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Members of the genus  Cylindrospermopsis  represent an important environmental and health concern. Strains CS-508 and MVCC14 of  C. raciborskii  were isolated from freshwater reservoirs located in Australia and Uruguay, respectively. While CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We annotated the draft genomes of these  C. raciborskii  strains using the assembly of reads obtained from Illumina MiSeq sequencing. The final assemblies resulted in genome sizes close to 3.6 Mbp for both strains and included 3202 ORFs for CS-508 (in 163 contigs) and 3560 ORFs for MVCC14 (in 99 contigs). Finally, both the average nucleotide identity (ANI) and the similarity of gene content indicate that these two genomes should be considered as strains of the  C. raciborskii  species.   Electronic supplementary material  The online version of this article (10.1186/s40793-018-0323-1) contains supplementary material, which is available to authorized users.

Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay