New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

Strassert, Jürgen F. H.; Jamy, Mahwash; Mylnikov, Alexander P.; Tikhonenkov, Denis V.; Burki, Fabien

doi:10.1101/403329

Cited by 13 publications

(25 citation statements)

References 52 publications

(80 reference statements)

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“…Inferring the monophyly of Archaeplastida was only possible using the combined evidence from the four datasets, careful data curation, and the application of complex mixture models. Our analyses consistently recovered the monophyly of Archaeplastida with both ML and BI methods, in contrast to recent reports of conflicting ML and BI hypotheses (Brown et al 2018;Gawryluk et al 2019;Strassert et al 2019). The monophyly of Archaeplastida has also been recovered in two recent studies (Lax et al 2018;Price et al 2019) although these are a minority among the datasets with a broad sampling of the eukaryotic diversity (Hampl et al 2009;Baurain et al 2010;Parfrey et al 2010;Burki et al 2012Burki et al , 2016Brown et al 2013;Yabuki et al 2014;Janouškovec et al 2017).…”

Section: Implications For Eukaryotic Evolutioncontrasting

confidence: 43%

“…Haptophyta was the sister group of a Telonemia + SAR clade (TSAR; Strassert et al 2019). Archaeplastida was not recovered as monophyletic, with Cryptista being sister to Glaucophyta + Chloroplastida (with low support) to the exclusion of a Rhodophyta + Picozoa clade.…”

Section: Monophyly Of Archaeplastida and The Tree Of Eukaryotesmentioning

confidence: 99%

“…With a few exceptions (Lax et al 2018;Price et al 2019), the majority of nuclear phylogenomic studies have not recovered the monophyly of PPE (Hampl et al 2009;Baurain et al 2010;Parfrey et al 2010;Burki et al 2012Burki et al , 2016Brown et al 2013;Yabuki et al 2014;Janouškovec et al 2017), or did so with low statistical support (Burki et al 2007(Burki et al , 2009, or using a very sparse taxon sampling (Rodríguez-Ezpeleta et al 2005, 2007aDeschamps and Moreira 2009). Recent studies reported contradicting Bayesian and maximum likelihood trees regarding Archaeplastida monophyly (Brown et al 2018;Gawryluk et al 2019;Strassert et al 2019). Importantly, the majority of studies that did not to recover monophyletic PPE did not converge to a robust alternative topology either, leading to the current situation where the monophyly of Archaeplastida is clear from plastids but inconclusive from host data.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomic Insights into the Origin of Primary Plastids

Irisarri

Strassert

Burki

2020

Preprint

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The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and a cyanobacterium, presumably in a common ancestor of all primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, the monophyly of both plastid and host (nuclear) genomes is required to support a single ancestral endosymbiosis, whereas non-monophyletic hosts could be explained under scenarios of independent or serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the strength of the signal for the Archaeplastida host monophyly in four available phylogenomic datasets. The effect of phylogenetic methodology, data quality, alignment trimming strategy, gene and taxon sampling, and the presence of outlier genes loci were investigated. Our analyses revealed a general lack of support for host monophyly in the shorter individual datasets. However, when analyzed together under rigorous data curation and complex mixture evolutionary models, the combined dataset consistently recovered the monophyly of Archaeplastida hosts. This study represents an important step towards better understanding the eukaryotic evolution and the origin of plastids.

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Section: Implications For Eukaryotic Evolutioncontrasting

confidence: 43%

Section: Monophyly Of Archaeplastida and The Tree Of Eukaryotesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenomic Insights into the Origin of Primary Plastids

Irisarri

Strassert

Burki

2020

Preprint

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“…For sequences assigned at the kingdom level without conflicts between reference databases, the ML tree search was constrained by requiring that each kingdom form a monophyletic clade. Monophyly of the eukaryotic supergroups found in the samples was also constrained (Figure ) according to the current consensus of phylogenomic studies (Adl et al, 2019; Strassert et al, 2019). The position of sequences which were not identified to kingdom, or which received conflicting kingdom assignments from the different reference datasets, was not constrained.…”

Section: Methodsmentioning

confidence: 99%

Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding

Sahraei

Furneaux

Kluting

et al. 2022

Ecology and Evolution

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Long amplicon metabarcoding has opened the door for phylogenetic analysis of the largely unknown communities of microeukaryotes in soil. Here, we amplified and sequenced the ITS and LSU regions of the rDNA operon (around 1500 bp) from grassland soils using PacBio SMRT sequencing. We tested how three different methods for generation of operational taxonomic units (OTUs) effected estimated richness and identified taxa, and how well large‐scale ecological patterns associated with shifting environmental conditions were recovered in data from the three methods. The field site at Kungsängen Nature Reserve has drawn frequent visitors since Linnaeus's time, and its species rich vegetation includes the largest population of Fritillaria meleagris in Sweden. To test the effect of different OTU generation methods, we sampled soils across an abrupt moisture transition that divides the meadow community into a Carex acuta dominated plant community with low species richness in the wetter part, which is visually distinct from the mesic‐dry part that has a species rich grass‐dominated plant community including a high frequency of F. meleagris. We used the moisture and plant community transition as a framework to investigate how detected belowground microeukaryotic community composition was influenced by OTU generation methods. Soil communities in both moisture regimes were dominated by protists, a large fraction of which were taxonomically assigned to Ciliophora (Alveolata) while 30%–40% of all reads were assigned to kingdom Fungi. Ecological patterns were consistently recovered irrespective of OTU generation method used. However, different methods strongly affect richness estimates and the taxonomic and phylogenetic resolution of the characterized community with implications for how well members of the microeukaryotic communities can be recognized in the data.

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“…

Phylogenomic analyses have boosted our understanding of the evolutionary trajectories of all living forms by providing continuous improvements to the tree of life [1][2][3][4][5] . Within this tree, fungi represent an ancient eukaryote group 6 , having diverged from the animals ∼1.35 billion years ago 7 .

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confidence: 99%

Phylogenomics unravels the early diversification of fungi

Strassert

Monaghan

2021

Preprint

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Our understanding of the eukaryote tree of life is continually improving, although the branching events at some of the deepest nodes remain elusive. The fungi are an ancient group of eukaryotes with a wide range of morphologies, life-history strategies, and ecological roles. While several recent phylogenomic analyses have been shown to be a powerful tool for uncovering even earliest diversifications, no study has yet examined the entire tree of fungi using a taxonomically comprehensive data set and suitable models of evolution. Here, we assembled a data set of 299 proteins from all recognised fungal groups for which genomic/transcriptomic data were available and subjected this to a battery of analyses, including tree inferences using site-heterogeneous mixture models and the Multi-Species Coalescent model. Tree topology was highly congruent and well supported, and any incongruence was found to result from an inability of some frequently used evolutionary models to model fast-evolving and heterogeneous sites. Our results provide higher resolution among early-branching lineages than previous studies, and shed light on hitherto highly contested evolutionary origins of the major fungal groups.

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New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

Cited by 13 publications

References 52 publications

Phylogenomic Insights into the Origin of Primary Plastids

Phylogenomic Insights into the Origin of Primary Plastids

Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding

Phylogenomics unravels the early diversification of fungi

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