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Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member  Compsopogon caeruleus  was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater  Compsopogon caeruleus . It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species  Compsopogon caeruleus  and  Hildenbrandia rivularis  originated and evolved independently at the inland water, whereas the  Bangia atropurpurea ,  Batrachospermum arcuatum  and  Thorea hispida  are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative  Palmaria palmata  at approximately 415–484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.

Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence