Genetic determinism of phage-bacteria coevolution in natural populations

共同进化 决定论 自然(考古学) 生物 进化生物学 细菌 计算生物学
作者
Damien Piel,Maxime Bruto,Yannick Labreuche,François Blanquart,Sabine Chenivesse,Sophie Lepanse,Adèle James,Rubén Barcia-Cruz,Javier Dubert,Bruno Petton,Erica Lieberman,K. Mathias Wegner,Fatima A. Hussain,Kathryn M. Kauffman,Martin F. Polz,David Bikard,Sylvain Gandon,Frédérique Le Roux
出处
期刊:bioRxiv 被引量:1
标识
DOI:10.1101/2021.05.05.442762
摘要

ABSTRACT Coevolution between bacteriophage (or phage) and their bacterial host is thought to be key for the coexistence of these antagonists. Recent studies have revealed the major role of mobile genetic elements in the emergence of phage resistant hosts but how phage escape these defenses in the wild remained to be explored. Here we show a striking parallel in phage evolving counter defenses to host defenses in natural population. We established a large collection of phages and their bacterial hosts and we explored the genetic structure of their interaction. We find that clearly delineated genomic clusters of phage are specific for distinct clades within a bacterial species, Vibrio crassostreae , yet while all phages can adsorb, only a subset of hosts are killed due to intracellular defense mechanisms. Host genomes contain multiple mobile defense genes and susceptibility to phage is negatively correlated with genome size. Phages also display extensive gene content variation, but their genome size remains conserved. We show that this gene content variation in hosts and phage is due to rapid turnover of genes involved in defense and escape, and that by exchanging anti-defense genes, phages irreversibly switch host. This could be indicative of co-evolution following the matching-allele-model of specificity and the spatial and temporal variability of phage infectivity further suggests that negative-frequency dependent selection drives phage-vibrio coevolutionary dynamics. We propose a “pan-escape system” that can be shared among phages by homologous recombination within a population that infects a bacterial host.
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