Fig. 2

Extensive recent horizontal gene transfer (HGT) among the 50 Rhizobium strains. a Comparison of the predicted number of recent HGT genes and the number of highly conserved plasmid genes between the reference genome of R4-CFN42 (R. etli) and other sample strains. b Genomic locations of the predicted HGT genes between R4-CFN42 and other sample strains. c All HGT events in the tested Rhizobium strains. Connection thickness is scaled to the number of shared protein-coding sequences. The maximum likelihood tree is based on concatenated single-copy protein-coding gene alignments. d Bipartite network of 13 symbiosis plasmids from Rhizobium strains nodulating P. vulgaris. The two clusters of plasmids based on network clustering are represented as blue and orange nodes. Purple nodes represent gene families shared by at least two plasmids, while plasmid-specific gene families are indicated as green nodes. All edges connecting plasmids and gene families are denoted by gray lines