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Autotrophic eukaryotes have evolved by the endosymbiotic uptake of photosynthetic organisms. Interestingly, many algae and plants have secondarily lost the photosynthetic activity despite its great advantages.  Prototheca  and  Helicosporidium  are non-photosynthetic green algae possessing colourless plastids. The plastid genomes of  Prototheca wickerhamii  and  Helicosporidium  sp. are highly reduced owing to the elimination of genes related to photosynthesis. To gain further insight into the reductive genome evolution during the shift from a photosynthetic to a heterotrophic lifestyle, we sequenced the plastid and nuclear genomes of two  Prototheca  species,  P. cutis  JCM 15793 and  P. stagnora  JCM 9641, and performed comparative genome analyses among trebouxiophytes. Our phylogenetic analyses using plastid- and nucleus-encoded proteins strongly suggest that independent losses of photosynthesis have occurred at least three times in the clade of  Prototheca  and  Helicosporidium . Conserved gene content among these non-photosynthetic lineages suggests that the plastid and nuclear genomes have convergently eliminated a similar set of photosynthesis-related genes. Other than the photosynthetic genes, significant gene loss and gain were not observed in  Prototheca  compared to its closest photosynthetic relative  Auxenochlorella . Although it remains unclear why loss of photosynthesis occurred in  Prototheca , the mixotrophic capability of trebouxiophytes likely made it possible to eliminate photosynthesis.

Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca