Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Dataset Collection
2.2. Alignment
2.3. General Statistics and Linkage Disequilibrium
2.4. Genetic Structure of S. cerevisiae mtDNA
3. Results
3.1. Saccharomyces cerevisiae Mitochondrial Genome
3.2. Recombination and Linkage Disequilibrium in S. cerevisiae Mitochondrial DNA
3.3. Genetic Structure of S. cerevisiae Mitochondrial DNA
3.3.1. Principal Component Analysis (PCA)
3.3.2. Sparse Non-Negative Matrix Factorization (sNMF)
3.3.3. Neighbor-Joining Phylogenetic Trees
3.4. Population Structure Based on Strains’ Technological Sources and Geographical Origins
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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General Parameter | Statistics |
---|---|
Number of sequences | 6646 |
Size (bp) | 5475 |
Number of polymorphic sites | 526 |
Number of haplotypes | 1265 |
Number of observed transitions | 273 |
Number of observed transversion | 291 |
Nucleotide composition (%)—C | 13.09 |
Nucleotide composition (%)—T | 41.33 |
Nucleotide composition (%)—A | 30.95 |
Nucleotide composition (%)—G | 14.63 |
Gene diversity | 0.9665 ± 0.0032 |
Mean number of pairwise differences | 38.632869 ± 16.797110 |
Nucleotide diversity (average over loci) | 0.007354 ± 0.003535 |
Tajima’s D p-value | 0.10600 |
Fu’s FS p-value | 0.59400 |
Beer | Bread | Clinical | Laboratory | Natural | Other Fb | Saké | Wine and Vine | |
---|---|---|---|---|---|---|---|---|
- | 0.0031 | 0.0034 | 0.0543 | 0.0031 | 0.0009 | 0.0037 | 0.0025 | Beer |
- | 0.0016 | 0.0545 | 0.0075 | 0.0127 | 0.0097 | 0.0025 | Bread | |
- | 0.0666 | 0.0035 | 0.0073 | 0.0133 | 0.0056 | Clinical | ||
- | 0.0374 | 0.0312 | 0.0281 | 0.0235 | Laboratory | |||
- | 0.0003 | 0.0024 | 0.0028 | Natural | ||||
- | 0.0028 | 0.0038 | Other Fb | |||||
- | 0.0020 | Saké | ||||||
- | Wine and vine |
Africa_Central | Africa_Eastern | Africa_West | America_North | America_South | East_Asia | Island_Southeast_Asia | Asia_Japan | Mainland_Southeast_Asia | Europe_Britain | Central_Europe | Europe_Eastern | Europe_Mediterranean | Europe_Western | Near_East_and_Caucasus | Oceania | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
- | 0.0238 | 0.0127 | 0.0079 | 0.0054 | 0.0054 | 0.0222 | 0.0033 | 0.0268 | 0.0459 | 0.0215 | 0.0083 | 0.0152 | 0.0181 | 0.0162 | 0.0769 | Africa_Central |
- | 0.0263 | 0.0078 | 0.0002 | 0.0342 | 0.0316 | 0.0184 | 0.0484 | 0.0229 | 0.0179 | 0.0299 | 0.0185 | 0.0184 | 0.0295 | 0.0154 | Africa_Eastern | |
- | 0.0162 | 0.0012 | 0.0164 | 0.0120 | 0.0046 | 0.0322 | 0.0209 | 0.0245 | 0.0100 | 0.0150 | 0.0115 | 0.0170 | 0.0888 | Africa_West | ||
- | 0.0107 | 0.0091 | 0.0202 | 0.0452 | 0.0733 | 0.0018 | 0.0137 | 0.0252 | 0.0198 | 0.0186 | 0.0116 | 0.0904 | America_North | |||
- | 0.0149 | 0.0203 | 0.0067 | 0.0303 | 0.0129 | 0.0118 | 0.0220 | 0.0026 | 0.0069 | 0.0126 | 0.1132 | America_South | ||||
- | 0.0195 | 0.0383 | 0.0779 | 0.0031 | 0.0197 | 0.0211 | 0.0028 | 0.0073 | 0.0163 | 0.0460 | East_Asia | |||||
- | 0.0006 | 0.0247 | 0.0352 | 0.0224 | 0.0104 | 0.0177 | 0.0172 | 0.0109 | 0.0459 | Island_Souhteast_Asia | ||||||
- | 0.0082 | 0.0026 | 0.0185 | 0.0239 | 0.0098 | 0.0121 | 0.0344 | 0.1680 | Asia_Japan | |||||||
- | 0.0123 | 0.0071 | 0.0391 | 0.0339 | 0.0390 | 0.0638 | 0.1946 | Mainland_Southeast_Asia | ||||||||
- | 0.0164 | 0.0003 | 0.0218 | 0.0189 | 0.0175 | 0.0921 | Europe_Britain | |||||||||
- | 0.0167 | 0.0156 | 0.0146 | 0.0033 | 0.1049 | Central_Europe | ||||||||||
- | 0.0031 | 0.0031 | 0.0060 | 0.0424 | Europe_Eastern | |||||||||||
- | 0.0056 | 0.0031 | 0.1090 | Europe_Mediterranean | ||||||||||||
- | 0.0062 | 0.0892 | Europe_Western | |||||||||||||
- | 0.0490 | Near_East_and_Caucasus | ||||||||||||||
- | Oceania |
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Vieira, D.; Esteves, S.; Santiago, C.; Conde-Sousa, E.; Fernandes, T.; Pais, C.; Soares, P.; Franco-Duarte, R. Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes. Microorganisms 2020, 8, 1001. https://doi.org/10.3390/microorganisms8071001
Vieira D, Esteves S, Santiago C, Conde-Sousa E, Fernandes T, Pais C, Soares P, Franco-Duarte R. Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes. Microorganisms. 2020; 8(7):1001. https://doi.org/10.3390/microorganisms8071001
Chicago/Turabian StyleVieira, Daniel, Soraia Esteves, Carolina Santiago, Eduardo Conde-Sousa, Ticiana Fernandes, Célia Pais, Pedro Soares, and Ricardo Franco-Duarte. 2020. "Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes" Microorganisms 8, no. 7: 1001. https://doi.org/10.3390/microorganisms8071001
APA StyleVieira, D., Esteves, S., Santiago, C., Conde-Sousa, E., Fernandes, T., Pais, C., Soares, P., & Franco-Duarte, R. (2020). Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes. Microorganisms, 8(7), 1001. https://doi.org/10.3390/microorganisms8071001