Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution
Data files
May 23, 2024 version files 215.03 MB
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concatenated_multiprotein_alignment.zip
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gene_collections_and_trees.zip
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peptide_transcriptome_assemblies.zip
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README.md
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supplementary_spreadsheet.zip
Abstract
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.
README: Investigation of heterotrophs reveals new insights in dinoflagellate evolution
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.