Taxonomic implications of revealing dimorphism in the Pyrenomonadaceae (Cryptophyceae): how many genera?

The present study reevaluates the taxonomy of the Pyrenomonadaceae through an integrative approach, combining molecular phylogeny with detailed morphological analysis. By expanding taxon sampling and focusing on morphologically validated strains, this research addresses long-standing conflicts between traditional phenotypic markers and emerging genetic data. The congruence of key morphological traits delineating genera with molecular phylogenies inferred from the nuclear 18S rDNA, ITS/5.8S rDNA, 28S rDNA and nucleomorph 18S rDNA was assessed. Molecular evidence confirmed dimorphism within the Pyrenomonadaceae, revealing genetically identical pairs with distinct vestibular invagination and the inner periplast morphology. In addition, comprehensive examination of three novel cryptophyte strains isolated from the Black Sea, employing LM, SEM, flow cytometry and molecular phylogeny revealed that the transition between sheet-like and plate-like inner periplast components is strictly correlated with cell ploidy levels rather than evolutionary divergence. These findings confirm a dimorphic (haploid-diploid) life cycle within the family. The genetic identity between morphologically disparate morphotypes justifies the abolition of the genus Storeatula, relegating it to a life-cycle stage of other related genera. A revision of the Pyrenomonadaceae was performed to fill the gap in its classification according to the latest morphological and molecular phylogenetic findings, resulting in the erection of a novel genus, Eomonas gen. nov. accommodating previously recognized and two newly described taxa from the Black Sea, Eomonas fusiformis sp. nov. and Eomonas vitalis sp. nov. Furthermore, we address the nomenclatural challenges posed by the poorly defined type species, Rhodomonas baltica, which currently prevents a complete formal revision of the family. To navigate this instability, we introduce a set of unique molecular signatures that allow for robust species delineation regardless of morphological or life-cycle stage state. This study emphasizes a transition in cryptophyte systematics towards a diagnostic framework that prioritizes stable genomic and ploidy-related characters over plastic phenotypic traits.