Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Recombination Detection
3.2. Temporal Signal and Substitution Rate Estimation
3.3. RIM8 Evolutionary Rates
3.4. Variable Gene Families
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Data Set | Number of Genomes | Time Span (Years) | Number of Timepoints | Mean Length (nt) | p-Value Phi Test | r/m |
---|---|---|---|---|---|---|
RIM2 | 59 | 8 | 9 | 175,301 | 6.01 × 10−34 | 2.156 |
RIM2_A | 47 | 8 | 8 | 175,310 | 3.94 × 10−27 | 1.574 |
RIM2_B | 10 | 1 | 4 | 175,309 | 5.24 × 10−9 | 3.385 |
RIM8 | 10 | 17 | 10 | 170,485 | 0.0151 | 7.833 |
RIM12 | 21 | 13 | 9 | 174,726 | 5.98 × 10−10 | 8.421 |
RIM12_A | 10 | 13 | 7 | 174,271 | 2.07 × 10−12 | 7.053 |
RIM12_C | 7 | 1 | 3 | 175,605 | 0.013 | 15.37 |
RIM14 | 9 | 2 | 6 | 179,756 | 9.79 × 10−8 | 2.214 |
RIM44 | 8 | 7 | 3 | 195,353 | 0.059 | 0.2884 |
Name | Group | r/m | Reference |
---|---|---|---|
Staphylococcus aureus | Bacteria | 0.283 | [36] |
Pseudomonas aeruginosa | Bacteria | 0.853 | [51] |
Escherichia coli | Bacteria | 1.024 | [52] |
Salmonella enterica | Bacteria | 1.14 | [53] |
Bacillus cereus | Bacteria | 3.4 | [54] |
Streptococcus pneumonia | Bacteria | 7.2 | [50] |
Cyanophage RIM8 | dsDNA phage | 7.8 | This study |
936 group of phages | dsDNA phage | 23.5 | [18] |
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Kupczok, A.; Dagan, T. Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage. Viruses 2019, 11, 720. https://doi.org/10.3390/v11080720
Kupczok A, Dagan T. Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage. Viruses. 2019; 11(8):720. https://doi.org/10.3390/v11080720
Chicago/Turabian StyleKupczok, Anne, and Tal Dagan. 2019. "Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage" Viruses 11, no. 8: 720. https://doi.org/10.3390/v11080720