Clade-specific gene distribution among Agrobacterium biovar 1

clade-specific sets of homologous gene clusters were determined using the ‘get_clade_specific_genes.r’ script from Pantagruel package (Lassalle et al., 2019) using the homologous gene family presence/absence matrix as input. Results are presented based on two criteria:- "bgclade_strict": where presence/absence of a gene family is deemed specific in contract to the absence/presence in other genomes of a background clade (defined to include at least 10 other genomes)- "bgclade_0.1": where absence/presence is allowed in up to 10% (rounded to the lower integer) of other genomes of a background clade, to allow the detection of genes specifically gained/lost by the ancestor of the focus clade strains but that may have independently gained/lost in close relatives; this relaxed approach often reveals large groups of contiguous clade-specific genes (Lassalle et al., 2011; Lassalle et al., 2017).