Rates of Molecular Evolution in a Marine <i>Synechococcus</i> Phage Lineage
Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and h...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-08-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/11/8/720 |
| _version_ | 1830415412309786624 |
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| author | Anne Kupczok Tal Dagan |
| author_facet | Anne Kupczok Tal Dagan |
| author_sort | Anne Kupczok |
| collection | DOAJ |
| description | Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of <i>Synechococcus</i>-infecting <i>Myoviridae</i> ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10<sup>−5</sup> substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity. |
| first_indexed | 2024-12-20T21:05:12Z |
| format | Article |
| id | doaj.art-96fc011f3276441ba4c7b80910911338 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-20T21:05:12Z |
| publishDate | 2019-08-01 |
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| series | Viruses |
| spelling | doaj.art-96fc011f3276441ba4c7b809109113382022-12-21T19:26:38ZengMDPI AGViruses1999-49152019-08-0111872010.3390/v11080720v11080720Rates of Molecular Evolution in a Marine <i>Synechococcus</i> Phage LineageAnne Kupczok0Tal Dagan1Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, GermanyGenomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, 24118 Kiel, GermanyCyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of <i>Synechococcus</i>-infecting <i>Myoviridae</i> ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10<sup>−5</sup> substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity.https://www.mdpi.com/1999-4915/11/8/720substitution raterecombination rategene turnovercyanophage |
| spellingShingle | Anne Kupczok Tal Dagan Rates of Molecular Evolution in a Marine <i>Synechococcus</i> Phage Lineage Viruses substitution rate recombination rate gene turnover cyanophage |
| title | Rates of Molecular Evolution in a Marine <i>Synechococcus</i> Phage Lineage |
| title_full | Rates of Molecular Evolution in a Marine <i>Synechococcus</i> Phage Lineage |
| title_fullStr | Rates of Molecular Evolution in a Marine <i>Synechococcus</i> Phage Lineage |
| title_full_unstemmed | Rates of Molecular Evolution in a Marine <i>Synechococcus</i> Phage Lineage |
| title_short | Rates of Molecular Evolution in a Marine <i>Synechococcus</i> Phage Lineage |
| title_sort | rates of molecular evolution in a marine i synechococcus i phage lineage |
| topic | substitution rate recombination rate gene turnover cyanophage |
| url | https://www.mdpi.com/1999-4915/11/8/720 |
| work_keys_str_mv | AT annekupczok ratesofmolecularevolutioninamarineisynechococcusiphagelineage AT taldagan ratesofmolecularevolutioninamarineisynechococcusiphagelineage |