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Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral Cooney, Elizabeth; Leander, Brian; Keeling, Patrick

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Abstract

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.

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Title	Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral
Creator	Cooney, Elizabeth; Leander, Brian; Keeling, Patrick
Date Issued	2022-08-25
Description	<b>Abstract</b><br/> <span lang="EN-US">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 </span><span lang="EN-US">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, </span><em><span lang="IT">Noctiluca scintillans</span></em><span lang="EN-US">, 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</span><span lang="ES-TRAD"> Noctilucales genera: </span><em><span lang="EN-US">Spatulodinium</span></em><span lang="EN-US">, <em>Kofoidinium</em>, and a new lineage, <em>Fabadinium</em> gen. nov. We also provide transcriptomes for undescribed species in <em>Amphidinium</em></span><span lang="DE"> and Abediniales</span><span lang="EN-US">, critical taxa for clarifying the phylogenetic position of </span><span lang="ES-TRAD">Noctilucales</span><span lang="EN-US">. Phylogenomic analyses suggest that the Noctilucales are sister to <em>Amphidinium</em> rather than an independent branch outside the core dinoflagellates. This topology is consistent with observations of shared characteristics between some members of Noctilucales and <em>Amphidinium</em> and provides the most compelling evidence to date that the unusual traits within this group are derived rather than ancestral. We also confirm that <em>Spatulodinium</em> </span><span lang="ES-TRAD">plastids are photosynthetic and of ancestral origin</span><span lang="EN-US">, and show that all non-photosynthetic Noctilucales retain plastid </span><span lang="ES-TRAD">genes</span><span lang="EN-US"> indicating a cryptic organelle.</span></p>
Subject	Other; Other; Noctilucales; dinoflagellate evolution; Amphidinium; Abediniales; single cell transcriptomics; Other; Noctilucales; dinoflagellate evolution; Amphidinium; Abediniales; single cell transcriptomics
Type	Dataset
Notes	Dryad version number: 6</p> Version status: submitted</p> Dryad curation status: Published</p> Sharing link: https://datadryad.org/stash/share/nAvxI4qHmjLr_fo2H9_kItg8rwqwdVrNyFtof3HjtsE</p> Storage size: 604474113</p> Visibility: public</p>
Date Available	2022-08-24
Provider	University of British Columbia Library
License	CC0 Waiver
DOI	10.14288/1.0417549
URI	https://doi.org/10.5683/SP3/YNRCPN
Publisher DOI	https://doi.org/10.5683/SP3/YNRCPN
Grant Funding Agency	Gordon and Betty Moore Foundation; Natural Sciences and Engineering Research Council of Canada; Natural Sciences and Engineering Research Council of Canada
Rights URI	https://creativecommons.org/publicdomain/zero/1.0/
Aggregated Source Repository	Dataverse

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