PCR-RFLP and total DNA homology revealed three related genomic species among broad-host-range Frankia strains

Restriction fragment length polymorphism (RFLP) analysis of the PCR amplified nifD-K intergenic spacer (IGS) region was used to cluster 22 Frankia strains of the Elaeagnus host specificity group into seven genomic groups and to measure the degree of genetic similarity among them. This PCR-RFLP analysis could assign freshly isolated strains to described genomic species and revealed genomic groups not yet described among Frankia strains of the Elaeagnus specificity group. Six broad-host-range Frankia strains, infective on both Alnus and Elaeagnus, fell into three closely related PCR-RFLP clusters, DNA-DNA hybridization was then used to establish the correlations between PCR-RFLP clusters and total DNA relatedness groups. The three PCR-RFLP clusters agreed with two new and one reference genomic species, indicating that Frankia ability to nodulate with Alnus and Elaeagnus is a monophyletic trait shared by three genomic species.