Proposal for practical multi-kingdom classification of eukaryotes based on monophyly and comparable divergence time criteria

Tedersoo, Leho

doi:10.1101/240929

Cited by 4 publications

(4 citation statements)

References 91 publications

(117 reference statements)

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“…Since nothing is known about the morphology of these clades, we consider these tentatively as subkingdom-level groups within Fungi, because of their supported monophyly with Fungi and divergence time of \ 1000 Ma. Many taxonomists place the unicellular Rozellomycota, Microsporidia and Aphelida within Fungi (James et al 2006a;Jones et al 2011a, Adl et al 2012James and Berbee 2012 and further studies on fungal classification), but other authors indicate the monophyly of Aphelida and Rozellomycota in a sister position to all other Fungi (Karpov et al 2013;2014b, 2017bLetcher et al 2013Letcher et al , 2017 and treat this socalled ARM clade as phylum Ophistosporidia (Karpov et al 2014b) or a part of the intentionally paraphyletic phylum Choanozoa, which includes protists at the base of Metazoa (Cavalier-Smith 2013; Ruggiero et al 2015). However, taxonomically more inclusive phylogenies place these groups separately-Rozellomycota and Microsporidia at the basal position of Fungi but Aphelida nested within 'chytrids' and/or zoopagaceous zygomycetes (Lazarus and James 2015;Tedersoo et al , 2018.…”

Section: Updated Classification Of Holomycota Including Fungimentioning

confidence: 99%

“…Tedersoo et al 2014;Maestre et al 2015). For better comparability across fungi and preferably across all organisms, taxonomic ranks should be monophyletic and exhibit at least roughly similar age (Hennig 1966;Avise and John 1999;Yilmaz et al 2014;Samarakoon et al 2016;Hyde et al 2017;Tedersoo 2017a). For example, orders and classes in chytrids and zygomycetes should ideally correspond to these ranks in Dikarya.…”

Section: Introductionmentioning

confidence: 99%

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High-level classification of the Fungi and a tool for evolutionary ecological analyses

et al. 2018

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High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

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Section: Updated Classification Of Holomycota Including Fungimentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

High-level classification of the Fungi and a tool for evolutionary ecological analyses

et al. 2018

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“…For metazoans and fungi, we use the versions modified in BOLD v4 ( 30 ) and Outline of Fungi ( 31 ), respectively. For protists, we use the taxonomy updates of PR2, except at kingdom level where we use a modification of Tedersoo ( 32 ) and Burki et al . ( 33 ).…”

Section: Methodsmentioning

confidence: 99%

EUKARYOME: the rRNA gene reference database for identification of all eukaryotes

Tedersoo,

Hosseyni Moghaddam,

Mikryukov

et al. 2024

Database

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Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers—ITS1, ITS2, 18S V4–V5 and 28S D1–D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding—a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.

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“…Differences in relative abundance of taxa were tested using one‐way ANOVAs followed by post‐hoc tests for unequal n. Differences in OTU richness and proportion of artefacts were tested using two‐way ANOVAs (sample and primer as independent factors without interaction term) supplemented by post‐hoc tests for unequal n. All analyses were performed using Statistica 13.0 (StatSoft, Tulsa, OK). We follow the age‐calibrated taxonomy implemented in UNITE (Tedersoo ; Tedersoo et al . ).…”

Section: Methodsmentioning

confidence: 99%

Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences

Tedersoo

Anslan

2019

Environ Microbiol Rep

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Summary Development of high‐throughput sequencing techniques has greatly benefited our understanding about microbial ecology, yet the methods producing short reads suffer from species‐level resolution and uncertainty of identification. Here, we optimize Pacific Biosciences‐based metabarcoding protocols covering the internal transcribed spacer (ITS region) and partial small subunit of the rRNA gene for species‐level identification of all eukaryotes, with a specific focus on Fungi (including Glomeromycota) and Stramenopila (particularly Oomycota). Based on tests on composite soil samples and mock communities, we propose best suitable degenerate primers, ITS9munngs + ITS4ngsUni for eukaryotes and selected groups therein and discuss the pros and cons of long read‐based identification of eukaryotes.

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Proposal for practical multi-kingdom classification of eukaryotes based on monophyly and comparable divergence time criteria

Cited by 4 publications

References 91 publications

High-level classification of the Fungi and a tool for evolutionary ecological analyses

High-level classification of the Fungi and a tool for evolutionary ecological analyses

EUKARYOME: the rRNA gene reference database for identification of all eukaryotes

Towards PacBio‐based pan‐eukaryote metabarcoding using full‐length ITS sequences

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