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Background  The ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus  Frankia  can establish a symbiotic relationship with a diverse group of plants within eight different families from three different orders, the Cucurbitales, Fagales and Rosales. Phylogenetically,  Frankia  strains can be divided into four clusters, three of which (I, II, III) contain symbiotic strains. Members of Cluster II nodulate the broadest range of host plants with species from four families from two different orders, growing on six continents. Two Cluster II genomes were sequenced thus far, both from Asia.    Results  In this paper we present the first  Frankia  cluster II genome from North America (California), Dg2, which represents a metagenome of two major and one minor strains. A phylogenetic analysis of the core genomes of 16  Frankia  strains shows that Cluster II the ancestral group in the genus, also ancestral to the non-symbiotic Cluster IV. Dg2 contains the canonical  nod  genes  nodABC  for the production of lipochitooligosaccharide Nod factors, but also two copies of the sulfotransferase gene  nodH.  In rhizobial systems, sulfation of Nod factors affects their host specificity and their stability.    Conclusions  A comparison with the  nod  gene region of the previously sequenced Dg1 genome from a Cluster II strain from Pakistan shows that the common ancestor of both strains should have contained  nodABC  and  nodH.  Phylogenetically, Dg2 NodH proteins are sister to rhizobial NodH proteins. A  glnA -based phylogenetic analysis of all Cluster II strains sampled thus far supports the hypothesis that Cluster II  Frankia  strains came to North America with  Datisca glomerata f ollowing the Madrean-Tethyan pattern.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3140-1) contains supplementary material, which is available to authorized users.

An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH