Fig. 1
Phylogenetic tree based on whole-genome sequences inferred using the neighbor-joining algorithm as implemented in the PHYLIP package [22]. The tree was built for 34 Frankia genomes out of a core of 214 genes per genome, 7276 in total, by EDGAR 2.0 [23, 24]. The core has 92,816 amino acid residues per genome, 3,155,744 in total. Genomes used were Candidatus Frankia datisca Dg1 (NC_015656.1), Frankia coriariae BMG5.1 (NZ_JWIO00000000.1), Candidatus Frankia californiensis Dg2 (FLUV00000000.1), Candidatus Frankia meridionalis Cppng1 (CADDZT010000001-CADDZT010000101), Frankia asymbiotica M16386 (NZ_MOMC00000000.1), Frankia saprophytica CN3 (NZ_AGJN00000000.2), Frankia inefficax EuI1c (NC_014666.1), Frankia irregularis DSM45899 (NZ_FAOZ00000000.1), Frankia elaeagni BMG5.12 (NZ_ARFH00000000.1), Frankia discariae BCU110501 (NZ_ARDT00000000.1), Frankia soli NRRL B-16219 (MAXA00000000.1), Frankia casuarinae CcI3 (NC_007777.1), Frankia canadensis ARgP5 (GCF_900241035.1), Candidatus Frankia nodosporulans AgTrS (NZ_CADCWS000000000.1), Candidatus Frankia alpina AiOr (GCA_902806485), Frankia alni ACN14a (NC_008278.1), Frankia torreyi CpI1 (NZ_JYFN00000000.1) and Frankia sp. QA3 (AJWA00000000). The genomes of Cryptosporangium arvum DSM44712 (JFBT01000000) and Jatrophihabitans endophyticus DSM45617 (NZ_FQVU00000000.1) were added for rooting. Bootstrap values are 100 for every branch; they were calculated in R [25] using the packages APE [26] and phangorn [27]. The genomes sequenced from nodules of Coriaria myrtifolia induced by the inoculum from the Philippines, CiP1, are labeled by a green outline. The size bar denotes 0.01 changes