Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics
Abstract
:1. Introduction
2. Results
2.1. General Features of 40 Mitogenomes of T. ganbajun
2.2. Structure of Standard Protein-Coding Genes
2.3. Multicopy HTs Verification in cox1 and nad5
2.4. Intron and HEs Dynamics of Mitogenomes
2.4.1. Intron Distribution
2.4.2. Intronic Polymorphism
2.5. Correlation Analysis of the Main Characteristics of the Mitochondrial Genomes
2.6. Horizontal Gene Transfer of HEs
2.7. Population Genetics
3. Discussion
3.1. Variations of HTs
3.2. The Effect of Heterogeneity
3.3. Intron Dynamics
3.4. Population Structure
4. Materials and Methods
4.1. Sampling, DNA Isolation, and Genome Sequencing
4.2. De Novo Assembly, Annotation, and Comparative Analysis of Mitogenomes
4.3. Existence of Multicopy Heterogeneity in the nad5 and cox1 Genes Verified by qPCR
4.4. Population Genetics
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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Strains | Genome Size (bp) | GC Content (%) | Standard Protein-Encoding Genes (PCGs) Size (bp) | Tot. Multicopy Genes Size (bp) | HEGs Size (bp) | Normalintrons Size (bp) (No.) | No. HE | Tot. Introns | GenBank Accession |
---|---|---|---|---|---|---|---|---|---|
JS-1 | 65,668 | 26.04 | 22,096 | 11,172 | 4022 | 1567 (5) | 11 | 16 | PQ126529 |
JS-11 | 65,543 | 25.90 | 24,854 | 12,013 | 4022 | 1397 (6) | 11 | 17 | PQ149496 |
JS-12 | 64,773 | 25.89 | 22,177 | 11,135 | 4121 | 1850 (8) | 11 | 19 | PQ149497 |
JS-13 | 66,588 | 26.04 | 24,816 | 11,975 | 4723 | 2078 (8) | 13 | 21 | PQ149498 |
JS-4 | 64,130 | 25.85 | 22,505 | 8428 | 3456 | 2101 (6) | 9 | 15 | PQ149493 |
JS-6 | 65,686 | 25.86 | 23,799 | 11,968 | 3150 | 1500 (7) | 9 | 16 | PQ149494 |
JS-7 | 68,725 | 25.94 | 24,078 | 10,039 | 4116 | 2396 (8) | 12 | 20 | PQ149495 |
KM112 | 64,682 | 25.86 | 21,813 | 9868 | 4121 | 1940 (6) | 11 | 18 | PQ149499 |
LF-8 | 65,622 | 26.00 | 23,710 | 10,746 | 4022 | 1129 (4) | 11 | 15 | PQ149500 |
LF-9 | 64,911 | 25.88 | 23,941 | 10,813 | 3162 | 2497 (9) | 9 | 18 | PQ149501 |
LQ-1 | 67,472 | 25.93 | 25,158 | 12,040 | 4425 | 1980 (6) | 12 | 18 | PQ149502 |
LQ-5 | 65,082 | 25.87 | 20,697 | 9655 | 4431 | 1157 (6) | 12 | 18 | PQ149503 |
LQ-6 | 64,913 | 25.93 | 23,545 | 9925 | 4121 | 2286 (7) | 11 | 18 | PQ149504 |
LQ-7 | 68,859 | 25.95 | 25,190 | 11,679 | 4022 | 2396 (8) | 11 | 19 | PQ149505 |
LQ-8 | 67,071 | 25.76 | 23,873 | 10,000 | 3107 | 2085 (7) | 8 | 15 | PQ149506 |
LT-1 | 65,543 | 25.89 | 24,854 | 12,013 | 4022 | 1397 (6) | 11 | 17 | PQ149507 |
LT-10 | 65,796 | 26.03 | 23,723 | 9874 | 4121 | 2343 (8) | 11 | 19 | PQ149509 |
LT-5 | 66,733 | 26.03 | 24,854 | 12,013 | 4376 | 1397 (6) | 11 | 17 | PQ149508 |
LX-2 | 65,573 | 26.03 | 25,012 | 12,171 | 4022 | 1408 (6) | 11 | 17 | PQ149510 |
LX-5 | 65,635 | 25.98 | 24,381 | 11,127 | 4061 | 2430 (9) | 11 | 20 | PQ149511 |
LX-7 | 65,709 | 26.05 | 24,952 | 12,111 | 4022 | 1300 (5) | 11 | 16 | PQ149512 |
LX-8 | 64,567 | 26.23 | 19,515 | 9205 | 3580 | 1164 (6) | 11 | 17 | PQ149513 |
SL-1 | 64,806 | 25.86 | 23,091 | 9868 | 4121 | 2383 (8) | 11 | 19 | PQ149514 |
SL-4 | 64,475 | 26.11 | 22,798 | 10,746 | 4332 | 1206 (5) | 12 | 17 | PQ149515 |
SL-7 | 67,542 | 25.92 | 22,654 | 10,585 | 4949 | 2059 (8) | 14 | 22 | PQ149516 |
SL-8 | 65,207 | 25.83 | 21,530 | 8998 | 3249 | 1806 (6) | 9 | 15 | PQ149517 |
SL-9 | 65,631 | 26.00 | 23,710 | 10,746 | 4022 | 1129 (4) | 11 | 15 | PQ149518 |
SZ-12 | 65,060 | 25.93 | 25,335 | 11,461 | 4407 | 1941 (6) | 12 | 18 | PQ149521 |
SZ-13 | 66,778 | 26.07 | 24,842 | 10,746 | 4236 | 1760 (7) | 12 | 19 | PQ149522 |
SZ-14 | 67,314 | 25.99 | 20,216 | 9322 | 4071 | 2688 (8) | 12 | 20 | PQ149523 |
SZ-15 | 64,879 | 25.95 | 22,862 | 9356 | 3800 | 2134 (7) | 11 | 18 | PQ149524 |
SZ-7 | 65,570 | 26.03 | 24,854 | 12,013 | 4332 | 1397 (6) | 12 | 18 | PQ149519 |
SZ-8 | 65,539 | 26.04 | 24,854 | 12,013 | 4022 | 1397 (6) | 11 | 17 | PQ149520 |
TT-3 | 65,809 | 25.90 | 23,779 | 9874 | 4121 | 2351 (7) | 11 | 18 | PQ149525 |
TT-5 | 65,824 | 25.90 | 25,053 | 11,148 | 4121 | 2733 (9) | 11 | 20 | PQ149526 |
YL-14 | 64,831 | 25.86 | 23,091 | 9868 | 3586 | 2428 (9) | 10 | 19 | PQ149530 |
YL-15 | 64,414 | 25.69 | 20,413 | 8468 | 3456 | 1263 (5) | 9 | 14 | PQ149531 |
YL-2 | 64,840 | 25.85 | 22,642 | 11,069 | 3237 | 1729 (8) | 9 | 17 | PQ149527 |
YL-5 | 66,855 | 25.80 | 24,501 | 10,707 | 3772 | 2217 (7) | 10 | 17 | PQ149528 |
YL-6 | 64,799 | 25.87 | 21,441 | 9868 | 4121 | 1612 (7) | 11 | 18 | PQ149529 |
Geographic Population | Sampling Site | Long. (E) | Lat. (N) | Region Sample Size | Local Geographic Population Sample Size |
---|---|---|---|---|---|
Honghe (HH) | Luxi | 103.76 | 24.52 | 11 | 4 |
Jianshui | 102.79 | 23.64 | 7 | ||
Kunming (KM) | Kunming | 102.83 | 24.88 | 11 | 1 |
Yiliang | 103.08 | 24.55 | 5 | ||
Shilin | 103.2 | 24.45 | 5 | ||
Qujing (QJ) | Longtan | 104.01 | 26.41 | 11 | 3 |
Tangtang | 104.21 | 26.48 | 2 | ||
Shizong | 103.59 | 24.49 | 6 | ||
Chuxiong (CX) | Lufeng | 102.04 | 25.09 | 7 | 2 |
Luquan | 102.28 | 25.33 | 5 |
SNPs Type | All Sites | Parsimony Information Sites | Singleton Variable Sites | Nucleotide Diversity (Pi) | Pi of per Population | |||
---|---|---|---|---|---|---|---|---|
Honghe | Kunming | Qujing | Chuxiong | |||||
All SNPs | 2463 | 1911 | 552 | 0.230 | 0.240 | 0.206 | 0.222 | 0.246 |
Intergenic SNPs | 1467 | 1160 | 310 | 0.233 | 0.215 | 0.199 | 0.235 | 0.240 |
Exon SNPs | 921 | 692 | 229 | 0.263 | 0.282 | 0.215 | 0.199 | 0.259 |
Intron SNPs | 66 | 53 | 13 | 0.252 | 0.227 | 0.254 | 0.258 | 0.199 |
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Li, H.; Liang, T.; Liu, Y.; Wang, P.; Wang, S.; Zhao, M.; Zhang, Y. Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics. Int. J. Mol. Sci. 2024, 25, 9013. https://doi.org/10.3390/ijms25169013
Li H, Liang T, Liu Y, Wang P, Wang S, Zhao M, Zhang Y. Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics. International Journal of Molecular Sciences. 2024; 25(16):9013. https://doi.org/10.3390/ijms25169013
Chicago/Turabian StyleLi, Haixia, Tong Liang, Yongju Liu, Pengfei Wang, Shaojuan Wang, Min Zhao, and Ying Zhang. 2024. "Exploring Mitochondrial Heterogeneity and Evolutionary Dynamics in Thelephora ganbajun through Population Genomics" International Journal of Molecular Sciences 25, no. 16: 9013. https://doi.org/10.3390/ijms25169013