Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral

Dinoflagellates are a diverse group of protists that possess many unique
traits. These include (but are not limited to) expansive genomes packaged
into permanently condensed chromosomes, photosynthetic or cryptic plastids
acquired vertically or horizontally in serial endosymbioses, and a
ruffle-like transverse flagellum attached along its length to the cell.
When reconstructing character evolution, early branching lineages with
unusual features that distinguish them from the rest of the group have
proven useful for inferring ancestral states. The Noctilucales are one
such lineage, possessing relaxed chromosomes in some life stages and a
trailing, thread-like transverse flagellum. However, most of the cellular
and molecular data for the entire group come from a single cultured
species, Noctiluca scintillans, and because its phylogenetic position is
unresolved, it remains unclear if these traits are ancestral or derived.
Here, we use single cell transcriptomics to characterize three diverse
Noctilucales genera: Spatulodinium, Kofoidinium, and a new lineage,
Fabadinium gen. nov. We also provide transcriptomes for undescribed
species in Amphidinium and Abediniales, critical taxa for clarifying the
phylogenetic position of Noctilucales. Phylogenomic analyses suggest that
the Noctilucales are sister to Amphidinium rather than an independent
branch outside the core dinoflagellates. This topology is consistent with
observations of shared characteristics between some members of
Noctilucales and Amphidinium and provides the most compelling evidence to
date that the unusual traits within this group are derived rather than
ancestral. We also confirm that Spatulodinium plastids are photosynthetic
and of ancestral origin, and show that all non-photosynthetic Noctilucales
retain plastid genes indicating a cryptic organelle.