Phylogenomics of the Intracellular Parasite Mikrocytos mackini Reveals Evidence for a Mitosome in Rhizaria

Burki, Fabien; Corradi, Nicolas; Sierra, Roberto; Pawłowski, Jan; Meyer, Gary R.; Abbott, Cathryn L.; Keeling, Patrick J.

doi:10.1016/j.cub.2013.06.033

Cited by 73 publications

(87 citation statements)

References 60 publications

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“…Building on previously published datasets [25,39], we more than doubled the taxon sampling, mostly using recently released high-quality transcriptomes for marine microbial species [28] (electronic supplementary material, table S3). Our carefully curated taxon sampling contained 150 OTUs for 250 genes (55 554 aa positions), globally characterized by only 21% of missing data (electronic supplementary material, table S1).…”

Section: Results (A) Improved Dataset and Model Selectionmentioning

confidence: 99%

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

et al. 2016

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Assembling the global eukaryotic tree of life has long been a major effort of Biology. In recent years, pushed by the new availability of genome-scale data for microbial eukaryotes, it has become possible to revisit many evolutionary enigmas. However, some of the most ancient nodes, which are essential for inferring a stable tree, have remained highly controversial. Among other reasons, the lack of adequate genomic datasets for key taxa has prevented the robust reconstruction of early diversification events. In this context, the centrohelid heliozoans are particularly relevant for reconstructing the tree of eukaryotes because they represent one of the last substantial groups that was missing large and diverse genomic data. Here, we filled this gap by sequencing high-quality transcriptomes for four centrohelid lineages, each corresponding to a different family. Combining these new data with a broad eukaryotic sampling, we produced a gene-rich taxon-rich phylogenomic dataset that enabled us to refine the structure of the tree. Specifically, we show that (i) centrohelids relate to haptophytes, confirming Haptista; (ii) Haptista relates to SAR; (iii) Cryptista share strong affinity with Archaeplastida; and (iv) Haptista þ SAR is sister to Cryptista þ Archaeplastida. The implications of this topology are discussed in the broader context of plastid evolution.

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Section: Results (A) Improved Dataset and Model Selectionmentioning

confidence: 99%

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

et al. 2016

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“…The main issues have been the relationship between Radiolaria and Foraminifera (i.e. Retaria), the monophyly of Cercozoa, as well as the relationship between Rhizaria and its immediate neighbours in the SAR supergroup, Stramenopiles and Alveolata (Burki et al 2007, 2013, 2016, Parfrey et al 2010, Krabberød et al 2011, Sierra et al 2013, 2015, Katz & Grant 2014, Cavalier-Smith et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria

Krabberoed

Orr

Braate

et al. 2016

Preprint

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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, freeliving 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 a and b 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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“…The rhizarian Mikrocytos is an intracellular parasite of oysters [113,114]. In a recent transcriptomic survey, the authors were only able to identify ISC system components and not genes that encode typical mitochondrial proteins (e.g.…”

Section: (C) Rhizariamentioning

confidence: 99%

Diversity and origins of anaerobic metabolism in mitochondria and related organelles

Stairs

Leger

Roger

2015

Phil. Trans. R. Soc. B

135

172

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One contribution of 17 to a theme issue 'Eukaryotic origins: progress and challenges'. Across the diversity of life, organisms have evolved different strategies to thrive in hypoxic environments, and microbial eukaryotes ( protists) are no exception. Protists that experience hypoxia often possess metabolically distinct mitochondria called mitochondrion-related organelles (MROs). While there are some common metabolic features shared between the MROs of distantly related protists, these organelles have evolved independently multiple times across the breadth of eukaryotic diversity. Until recently, much of our knowledge regarding the metabolic potential of different MROs was limited to studies in parasitic lineages. Over the past decade, deep-sequencing studies of free-living anaerobic protists have revealed novel configurations of metabolic pathways that have been co-opted for life in low oxygen environments. Here, we provide recent examples of anaerobic metabolism in the MROs of free-living protists and their parasitic relatives. Additionally, we outline evolutionary scenarios to explain the origins of these anaerobic pathways in eukaryotes.

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Phylogenomics of the Intracellular Parasite Mikrocytos mackini Reveals Evidence for a Mitosome in Rhizaria

Cited by 73 publications

References 60 publications

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria

Diversity and origins of anaerobic metabolism in mitochondria and related organelles

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