Microcystis botrys in a toxic cyanobacterias freshwater species that forms blooms in many lakes, including freshwater drinking reservoirs. The toxins produced are known as micocystins and consist of a suite of compounds that are regulated by the microcystis gene complex. Within a Formas financed project we are investigating when and why certain blooms have high levels of toxicity and others do not. Blooms are composed of toxic strains and those that do not produce microcystins. The proportion of toxic to non-toxic strains varies temporally and spatially. A first step in the investigation is to establish reference genomes for Microcystis botrys based on a toxic and a non-toxic strain. For this purpose we are using PacBIo technology. Resequencing of additional strains will be made with Illumina. Microcystis botrys genomes will be compared to available Microcystis aeruginosa strains.