First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group

Pánek, Tomáš; Zadrobílková, Eliška; Walker, Gordon; Brown, Matthew W.; Gentekaki, Eleni; Hroudová, Miluše; Kang, Seungho; Roger, Andrew J.; Tice, Alexander K.; Vlček, Čestmı́r; Čepička, Ivan

doi:10.1016/j.ympev.2016.01.011

Cited by 23 publications

(27 citation statements)

References 50 publications

(94 reference statements)

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“…Lineages with organisms that use cellulose structurally are marked with a green dot. The relationships between phyla are based on Adl et al (2012, 2019) and Pánek et al () for Eukaryota and Hug et al () for Bacteria.…”

Section: Resultsmentioning

confidence: 99%

Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution

et al. 2020

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Summary Plants must rearrange the network of complex carbohydrates in their cell walls during normal growth and development. To accomplish this, all plants depend on proteins called expansins that nonenzymatically loosen noncovalent bonding between cellulose microfibrils. Surprisingly, expansin genes have more recently been found in some bacteria and microbial eukaryotes, where their biological functions are largely unknown. Here, we reconstruct a comprehensive phylogeny of microbial expansin genes. We find these genes in all eukaryotic microorganisms that have structural cell wall cellulose, suggesting expansins evolved in ancient marine microorganisms long before the evolution of land plants. We also find expansins in an unexpectedly high diversity of bacteria and fungi that do not have cellulosic cell walls. These bacteria and fungi inhabit varied ecological contexts, mirroring the diversity of terrestrial and aquatic niches where plant and/or algal cellulosic cell walls are present. The microbial expansin phylogeny shows evidence of multiple horizontal gene transfer events within and between bacterial and eukaryotic microbial lineages, which may in part underlie their unusually broad phylogenetic distribution. Overall, expansins are unexpectedly widespread in bacteria and eukaryotes, and the contribution of these genes to microbial ecological interactions with plants and algae has probbaly been underappreciated.

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Section: Resultsmentioning

confidence: 99%

Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution

et al. 2020

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“…In additon to the Bayesian analyses, we employed C-series models [34] that account for heterogeneous site-specific features of sequence evolution in the phylogenomic dataset under a maximum-likelihood (ML) framework in IQ-TREE v1.3.3 [38]. The best-fitting model available under ML analyses that we were capable of running with computational constraints was LG + Γ4 + C20 + F with class weights optimized from the dataset using the exchangeabilities from the LG Q-Matrix (LG + Γ4 + FMIX (empirical, C20pi1-C20pi10)) [39, 40]. Topological support was estimated from 1,000 ultrafast ML bootstrap (ML BS) replicates in IQ-TREE.…”

Section: Methodsmentioning

confidence: 99%

Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

Tice¹,

Shadwick²,

Fiore-Donno³

et al. 2016

Biol Direct

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BackgroundAcanthamoebidae is a “family” level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses.ResultsHere we show using a phylogenomic approach that the Acanthamoebidae is a fully supported monophyletic group within Amoebozoa with both ML and Bayesian analyses. We also expand the known range of morphological and life cycle diversity found in the Acanthamoebidae by demonstrating that the amoebozoans “Protostelium” arachisporum, Dracoamoeba jormungandri n. g. n. sp., and Vacuolamoeba acanthoformis n.g. n.sp., belong within the group. We also found that “Protostelium” pyriformis is clearly a species of Acanthamoeba making it the first reported sporocarpic member of the genus, that is, an amoeba that individually forms a walled, dormant propagule elevated by a non-cellular stalk. Our phylogenetic analyses recover a fully supported Acanthamoebidae composed of five genera. Two of these genera (Acanthamoeba and Luapeleameoba) have members that are sporocarpic.ConclusionsOur results provide high statistical support for an Acanthamoebidae that is composed of five distinct genera. This study increases the known morphological diversity of this group and shows that species of Acanthamoeba can include spore-bearing stages. This further illustrates the widespread nature of spore-bearing stages across the tree of Amoebozoa.ReviewersThis article was reviewed by Drs. Eugene Koonin, Purificacion Lopez-Garcia and Sandra Baldauf. Sandra Baldauf was nominated by Purificacion Lopez-Garcia, an Editorial Board member.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-016-0171-0) contains supplementary material, which is available to authorized users.

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“…Andalucia . ••••Stygiellidae Pánek et al. Anaerobic, mitochondria acristate. Stygiella, Velundella . •••Histionina Cavalier‐Smith 2013Free‐swimming or sessile cells, some genera with lorica; aerobes with flat mitochondrial cristae.…”

Section: Systematicsmentioning

confidence: 99%

“…Andalucia . ••••Stygiellidae Pánek et al. Anaerobic, mitochondria acristate. Stygiella, Velundella . …”

Section: Systematicsmentioning

confidence: 99%

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Adl

Bass

Lane

et al. 2019

J Eukaryotic Microbiology

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990

799

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This revision of the classification of eukaryotes follows that of Adl et al., 2012 [ J. Euk. Microbiol . 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

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First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group

Cited by 23 publications

References 50 publications

Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution

Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution

Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

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