A new 18S rRNA phylogeny of uncultured predacious fungi (Zoopagales)

Davis, William J.; Amses, Kevin R.; James, E S; James, Timothy Y.

doi:10.1080/00275514.2018.1546066

Cited by 11 publications

(6 citation statements)

References 36 publications

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“…More recent studies relying on 18S sequences showed that with increased taxon sampling, Zoopagales is recovered as a monophyletic lineage, though internal nodes often have < 80% bootstrap support (Corsaro et al, 2018;Davis et al, in press). In agreement with previous studies (i.e., Corsaro et al, 2018;Davis et al, in press) we resolve a monophyletic Zoopagales but do so with strong bootstrap support for all internal nodes. We recover a Zoophagus insidians + Stylopage hadra clade and a Syncephalis + Thamnocephalis clade.…”

Section: Discussionsupporting

confidence: 92%

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

Davis

Amses

Benny

et al. 2019

Molecular Phylogenetics and Evolution

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Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.

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Section: Discussionsupporting

confidence: 92%

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

Davis

Amses

Benny

et al. 2019

Molecular Phylogenetics and Evolution

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“…Within the microbial world, a large fraction remains uncultured. This is more commonly encountered within the bacterial and archaeal domains, although a similar pattern has been suggested with Fungi [40][41][42][43]. Within the anaerobic fungal phylum Neocallimastigomycota, multiple putative novel genera were identified in culture-independent studies [20,21,35].…”

Section: Discussionsupporting

confidence: 55%

Aestipascuomyces dupliciliberatus gen. nov, sp. nov., the First Cultured Representative of the Uncultured SK4 Clade from Aoudad Sheep and Alpaca

Stabel¹,

Hanafy²,

Schweitzer³

et al. 2020

Preprint

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We report on the isolation of the previously uncultured Neocallimastigomycota SK4 lineage by two independent research groups from a wild aoudad sheep rumen sample (Texas, USA) and an alpaca fecal sample (Baden-Württemberg, Germany). Isolates from both locations showed near identical morphological and microscopic features, forming medium-sized white filamentous colonies with a white center of sporangia on agar roll tubes and a heavy biofilm in liquid media. Microscopic analysis revealed monocentric thalli, and spherical polyflagellated zoospores with 7–20 flagella. Zoospore release occurred through an apical pore as well as by sporangial wall rupturing, a duality that is unique amongst described AGF strains. Isolates were capable of growing on a wide range of mono-, oligo-, and polysaccharides substrates. Phylogenetic assessment based on the D1-D2 large rRNA subunit (D1-D2 LSU) and internal transcribed spacer-1 (ITS-1) regions demonstrated high sequence identity (minimum identity of 99.07% and 96.96%, respectively) between all isolates; but low sequence identity (92.4% and 86.7%, respectively) to their closest cultured relatives. D1-D2 LSU phylogenetic trees grouped the isolates as a new monophyletic clade within the Orpinomyces-Neocallimastix-Pecoramyces-Feramyces-Ghazallamyces supragenus group. D1-D2 LSU and ITS-1 sequences from the obtained isolates were either identical, or displayed extremely high sequence similarity to sequences recovered from the same Aoudad sheep sample on which isolation was conducted, as well as several sequences recovered from domestic sheep and few other herbivores. Interestingly, members of the SK4 clade seem to be encountered in animals grazing on summer pasture. We hence propose accommodating these novel isolates in a new genus, Aestipascuomyces (derived from the Latin word for “summer pasture”), and a new species, A. dupliciliberatus. The type strain is Aestipascuomyces dupliciliberatus strain R4.

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“…Both sexual and asexual spores have been described. The evolutionary relationships among the different families are not well resolved, mostly due to the difficulty of working with such small and usually unculturable fungi (Davis et al ., ). Additionally, molecular analyses suggest that members of this clade show high evolutionary rates (Ahrendt et al ., ; Davis et al ., ), and some of the most commonly used primers for barcode sequences of fungi or eukaryotes work poorly for this group (Tedersoo & Lindahl, ).…”

Section: Zygomycetous Fungimentioning

confidence: 97%

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

2019

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The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely unicellular monopolar organisms to highly complex syncitial filaments that may form macroscopic structures. Fungi emerged as a 'Third Kingdom', embracing organisms that were outside the classical dichotomy of animals versus vegetals. The taxonomy of this group has a turbulent history that is only now starting to be settled with the advent of genomics and phylogenomics. We here review the current status of the phylogeny and taxonomy of fungi, providing an overview of the main defined groups. Based on current knowledge, nine phylum-level clades can be defined: Opisthosporidia, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Zoopagomycota, Mucoromycota, Glomeromycota, Basidiomycota and Ascomycota. For each group, we discuss their main traits and their diversity, focusing on the evolutionary relationships among the main fungal clades. We also explore the diversity and phylogeny of several groups of uncertain affinities and the main phylogenetic and taxonomical controversies and hypotheses in the field.

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A new 18S rRNA phylogeny of uncultured predacious fungi (Zoopagales)

Cited by 11 publications

References 36 publications

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

Aestipascuomyces dupliciliberatus gen. nov, sp. nov., the First Cultured Representative of the Uncultured SK4 Clade from Aoudad Sheep and Alpaca

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

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