Fig. 1

Maximum likelihood phylogenetic tree of 109 Microcystis colony genomes and previously sequenced reference genomes. Microcystis genomes were classified in 18 genotypes based on Average Nucleotide Identity (ANI) greater or equal to 99%. A core genome was inferred based on 109 Microcystis genomes and 122 Microcystis reference genomes downloaded from NCBI. The alignment of the 115 core genes (68,145 bp in total after excluding positions with gaps) was used to infer the Maximum Likelihood phylogeny. The tree was rooted using two cyanobacteria (Anabaena variabilis ATCC29413 and Synechocystis sp. PCC6803) as outgroups. The clades highlighted in different colours indicate Microcystis genotypes (G01 to G18) from this study; uncoloured clades are other reference genomes from the literature. The purple circles on the tree branches indicate bootstrap values greater or equal to 70%. The empty and filled triangles around the tree indicate absence and presence of the mcy cluster, respectively. The small coloured and filled dots indicate the most prevalent AB genera related to each Microcystis genome. The outermost circle indicates the geographic origin of the Microcystis genomes. Several reference genomes of Microcystis genotypes recovered from environments with high and low phosphorus are indicated as LL/LG (Low Phosphorus Lake/Low Phosphorus genotype), HL/LG (High-Phosphorus Lake/Low-Phosphorus Genotype) and HL/HG (High-Phosphorus Lake/High-Phosphorus Genotype). For details about the names of the strains, please refer to Supplementary Table 2