Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. Primer Design, PCR Amplification, and Sequencing
2.3. Mitogenome Annotation and Sequence Analyses
2.4. Genetic Distance
2.5. Phylogenetic Analyses
2.6. Detecting Selective Pressure
3. Results
3.1. Mitogenome Organization and Structure
3.2. Protein-Coding Genes and Codon Usages
3.3. Ribosomal and Transfer RNAs
3.4. Intergenic Regions and L-Strand Origin of Replication
3.5. Genetic Distance
3.6. Phylogeny of Hylidae
3.7. Detecting Selective Pressure
4. Discussion
4.1. Mitogenome Structure
4.2. Genetic Distance and Phylogeny of Hylidae
4.3. Detecting Selective Pressure
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Family | Genus | Species | Length (bp) | GenBank Accession Number | Reference |
---|---|---|---|---|---|
Hylidae | Bokermannohyla | Bokermannohyla alvarengai | 17,325 | KY829114 | [57] |
Boana | Boana aff. courtoisae | 15,840 | MW575899 | [58] | |
Boana aff. lanciformis | 17,150 | MW575918 | |||
Boana alfaroi | 17,219 | MW575923 | |||
Boana almendarizae | 17,439 | MW575920 | |||
Boana boans | 17,021 | MW575903 | |||
Boana calcarata | 16,251 | MW575909 | |||
Boana cinerascens | 17,684 | MW575925 | |||
Boana dentei | 17,587 | MW575906 | |||
Boana diabolica | 14,606 | MW575901 | |||
Boana fasciata | 17,438 | MW575919 | |||
Boana leucocheila | 18,042 | MW575912 | |||
Boana maculateralis | 16,301 | MW575922 | |||
Boana ornatissima | 17,656 | MW575902 | |||
Boana punctata | 17,899 | MW575907 | |||
Boana raniceps | 17,180 | MW575911 | |||
Boana steinbachi | 18,107 | MW575910 | |||
Boana tetete | 16,107 | MW575921 | |||
Boana xerophylla | 18,062 | MW575900 | |||
Dendrobates | Dendrobates auratus | 14,963 | JX564862 | [32] | |
Dryophytes | Dryophytes andersonii isolate | 15,423 | MW002721 | [59] | |
Dryophytes cinereus voucher | 15,418 | MF198328 | [60] | ||
Dryophytes femoralis isolate | 15,415 | MW002723 | [59] | ||
Dryophytes suweonensis | 17,448 | KX854020 | [61] | ||
18,611 | KY419887 | [27] | |||
18,288 | KY700829 | Unpublished | |||
Dryophytes versicolor | 18,800 | MH087467 | [26] | ||
Hyla | Hyla annectans | 17,973 | KM271781 | [62] | |
Hyla chinensis | 18,180 | AY458593 | [63] | ||
Hyla japonica | 19,519 | AB303949 | [64] | ||
Hyla sanchiangensis LS | 15,664 | MT561180 | [31] | ||
Hyla sanchiangensis JX | 15,675 | MK388867 | This study | ||
Hyla sanchiangensis WC | 15,977 | MK388868 | This study | ||
Hyla sanchiangensis MX | 15,694 | MZ508281 | Direct Submission | ||
Hyla tsinlingensis | 18,305 | KU601448 | [65] | ||
Nyctimystes | Nyctimystes kubori | 14,983 | JX564879 | [32] | |
Osteocephalus | Osteocephalus taurinus | 14,970 | JX564881 | [32] | |
Pithecopus | Pithecopus megacephalus | 18,050 | MG772558 | Unpublished | |
Phyllomedusa | Phyllomedusa tomopterna | 14,926 | JX564887 | [32] | |
Pseudis | Pseudis tocantins | 15,564 | MH571152 | [66] | |
Dendrobatidae | Dendrobates | Dendrobates auratus | 14,863 | JX564862 | [32] |
Mannophryne | Mannophryne trinitatis | 14,939 | JX564878 | ||
Alsodidae | Odontophrynus | Odontophrynus occidentalis | 14,908 | JX564880 | |
Rhinodermatidae | Rhinoderma | Rhinoderma darwinii | 14,943 | JX564891 |
Gene/Region | Position JX/WC | Length (bp) JX/WC | Spacer (+) Overlap (−) JX/WC | Start Codon | Stop Codon | Strand |
---|---|---|---|---|---|---|
trnL1 (cta) | 1–72 | 72 | 0 | H | ||
trnT (aca) | 73–143 | 71 | −1 | H | ||
trnP (cca) | 143–211 | 69 | −1 | L | ||
trnF (ttc) | 211–278 | 68 | 0 | H | ||
12S rRNA | 279–1211/279–1210 | 933/932 | 0 | H | ||
trnV (gta) | 1212–1280/1211–1279 | 69 | 0 | H | ||
16S rRNA | 1281–2884/1280–2876 | 1604/1597 | 0 | H | ||
trnL2 (tta) | 2885–2957/2877–2949 | 73 | 0 | H | ||
ND1 | 2958–3918/2950–3910 | 945 | 0 | TTG | T | H |
trnI (atc) | 3919–3989/3911–3981 | 71 | −1 | H | ||
trnQ (caa) | 3989–4059/3981–4051 | 71 | −1 | L | ||
trnM (atg) | 4059–4127/4051–4119 | 69 | 0 | H | ||
ND2 | 4128–5162/4120–5154 | 1029 | +7 | ATT | AGA | H |
trnW (tga) | 5170–5239/5162–5231 | 70 | 0 | H | ||
trnA (gca) | 5240–5308/5232–5300 | 69 | 0 | L | ||
trnN (aac) | 5309–5381/5301–5373 | 73 | L | |||
OL | 5382–5406/5374–5399 | 27/28 | 0 | |||
trnC (tgc) | 5407–5470/5400–5463 | 64 | 0 | L | ||
trnY (tac) | 5471–5540/5464–5533 | 70 | +4 | L | ||
COX1 | 5545–7086/5538–7079 | 1527 | +1 | ATA | AGA | H |
trnS2 (tca) | 7088–7158/7081–7151 | 71 | +1 | L | ||
trnD (gac) | 7160–7228/7153–7221 | 69 | +1 | H | ||
COX2 | 7230–7917/7223–7910 | 672 | 0 | ATG | T | H |
trnK (aaa) | 7918–7990/7911–7982 | 73/72 | 0 | H | ||
ATP8 | 7991–8155/7983–8147 | 159 | −25 | ATG | TAA | H |
ATP6 | 8131–8829/8123–8821 | 699 | −1 | ATC | TAA | H |
COX3 | 8829–9614/8821–9606 | 783 | −1 | ATG | TAA | H |
trnG (gga) | 9614–9682/9606–9674 | 69 | 0 | H | ||
ND3 | 9683–10022/9675–10014 | 327 | 0 | ATG | T | H |
trnR (cga) | 10023–10091/10015–10083 | 69 | +2 | H | ||
ND4L | 10094–10396/10086–10388 | 300 | −7 | ATG | TAG | H |
ND4 | 10390–11754/10382–11746 | 1359 | 0 | ATG | TAA | H |
trnH (cac) | 11755–11823/11747–11815 | 69 | 0 | H | ||
trnS1 (agc) | 11824–11890/11816–11882 | 67 | +36 | H | ||
ND5 | 11927–13729/11919–13721 | 1803 | −17 | ATG | AGA | H |
ND6 | 13713–14210/13705–14202 | 495 | 0 | ATG | AGA | L |
trnE (gaa) | 14211–14278/14203–14270 | 68 | +2 | L | ||
Cytb | 14281–15429/14273–15421 | 1149 | 0 | ATG | TAG | H |
Region | H. Sanchiangensis WC | H. sanchiangensis JX | H. sanchiangensis LS (MT561180) | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Length (bp) | AT% | AT-Skew | GC-Skew | Length (bp) | AT% | AT-Skew | GC-Skew | Length (bp) | AT% | AT-Skew | GC-Skew | |
Whole genome * | 15,977 | 60.1 | 0 | −0.275 | 15,675 | 59.9 | 0.002 | −0.278 | 15,664 | 59.8 | 0.001 | −0.275 |
PCGs | 11,331 | 59.6 | −0.075 | −0.278 | 11,331 | 59.8 | −0.074 | −0.279 | 11,316 | 59.6 | −0.078 | −0.274 |
tRNA | 1533 | 59.4 | 0.036 | 0.016 | 1533 | 59.9 | 0.053 | −0.012 | 1528 | 59.3 | 0.047 | −0.005 |
rRNA | 2529 | 59.9 | 0.142 | −0.120 | 2537 | 59.6 | 0.145 | −0.125 | 2533 | 59.8 | 0.144 | −0.119 |
Model | np | LnL | Estimates of Parameters | Model Compared | LRT p-Value | Positive Sites | ||||
---|---|---|---|---|---|---|---|---|---|---|
Model A | 83 | −169886.61 | Site class | 0 | 1 | 2a | 2b | Model A vs. Model A null | 0.000213429 | 1595 L 0.973 *, 2308 T 0.955 *, 2479 S 0.984 *, 2632 L 0.950 *, 3272 T 0.956 * |
f | 0.9212 | 0.073 | 0.0056 | 0.00045 | ||||||
ω0 | 0.0427 | 1 | 0.043 | 1 | ||||||
Model A null | 82 | −169893.47 | ω1 | 0.0427 | 1 | 149.39 | 149.39 | Not Allowed | ||
1 |
Genes | Postive Selection Sites | Amino Acids | BEB Value | Feature Key | Description | |
---|---|---|---|---|---|---|
Foreground | Background | |||||
Cytb | 316 | T/V/S | L | 0.973 * | Domain | CYTB_CTER |
ND3 | 85 | V/A/S | T/A/S | 0.955 * | / | / |
ND4 | 47 | N | S/P/A | 0.984 * | Domain | Oxidored_q5_N |
200 | T/M | L/V/M | 0.950 * | Domain | Proton_antipo_M | |
ND5 | 400 | V | T/A/S/V | 0.956 * | Domain | Proton_antipo_M |
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Hong, Y.-H.; Huang, H.-M.; Wu, L.; Storey, K.B.; Zhang, J.-Y.; Zhang, Y.-P.; Yu, D.-N. Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae. Animals 2023, 13, 1593. https://doi.org/10.3390/ani13101593
Hong Y-H, Huang H-M, Wu L, Storey KB, Zhang J-Y, Zhang Y-P, Yu D-N. Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae. Animals. 2023; 13(10):1593. https://doi.org/10.3390/ani13101593
Chicago/Turabian StyleHong, Yue-Huan, Hai-Ming Huang, Lian Wu, Kenneth B. Storey, Jia-Yong Zhang, Yong-Pu Zhang, and Dan-Na Yu. 2023. "Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae" Animals 13, no. 10: 1593. https://doi.org/10.3390/ani13101593
APA StyleHong, Y.-H., Huang, H.-M., Wu, L., Storey, K. B., Zhang, J.-Y., Zhang, Y.-P., & Yu, D.-N. (2023). Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae. Animals, 13(10), 1593. https://doi.org/10.3390/ani13101593