Symbiodiniaceae Minicircles Reveal Coral Reef Algae Genomic Variation

Members of the Symbiodiniaceae family of algae are symbiotic with a range of invertebrates, including members of the cnidaria phylum (jellyfish, anemones, and corals). Stony corals thrive from this relationship which permits them to construct tropical and subtropical coral reefs which support an enormous diversity of marine fauna. Symbiotic algae are vital to the health of the coral, providing a large amount of energy in the form of compounds generated via photosynthesis. The Symbiodiniaceae family, together with other dinoflagellate algae, is characterized by a uniquely organized chloroplast genome in which the DNA is fragmented into numerous small plasmid-like molecules, termed minicircles rather than existing as a single circular molecule. In the Symbiodiniacae, each of the minicircles identified to date contains a single gene which encodes for a core protein of the photosystem apparatus, or for an associated energy-transducing complexes, or a ribosomal RNA. Past studies that have identified minicircles in Symbiodiniacae have used minicircles from other algal taxa as a starting point for discovery and thus the full minicircle complement is unknown. Here we have used rolling circle amplification (RCA), an unbiased methodology, to identify circular DNA in the algae Breviolum psygmophilum (formerly Symbiodiaceae Clade B). The amplified minicircles were sequenced via Illumina MiSeq and Oxford Nanopore Technologies. Using this approach, we determined that B. psygmophilum cpDNA contains 14 minicircles, 4 of which have more than one variant. In addition, the relative abundance of individual minicircles is plastic, varying across physiological stages from the linear growth phase and the early declining growth phase. These observations raise the possibility that the evolution of chloroplast minicircles may provide a means of modulating gene dosage through variation in DNA relative abundance, a level of flexibility that may not be readily achievable in the typical single-circular chloroplast genomes found in most plants and algae.