Genomes of three facultatively symbiotic Frankia sp. strainsreflect host plant biogeography

Filamentous actinobacteria from the genus Frankia anddiverse woody trees and shrubs together form N2-fixing actinorhizal rootnodule symbioses that are a major source of new soil nitrogen in widelydiverse biomes 1. Three major clades of Frankia sp. strains are defined;each clade is associated with a defined subset of plants from among theeight actinorhizal plant families 2,3. The evolution arytrajectoriesfollowed by the ancestors of both symbionts leading to current patternsof symbiont compatibility are unknown. Here we show that the competingprocesses of genome expansion and contraction have operated in differentgroups of Frankia strains in a manner that can be related to thespeciation of the plant hosts and their geographic distribution. Wesequenced and compared the genomes from three Frankia sp. strains havingdifferent host plant specificities. The sizes of their genomes variedfrom 5.38 Mbp for a narrow host range strain (HFPCcI3) to 7.50Mbp for amedium host range strain (ACN14a) to 9.08 Mbp for a broad host rangestrain (EAN1pec.) This size divergence is the largest yet reported forsuch closely related bacteria. Since the order of divergence of thestrains is known, the extent of gene deletion, duplication andacquisition could be estimated and was found to be inconcert with thebiogeographic history of the symbioses. Host plant isolation favoredgenome contraction, whereas host plant diversification favored genomeexpansion. The results support the idea that major genome reductions aswell as expansions can occur in facultatively symbiotic soil bacteria asthey respond to new environments in the context of theirsymbioses