Abstract The cryptophytes of the Black Sea are a poorly studied group that has yet to be fully resolved using comprehensive taxonomic approaches, including electron microscopy and molecular genetics. This study describes Proteomonas agilis sp. nov. belonging to a marine cryptophyte genus formerly thought to be monotypic. The morphological characters of the new species align with those currently used to delineate the genus Proteomonas, and are similar to those of the haplomorph P. sulcata, the type species, with minor morphological and molecular modifications. Phylogenetic relationships inferred from nuclear-encoded SSU, LSU, and ITS2 rDNA datasets confirmed that the new species belongs to the monophyletic genus Proteomonas, which is divided into two unequal branches. The largest and relatively long branch contains 18 strains, including P. agilis sp. nov. Comparison of ITS2 rRNA secondary structures using the compensatory base changes approach confirmed the distinction of P. agilis sp. nov. from the other Proteomonas strains. Our findings revealed that the cryptophyte genus Proteomonas is not monotypic but includes a range of unstudied species besides the type species P. sulcata and P. agilis sp. nov. described in this study. Therefore, an integrated approach is required for a careful revision of the genus.
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