DOI: 10.5061/dryad.x95x69prq
title: Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution

description: 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.
description: # Investigation of heterotrophs reveals new insights in dinoflagellate
 evolution
 [https://doi.org/10.5061/dryad.x95x69prq](https://doi.org/10.5061/dryad.x95x69prq) Dryad-stored material consists of: A zipped folder containing all peptide single cell transcriptome assemblies:      peptide_transcriptome_assemblies.zip A zipped folder containing *.contree files that can be viewed in FigTree v.1.4.4 (free download at https://github.com/rambaut/figtree/releases):      gene_collections_and_trees.zip A zipped excel file of plastid targeting extensions on isoprenoid transcripts, and spliced leader sequences in Dinophysis acuminata:      supplementary_spreadsheet.zip A zipped fasta file of the concatenated alignment used to make the multi-protein phylogeny:      concatenated_multiprotein_alignment.fasta.zip A zipped folder containing videos of all cells:      videos.zip ## Description of the data and file structure Peptide assemblies of all transcriptomes have been made available so they can be used for gene searches and added to larger datasets for analyses. Curated gene collections for each single gene discussed in the study are given with corresponding trees in which all counted taxa are colored. The trees generated for Fig. S3 are included. Trees (*.tre) can be viewed in FigTree while curated gene collections, which are unaligned and untrimmed, can be used to reproduce results, or used as queries in blast searches against other transcriptomes. The concatenated multi-protein alignment can be used to generate phylogenies using any model or statistical method. Videos can be viewed in most standard video-viewing programs.