Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny

Krabberød, Anders K.; Bråte, Jon; Dolven, Jane K.; Ose, Randi F.; Klaveness, Dag; Kristensen, Tom; Bjørklund, Kjell R.; Shalchian-Tabrizi, Kamran

doi:10.1371/journal.pone.0023526

Cited by 52 publications

(44 citation statements)

References 47 publications

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“…The Rhizaria tree (Fig. 3B) showed the grouping of Chlorarachniophyta and Monadofilosa (from the phylum Cercozoa), while Radiolaria was not well defined as described in previous phylogenies [23]: the class Polycystinea did not appear monophyletic and was separated into the respective orders except Collodaria and Nassellaria that were grouped (as Nassellaria*). These trees confirmed that the final dataset did not contain misclassified sequences.…”

Section: Resultsmentioning

confidence: 72%

General Patterns of Diversity in Major Marine Microeukaryote Lineages

Pernice

Logares²,

Guillou³

et al. 2013

PLoS ONE

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Microeukaryotes have vital roles for the functioning of marine ecosystems, but still some general characteristics of their current diversity and phylogeny remain unclear. Here we investigated both aspects in major oceanic microeukaryote lineages using 18S rDNA (V4–V5 hypervariable regions) sequences from public databases that derive from various marine environmental surveys. A very carefully and manually curated dataset of 8291 Sanger sequences was generated and subsequently split into 65 taxonomic groups (roughly to Class level based on KeyDNATools) prior to downstream analyses. First, we calculated genetic distances and clustered sequences into Operational Taxonomic Units (OTUs) using different distance cut-off levels. We found that most taxonomic groups had a maximum pairwise genetic distance of 0.25. Second, we used phylogenetic trees to study general evolutionary patterns. These trees confirmed our taxonomic classification and served to run Lineage Through Time (LTT) plots. LTT results indicated different cladogenesis dynamics across groups, with some displaying an early diversification and others a more recent one. Overall, our study provides an improved description of the microeukaryote diversity in the oceans in terms of genetic differentiation within groups as well as in the general phylogenetic structure. These results will be important to interpret the large amount of sequence data that is currently generated by High Throughput Sequencing technologies.

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Section: Resultsmentioning

confidence: 72%

General Patterns of Diversity in Major Marine Microeukaryote Lineages

Pernice

Logares²,

Guillou³

et al. 2013

PLoS ONE

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“…Taxopodida and Acantharia have been grouped together as Spasmaria based on the existence of contractile myonemes in both groups (Cavalier-Smith 1993), a grouping also supported in combined 18S and 28S rDNA phylogeny (Krabberød et al 2011). Myonemes give taxopodidans the ability to swim using their pseudopodia like oars, while giving acantharians the ability to regulate their buoyancy by altering their cell volume (Cachon et al 1977; Febvre 1981).…”

Section: Discussionmentioning

confidence: 96%

Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria

Krabberød

Orr

Bråte

et al. 2017

Molecular Biology and Evolution

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The innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport, and cytokinesis, and is largely responsible for the diversity of morphologies among eukaryotes. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton, we provide the first single cell transcriptomes from uncultured, free-living unicellular eukaryotes: the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida). A phylogenomic approach using 255 genes finds Radiolaria and Foraminifera as separate monophyletic groups (together as Retaria), while Cercozoa is shown to be paraphyletic where Endomyxa is sister to Retaria. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these on the revised phylogeny of Rhizaria reveal lineage-specific gene duplications and neofunctionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution in uncultured protist species.

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“…; Krabberød et al. ), the sequence data need to be sampled from both subgroups to accurately elucidate the evolution of EF‐1α/EFL gene in Radiolaria, as well as that in Rhizaria as a whole.…”

mentioning

confidence: 99%

Evolution of Elongation Factor‐Like (EFL) Protein in Rhizaria is Revised by Radiolarian EFL Gene Sequences

Ishitani

Kamikawa

Yabuki

et al. 2012

J Eukaryotic Microbiology

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Elongation factor 1α (EF-1α) and elongation factor-like (EFL) proteins are considered to carry out equivalent functions in translation in eukaryotic cells. Elongation factor 1α and EFL genes are patchily distributed in the global eukaryotic tree, suggesting that the evolution of these elongation factors cannot be reconciled without multiple lateral gene transfer and/or ancestral co-occurrence followed by differential loss of either of the two factors. Our current understanding of the EF-1α/EFL evolution in the eukaryotic group Rhizaria, composed of Foraminifera, Radiolaria, Filosa, and Endomyxa, remains insufficient, as no information on EF-1α/EFL gene is available for any members of Radiolaria. In this study, EFL genes were experimentally isolated from four polycystine radiolarians (i.e. Dictyocoryne, Eucyrtidium, Collozoum, and Sphaerozoum), as well as retrieved from publicly accessible expressed sequence tag data of two acantharean radiolarians (i.e. Astrolonche and Phyllostaurus) and the endomyxan Gromia. The EFL homologs from radiolarians, foraminiferans, and Gromia formed a robust clade in both maximum-likelihood and Bayesian phylogenetic analyses, suggesting that EFL genes were vertically inherited from their common ancestor. We propose an updated model for EF-1α/EFL evolution in Rhizaria by incorporating new EFL data obtained in this study.

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Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny

Cited by 52 publications

References 47 publications

General Patterns of Diversity in Major Marine Microeukaryote Lineages

General Patterns of Diversity in Major Marine Microeukaryote Lineages

Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria

Evolution of Elongation Factor‐Like (EFL) Protein in Rhizaria is Revised by Radiolarian EFL Gene Sequences

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