Fig. 1

Genome divergence among Symbiodiniaceae. a Similarity between Symbiodiniaceae (and the outgroup P. glacialis) based on pairwise whole-genome sequence alignments. The colour of the square depicts the average percent identity of the best reciprocal one-to-one aligned regions (I) between each genome pair and the size of the square is proportional to the percent of the query genome that aligned to the reference (Q), as shown in the legend. The tree topologies on the left and bottom indicate the known phylogenetic relationship [26] among the isolates. Isolates in Symbiodinium are highlighted in grey, and their comparisons are highlighted in a bounded box. b Neighbour-joining tree based on 21-mers shared by genomes of Suessiales; branch lengths are proportional to the estimated distances. The shortest and longest distances (d) in the tree, as well as average distances (δ) among representative clades are shown following the bottom-left colour code. ‘Clade BCF’: clade including B. minutum, the two Cladocopium isolates, and F. kawagutii