.5. Selection Pressure Analyses
3. Result
3.1. Mitogenome Organization and Structure
3.2. Protein-Coding Genes
3.3. RNA Genes in C. vicina Mitogenomes
3.4. Comparing Mitogenomes Among Species
3.5. Phylogenetic Analyses
3.6. Evolutionary Analysis
4. Discussion
4.1. Mitochondrial Genome Characteristics
4.2. Phylogenetic Analysis
4.3. Evolutionary Analysis of Terrestrial Adaptability
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Start | Stop | Strand | Length | Intergenic Nucleotide | Star | Stop |
---|---|---|---|---|---|---|---|
tRNAPhe | 1 | 70 | + | 70 | 0 | ||
12s rRNA | 71 | 1039 | + | 969 | 0 | ||
tRNAVal | 1040 | 1110 | + | 71 | 14 | ||
16s rRNA | 1125 | 2717 | + | 1593 | 1 | ||
tRNALeu | 2719 | 2794 | + | 76 | 1 | ||
ND1 | 2796 | 3767 | + | 972 | −1 | ATG | TAG |
tRNAIle | 3767 | 3836 | + | 70 | −1 | ||
tRNAGln | 3836 | 3906 | − | 71 | −1 | ||
tRNAMet | 3906 | 3974 | + | 69 | 0 | ||
ND2 | 3975 | 5015 | + | 1041 | −2 | ATG | TAG |
tRNATrp | 5014 | 5088 | + | 75 | 1 | ||
tRNAAla | 5090 | 5158 | − | 69 | 2 | ||
tRNAAsn | 5161 | 5234 | − | 74 | 3 | ||
tRNACys | 5261 | 5326 | − | 66 | 26 | ||
tRNATyr | 5327 | 5397 | − | 71 | 1 | ||
COX1 | 5399 | 6946 | + | 1548 | 3 | GTG | AGG |
tRNASer | 6938 | 7008 | − | 71 | 0 | ||
tRNAAsp | 7009 | 7078 | + | 70 | 0 | ||
COX2 | 7079 | 7765 | + | 687 | 5 | ATG | TAA |
tRNALys | 7771 | 7840 | + | 70 | 1 | ||
ATP8 | 7842 | 8006 | + | 165 | −10 | ATG | TAA |
ATP6 | 7997 | 8680 | + | 684 | −1 | ATG | TAA |
COX3 | 8680 | 9464 | + | 785 | −1 | ATG | TA |
tRNAGly | 9464 | 9531 | + | 68 | 0 | ||
ND3 | 9532 | 9883 | + | 180 | 0 | ATG | TA |
tRNAArg | 9882 | 9951 | + | 70 | 1 | ||
ND4L | 9952 | 10,248 | + | 297 | 0 | ATG | TAA |
ND4 | 10,242 | 11,619 | + | 1378 | −7 | ATG | T |
tRNAHis | 11,620 | 11,689 | + | 70 | 0 | ||
tRNASer | 11,690 | 11,755 | + | 66 | 0 | ||
tRNALeu | 11,765 | 11,836 | + | 72 | 9 | ||
ND5 | 11,837 | 13,633 | + | 1797 | 0 | ATG | TAA |
ND6 | 13,629 | 14,153 | − | 525 | −5 | ATG | AGG |
tRNAGlu | 14,154 | 14,221 | − | 68 | 0 | ||
Cytb | 14,226 | 15,357 | + | 1132 | 4 | ATG | TA |
tRNAThr | 15,370 | 15,438 | + | 69 | 2 | ||
tRNAPro | 15,440 | 15,508 | − | 69 | 1 |
C. vicina | Size | A % | T % | G % | C % | AT % | GC % | AT Skew | GC Skew |
---|---|---|---|---|---|---|---|---|---|
mtDNA | 16,440 | 34.83 | 24.60 | 12.57 | 28.00 | 59.43 | 40.57 | 0.17 | −0.38 |
PCGs | 11,340 | 34.02 | 24.87 | 11.34 | 29.77 | 58.89 | 41.11 | 0.16 | −0.45 |
tRNAs | 1545 | 35.86 | 25.63 | 15.08 | 23.43 | 61.49 | 38.51 | 0.17 | −0.22 |
rRNAs | 2562 | 38.37 | 20.07 | 16.74 | 24.82 | 58.44 | 41.56 | 0.31 | −0.19 |
D-Loop | 932 | 34.44 | 31.97 | 11.92 | 21.67 | 66.41 | 33.59 | 0.04 | −0.29 |
Spcies | T(U)% | A% | AT% | AT Skew | G% | C% | GC% | GC Skew |
---|---|---|---|---|---|---|---|---|
Bungarus fasciatus | 31.3 | 33.5 | 64.8 | 0.034 | 11.2 | 24 | 35.2 | −0.362 |
Bungarus multicinctus | 29.9 | 32.2 | 62.1 | 0.037 | 12.1 | 25.8 | 37.9 | −0.362 |
Micrurus fulvius | 27.7 | 30.8 | 58.5 | 0.053 | 13.0 | 28.5 | 41.5 | −0.373 |
Naja naja | 26.2 | 32.1 | 58.3 | 0.102 | 13.2 | 28.5 | 41.7 | −0.367 |
Naja kaouthia | 26.2 | 32.2 | 58.3 | 0.103 | 13.2 | 28.5 | 41.7 | −0.368 |
Naja atra | 26.2 | 32.2 | 58.4 | 0.101 | 13.1 | 28.5 | 41.6 | −0.371 |
Ophiophagus hannah | 26.1 | 32.7 | 58.8 | 0.113 | 12.1 | 29.1 | 41.2 | −0.413 |
Sinomicrurus peinani | 29.3 | 32.4 | 61.7 | 0.051 | 11.8 | 26.5 | 38.3 | −0.383 |
Sinomicrurus macclellandi | 27.7 | 32.0 | 59.6 | 0.072 | 12.2 | 28.2 | 40.4 | −0.397 |
Aldabrachelys gigantea | 26.4 | 32.8 | 59.2 | 0.107 | 12.4 | 28.4 | 40.8 | −0.392 |
Chelonoidis microphyes | 26.4 | 32.3 | 58.8 | 0.100 | 12.5 | 28.7 | 41.2 | −0.394 |
Chelonoidis vandenburghi | 26.4 | 32.4 | 58.8 | 0.100 | 12.4 | 28.7 | 41.2 | −0.396 |
Chelonoidis guntheri | 26.4 | 32.4 | 58.8 | 0.109 | 12.4 | 28.7 | 41.2 | −0.396 |
Chelonoidis donfaustoi | 26.4 | 32.4 | 58.8 | 0.102 | 12.4 | 28.8 | 41.2 | −0.397 |
Chelonoidis darwini | 26.4 | 32.5 | 58.8 | 0.104 | 12.4 | 28.8 | 41.2 | −0.399 |
C. vicina | 26.4 | 32.4 | 58.8 | 0.108 | 12.5 | 28.7 | 41.2 | −0.395 |
Chelonoidis porteri | 26.4 | 32.4 | 58.8 | 0.108 | 12.4 | 28.8 | 41.2 | −0.399 |
Chelonoidis duncanensis | 26.3 | 32.5 | 58.8 | 0.104 | 12.4 | 28.8 | 41.2 | −0.399 |
Chelonoidis hoodensis | 26.4 | 32.4 | 58.8 | 0.102 | 12.4 | 28.8 | 41.2 | −0.397 |
Chelonoidis abingdonii | 26.4 | 32.4 | 58.8 | 0.102 | 12.4 | 28.8 | 41.2 | −0.397 |
Gopherus evgoodei | 27.4 | 32.3 | 59.7 | 0.082 | 12.9 | 27.4 | 40.3 | −0.358 |
Geochelone elegans | 25.6 | 32.0 | 57.6 | 0.112 | 13.2 | 29.3 | 42.4 | −0.380 |
Malacochersus tornieri | 27.7 | 33.0 | 60.7 | 0.087 | 11.8 | 27.5 | 39.3 | −0.399 |
Testudo kleinmanni | 27.9 | 32.3 | 60.2 | 0.073 | 12.5 | 27.2 | 39.8 | −0.370 |
Testudo marginata | 27.8 | 32.3 | 60.1 | 0.076 | 12.7 | 27.3 | 39.9 | −0.366 |
Testudo horsfieldii | 27.5 | 32 | 59.5 | 0.077 | 12.8 | 27.7 | 40.5 | −0.369 |
Indotestudo forstenii | 27.8 | 32.8 | 60.7 | 0.082 | 12.1 | 27.2 | 39.3 | −0.382 |
Stigmochelys pardalis | 27.5 | 32.5 | 60.1 | 0.084 | 12.6 | 27.4 | 39.9 | −0.371 |
Manouria emys | 27.5 | 31.7 | 59.2 | 0.069 | 13.3 | 27.5 | 40.8 | −0.350 |
Testudo graeca | 28.3 | 32.9 | 61.2 | 0.074 | 12.2 | 26.6 | 38.8 | −0.372 |
Indotestudo elongata | 28.1 | 33.0 | 61.1 | 0.079 | 12.0 | 26.9 | 38.9 | −0.384 |
Manouria impressa | 28.0 | 31.6 | 59.6 | 0.059 | 13.3 | 27.1 | 40.4 | −0.341 |
Astrochelys yniphora | 27.5 | 32.5 | 60.1 | 0.083 | 12.5 | 27.4 | 39.9 | −0.371 |
Laticauda semifasciata | 27.3 | 31.9 | 59.2 | 0.079 | 13.2 | 27.6 | 40.8 | −0.352 |
Laticauda colubrina | 29.1 | 33.1 | 62.2 | 0.065 | 12.1 | 25.7 | 37.8 | −0.360 |
Laticauda laticaudata | 28.0 | 32.1 | 60.2 | 0.068 | 12.8 | 27.1 | 39.8 | −0.358 |
Aipysurus eydouxii | 26.8 | 31.9 | 58.7 | 0.086 | 12.7 | 28.6 | 41.3 | −0.384 |
Emydocephalus ijimae | 28.0 | 31.9 | 59.9 | 0.066 | 12.6 | 27.6 | 40.1 | −0.373 |
Hydrophis curtus | 28.3 | 31.0 | 59.3 | 0.046 | 13.5 | 27.2 | 40.7 | −0.337 |
Hydrophis cyanocinctus | 28.2 | 31.4 | 59.6 | 0.054 | 13.0 | 27.3 | 40.4 | −0.354 |
Gene | Model | 2Δlnl | p-Value | Positively Selected Sites (BEB Analysis) |
---|---|---|---|---|
COX2 | Model A vs. Null Mode | 0 | 1 | 5 T 0.986 *, 16 T 0.985 * |
COX3 | 0 | 1 | 22 M 0.955 *, 175 A 0.962 * | |
CYtb | 0 | 1 | 324 T 0.994 ** | |
ND3 | 0 | 1 | 14 S 0.998 **, 16 L 0.975 * | |
ND4 | 0 | 1 | 30 Y 0.975 *, 431 I 0.994** | |
ND4L | 0 | 1 | 15 T 0.990 *,56 Q 0.962 * | |
ND5 | 0 | 1 | 535 S 0.970 * | |
ND6 | 0 | 1 | 130 G 0.977 * |
Gene | Model Compared | |2ΔlnL| | p-Value | ωAR | ωTR |
---|---|---|---|---|---|
ATP6 | M2 vs. M0 | 0.635 | 0.426 | 0.095 | 0.085 |
ATP8 | 0.049 | 0.825 | 0.209 | 0.198 | |
COX1 | 0.518 | 0.472 | 0.017 | 0.015 | |
COX2 | 6.322 | 0.012 * | 0.024 | 0.039 | |
COX3 | 0.021 | 0.885 | 0.033 | 0.034 | |
Cytb | 0.087 | 0.768 | 0.044 | 0.046 | |
ND1 | 8.989 | 0.003 ** | 0.049 | 0.035 | |
ND2 | 0.133 | 0.715 | 0.067 | 0.064 | |
ND3 | 10.256 | 0.002 ** | 0.060 | 0.112 | |
ND4 | 3.462 | 0.063 | 0.061 | 0.050 | |
ND4L | 0.017 | 0.898 | 0.057 | 0.055 | |
ND5 | 0.609 | 0.435 | 0.071 | 0.066 | |
ND6 | 2.074 | 0.150 | 0.090 | 0.116 |
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Chen, Y.; Wang, X.; Wu, X.; Shang, Y.; Wei, Q.; Cai, H.; Sha, W.; Qi, Y.; Liu, S.; Zhang, H. Terrestrial Adaptation in Chelonoidis vicina as Revealed Based on Analysis of the Complete Mitochondrial Genome. Genes 2025, 16, 173. https://doi.org/10.3390/genes16020173
Chen Y, Wang X, Wu X, Shang Y, Wei Q, Cai H, Sha W, Qi Y, Liu S, Zhang H. Terrestrial Adaptation in Chelonoidis vicina as Revealed Based on Analysis of the Complete Mitochondrial Genome. Genes. 2025; 16(2):173. https://doi.org/10.3390/genes16020173
Chicago/Turabian StyleChen, Yao, Xibao Wang, Xiaoyang Wu, Yongquan Shang, Qinguo Wei, Haotian Cai, Weilai Sha, Yan Qi, Shuli Liu, and Honghai Zhang. 2025. "Terrestrial Adaptation in Chelonoidis vicina as Revealed Based on Analysis of the Complete Mitochondrial Genome" Genes 16, no. 2: 173. https://doi.org/10.3390/genes16020173
APA StyleChen, Y., Wang, X., Wu, X., Shang, Y., Wei, Q., Cai, H., Sha, W., Qi, Y., Liu, S., & Zhang, H. (2025). Terrestrial Adaptation in Chelonoidis vicina as Revealed Based on Analysis of the Complete Mitochondrial Genome. Genes, 16(2), 173. https://doi.org/10.3390/genes16020173