Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria.
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.
Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway.
Anders K
AK
Krabberød
Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway.
Russell J S
RJS
Orr
Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway.
Jon
J
Bråte
Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway.
Tom
T
Kristensen
Department of Research and Collections, Natural History Museum, University of Oslo, Oslo, Norway.
Kjell R
KR
Bjørklund
Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway.
Kamran
K
Shalchian-Tabrizi
D001499:Bayes Theorem; D005075:Biological Evolution; D056890:Eukaryota / Q000235:genetics; D005057:Eukaryotic Cells; D019143:Evolution, Molecular; D010802:Phylogeny; D056901:Rhizaria / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis / Q000379:methods; D059467:Transcriptome / Q000235:genetics; D014404:Tubulin / Q000235:genetics
D014404:Tubulin
Radiolaria; Rhizaria; SAR; cytoskeleton; phylogeny; protists; single-cell transcriptomics