Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution

Dinoflagellates are diverse and ecologically important protists
characterized by many morphological and molecular traits that set them
apart from other eukaryotes. These features include, but are not limited
to, massive genomes organized using bacterially-derived histone-like
proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than
histones, and a complex history of photobiology with many independent
losses of photosynthesis, numerous cases of serial secondary and tertiary
plastid gains, and the presence of horizontally acquired bacterial
rhodopsins and type II RuBisCo. Elucidating how this all evolved depends
on knowing the phylogenetic relationships between dinoflagellate lineages.
Half of these species are heterotrophic, but existing molecular data is
strongly biased toward the photosynthetic dinoflagellates due to their
amenability to cultivation and prevalence in culture collections. These
biases make it impossible to interpret the evolution of photosynthesis,
but may also affect phylogenetic inferences that impact our understanding
of character evolution. Here, we address this problem by isolating
individual cells from the Salish Sea and using single cell, culture-free
transcriptomics to expand molecular data for dinoflagellates to include 27
more heterotrophic taxa, resulting in a roughly balanced representation.
Using these data, we performed a comprehensive search for proteins
involved in chromatin packaging, plastid function, and photoactivity
across all dinoflagellates. These searches reveal that 1) photosynthesis
was lost at least 21 times, 2) two known types of HLP were horizontally
acquired around the same time rather than sequentially as previously
thought; 3) multiple rhodopsins are present across the dinoflagellates,
acquired multiple times from different donors; 4) kleptoplastic species
have nucleus-encoded genes for proteins targeted to their temporary
plastids and they are derived from multiple lineages, and 5) warnowiids
are the only heterotrophs that retain a whole photosystem, although some
photosynthesis-related electron transport genes are widely retained in
heterotrophs, likely as part of the iron-sulfur cluster pathway that
persists in non-photosynthetic plastids.