The class Pedinophyceae was established for asymmetric uniflagellate green algae, and was originally considered as an ancestral lineage of viridiplants. However, analyses of 71 concatenated plastid proteins [Turmel et al. (2009): Mol. Biol. Evol. 26: 2317-2331] recovered Pedinomonas within the Chlorellales (Trebouxiophyceae), thereby questioning the Pedinophyceae as an independent class. For the present study, complete nuclear and plastid-encoded rRNA operon sequences have been determined for 37 taxa of green algae including 6 members of the Pedinophyceae, providing 9272 aligned nucleotide positions. Phylogenies using both rRNA operons consistently rejected any relationship between Pedinophyceae and the Chlorellales. Instead, the Pedinophyceae were significantly resolved as sister of all phycoplast-containing 'core' chlorophytes, i.e. Chlorodendrophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Reinvestigation of plastid proteins discovered biased phylogenetic signal among protein partitions, indicating the published Pedinomonas + Chlorellales association as likely artificial. Marine pedinophytes (Resultomonas and Marsupiomonas; Marsupiomonadales ord. nov.), formed a sister clade to the order Pedinomonadales, occurring in freshwater and soil habitats. Synapomorphies in rRNA secondary structures were integrated in taxonomic diagnoses of the Pedinophyceae and were also used for BLAST searches targeting environmental sequence databases. The latter approach revealed conserved habitat preferences for the Marsupiomonadales and Pedinomonadales, and identified several novel pedinophyte lineages.
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