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Here, we report the draft genome sequence of the estuarine Synechococcus sp. strain CB0101. The genomics information of this strain will facilitate the study of the poorly understood Synechococcus subcluster 5.2 and how this strain is capable of thriving in a dynamic estuarine system, such as the Chesapeake Bay.

Draft Genome Sequence of Synechococcus sp. Strain CB0101, Isolated From the Chesapeake Bay Estuary