Combined molecular and morphological data for improving phylogenetic hypothesis in Dacrymycetes

Shirouzu, Takashi; Hirose, Dai; Oberwinkler, Franz; Shimomura, Norihiro; Maekawa, Nitaro; Tokumasu, Seiji

doi:10.3852/12-147

Cited by 32 publications

(56 citation statements)

References 35 publications

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“…In contrast, small or large subunit rRNA are more conserved across the fungal kingdom than the ITS region. Therefore, the simultaneous use of ITS and small/large subunit regions is becoming integral in taxonomic and phylogenetic fingerprinting analysis (Weber et al 2009;Monchy et al 2011;Liu et al 2012;Singh et al 2012;Reblova et al 2013;Shirouzu et al 2013;Wang et al 2013;Dal Grande et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE

Liu

Cai

et al. 2015

World J Microbiol Biotechnol

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Both the internal transcribed spacer (ITS) region and 18S rRNA genes are broadly applied in molecular fingerprinting studies of fungi. However, the differences in those two ribosomal RNA regions are still largely unknown. In the current study, three sets of most suitable subunit ribosomes in ITS and 18S rRNA were compared using denaturing gradient gel electrophoresis (DGGE) under the optimum experimental conditions. Ten samples from both aquatic and soil environments were tested. The results revealed that the ITS region produced range-weighted richness in the range 36-361, which was significantly higher than that produced by 18S rDNA. There was a similar tendency in terms of the Shannon-Weaver diversity index and community dynamics in both water and soil samples. Samples from water and soil were better separated using ITS than 18S rDNA in principal component analysis of DGGE bands. Our study suggests that the ITS region is more precise and has more potential than 18S rRNA genes in fungal community analysis.

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Section: Discussionmentioning

confidence: 99%

Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE

Liu

Cai

et al. 2015

World J Microbiol Biotechnol

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“…The Dacrymycetes include a small group of wood‐decaying fungi that produce gelatinous and usually highly pigmented fruting bodies. They are characterized by a unique basidial morphology (Hibbett, ; Shirouzu et al ., , ). Shirouzu et al .…”

Section: Dikaryamentioning

confidence: 99%

“…Shirouzu et al . () described a second order, Unilacrymales, although its monophyly is questioned (Zhao et al ., ).…”

Section: Dikaryamentioning

confidence: 99%

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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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“…Although OTUs belonging to clades H, I, K, P, and Q were detected using the eDNA or culture method, their fruiting bodies were not identified at any time during this investigation. Clades I and Q, Unilacryma spp., and Dacryonaema spp., which branched deep in the phylogenetic tree, are considered to be important lineages for studying the early evolution of Dacrymycetes 29,33 . Lineages that diverged early in the phylogeny of Dacrymycetes tend to feature small or thin fruiting bodies 4,33 .…”

Section: Discussionmentioning

confidence: 99%

Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms

Shirouzu

Matsuoka

Doi

et al. 2020

Sci Rep

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Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DnA (eDnA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDnA sequences. eDnA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. further, eDnA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.Microorganism diversity has been challenging to comprehensively investigate owing to their microscopic-size and high species diversity. This statement generally applies to many terrestrial microorganisms. However, mushroom-forming fungi are an exception as they grow visible fruiting bodies, allowing for their diversity and phylogeny to be relatively well studied 1 . Mushroom diversity has been investigated using morphological and phylogenetic analyses based on collected fruiting bodies. However, in most mushroom species, fruiting bodies appear in a temporally sporadic manner, with the small and ephemeral fruiting bodies frequently being overlooked. Therefore, despite the importance of mushroom-forming fungi as decomposers or symbionts in terrestrial ecosystems, a large proportion of the mushroom species diversity remains poorly described 2 . Furthermore, the early-diverged lineages of mushroom-forming fungi tend to feature inconspicuously small or thin fruiting bodies 1,3,4 . Thus, even though the fruiting bodies may not always be detectable within a sampling site, various mushroom strains may nevertheless inhabit the same location as inconspicuous mycelia 4,5 . These lineages account

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Combined molecular and morphological data for improving phylogenetic hypothesis in Dacrymycetes

Cited by 32 publications

References 35 publications

Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE

Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

Complementary molecular methods reveal comprehensive phylogenetic diversity integrating inconspicuous lineages of early-diverged wood-decaying mushrooms

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