アブストラクト
| Date | Jul 26, 2018 |
| Speaker |
Anne Kupczok,
Institute of General Microbiology, Kiel University, Kiel, Germany
http://www.mikrobio.uni-kiel.de/de/ag-dagan/mitarbeiterinnen/dr.-rer.-nat.-anne-kupczok |
| Title | Evolutionary rate estimation for bacteriophages based on time series data sets |
| Abstract | Time series samples of isolates or communities provide yet unexplored evidence for the evolutionary processes that shape the populations over the sampling time. The evolutionary processes that affect genomic diversity include point mutation, recombination, and gene turnover. The temporal dynamics of these molecular events are crucial for our understanding of genome evolution. Methods for evolutionary rate estimation have been developed for isolates of bacteria and eukaryotic viruses, however, rates of molecular evolution in bacteriophages are not well investigated. Here we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We first analyze 34 isolates of the 936 group of Siphoviridae phages that were sampled using a constant Lactococcus lactis strain from a single dairy over 29 years. The estimated substitution rate of 1.9x10-4 substitutions per site per year due to mutation is within the range of estimates for eukaryotic viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5x10-3 nucleotide alterations due to recombination per site per year. The recombination rate thus exceeds the substitution rate to a great extent, resulting in a relative effect of recombination to mutation (r/m) of ~24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with other phages of the 936 group, demonstrating the role of the 936 group pangenome as reservoir of genetic variation. The second analysis involves two Myoviridae phage lineages infecting marine Synechococcus cyanobacteria that have been sampled over 2 years (8 isolates) and 13 years (6 isolates), respectively. We estimate a substitution rate of ~2x10-5 substitutions per site per year for each of the two lineages. Those rate estimates are consistent with the known negative association between genome size and evolutionary rate. Those analyses provide first estimations of phage substitution rates in natural environments. Phages are recognized as major contributors to bacterial evolution and ecology in nature. The rates estimated here can provide the basis for a quantitative assessment of phage evolutionary rates that are in action during phage bacteria antagonistic coevolution. |