To investigate patterns of shared gene content, we ran a principal component analysis (PCA) on the gene family distribution matrix using the panpca function (micropan R package). Around 34% of the total variation among the genomes was seen along the 2 principal components (Supplementary Figure 3). Genomes in the same clade formed non-overlapping groups. Species that formed clades (based on relatedness of core genome nucleotide sequences) were also more similar to each other in families of accessory genes.