Woronichinia naegeliana: a common nontoxigenic component of temperate freshwater cyanobacterial blooms with 30% of its genome in transposons

•The complete genome of Woronichinia naegeliana WA131 was determined from a microcystin-containing CyanoHAB in a US Pacific NW freshwater lake (2018).•The larger genome size of 7.9 Mpb, compared to other bloom-forming cyanobacteria, is mostly attributable to insertion elements and their transposase genes, which are often present in high copy number. Pseudogenes are also relatively abundant, but most of these are transposases.•The genome contains no genes for cyanotoxins or the common taste-and-odor compounds. Gene clusters for the production of anabaenopeptins, cyanopeptolins, microginins and some post-translationally modified peptides are present.•The genome of this planktonic, non-diazotrophic cyanobacterium contains genes commonly found in other bloom-forming cyanobacteria, but surprisingly lacks genes for nitrite and nitrate reductases, making this cyanobacterium dependent on reduced and organic forms of nitrogen.•In the US Pacific NW, Woronichinia naegeliana was a common component of freshwater HABs across the period 2007–2019, often being the dominant or subdominant cyanobacterium.