Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction

Abstract

Bacteriophages are recognized DNA vectors and transduction is considered as a common mechanism of lateral gene transfer (LGT) during microbial evolution. Anecdotal events of phage-mediated gene transfer were studied extensively, however, a coherent evolutionary viewpoint of LGT by transduction, its extent and characteristics, is still lacking. Here we report a large-scale evolutionary reconstruction of transduction events in 3982 genomes. We inferred 17 158 recent transduction events linking donors, phages and recipients into a phylogenomic transduction network view. We find that LGT by transduction is mostly restricted to closely related donors and recipients. Furthermore, a substantial number of the transduction events (9%) are best described as gene duplications that are mediated by mobile DNA vectors. We propose to distinguish this type of paralogy by the term autology. A comparison of donor and recipient genomes revealed that genome similarity is a superior predictor of species connectivity in the network in comparison to common habitat. This indicates that genetic similarity, rather than ecological opportunity, is a driver of successful transduction during microbial evolution. A striking difference in the connectivity pattern of donors and recipients shows that while lysogenic interactions are highly species-specific, the host range for lytic phage infections can be much wider, serving to connect dense clusters of closely related species. Our results thus demonstrate that DNA transfer via transduction occurs within the context of phage-host specificity, but that this tight constraint can be breached, on rare occasions, to produce long-range LGTs of profound evolutionary consequences.