Surveying the biodiversity of the Cryptomycota using a targeted PCR approach

Lazarus, Katherine L.; James, Timothy Y.

doi:10.1016/j.funeco.2014.11.004

Cited by 68 publications

(71 citation statements)

References 39 publications

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“…After a burnin of the first 10% of states, posterior estimates were summarized onto a maximum-clade-credibility (MCC) tree using TreeAnnotator from the BEAST 2 suite. Posterior stem ages for all groups Lazarus and James (2015), Torruella et al (2015), Spatafora et al (2016) and . The numbers of classes are adapted from the proposed taxonomy (Online Resource 2).…”

Section: Revised Classification Of Fungi Within Eukaryotesmentioning

confidence: 99%

“…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. Therefore, we suggest renaming of Aphelida to Aphelidiomycota to meet the standards of nomenclature.…”

Section: Updated Classification Of Holomycota Including Fungimentioning

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: Revised Classification Of Fungi Within Eukaryotesmentioning

confidence: 99%

Section: Updated Classification Of Holomycota Including Fungimentioning

confidence: 99%

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

et al. 2018

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“…Just over 10% of the studies investigated fungi (e.g. Rao et al 2012;Lazarus & James 2015). Research on micro-eukaryotes was relatively common, with multiple studies being conducted on the foraminifera, as well as diatoms and a number of other protist taxa (e.g.…”

Section: Organisms Studiedmentioning

confidence: 99%

“…Terrestrial samples -mainly soil -were studied almost as often as marine samples, with the most common focus of these studies being the analysis of fungi (e.g. Teasdale et al 2013;Lazarus & James 2015;Song et al 2015) followed by prokaryotes (e.g. Lin et al 2010;Kanokratana et al 2011).…”

Section: Study Environmentsmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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“…A preliminary molecular analysis placed them within the Fungi, close to 'zygomycota' (Wylezich et al 2004, White et al 2006. Since then, the Microsporidia have been placed near the root of the fungal kingdom (Capella-Gutiérrez et al 2012, Xiang et al 2014 as have the Cryptomycota (Lazarus and James 2015). The genus Nephridiophaga was introduced by Ivanić (1937) for N. apis, which infects honey bees.…”

Section: Introductionmentioning

confidence: 99%

Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota

Radek¹,

Wurzbacher²,

Gisder³

et al. 2017

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Nephridiophagids are poorly known unicellular eukaryotes, previously of uncertain systematic position, that parasitize the Malpighian tubules of insects. Their life cycle includes merogony with multinucleate plasmodia and sporogony leading to small, uninucleate spores. We examined the phylogenetic affiliations of three species of Nephridiophaga, including one new species, Nephridiophaga maderae, from the Madeira cockroach (Leucophaea maderae). In addition to the specific host, the new species differs from those already known by the size of the spores and by the number of spores within the sporogenic plasmodium. The inferred phylogenetic analyses strongly support a placement of the nephridiophagids in the fungal kingdom near its root and with a close, but unresolved, relationship to the chytids (Chytridiomycota). We found evidence for the nephridiophagidean speciation as being strongly coupled to host speciation. Copyright RESEARCH ARTICLERenate Radek et al. / MycoKeys 25: 31-50 (2017) 32

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Surveying the biodiversity of the Cryptomycota using a targeted PCR approach

Cited by 68 publications

References 39 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

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Morphologic and molecular data help adopting the insect-pathogenic nephridiophagids (Nephridiophagidae) among the early diverging fungal lineages, close to the Chytridiomycota

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