Epitypification of the Central African Cantharellus densifolius and C. luteopunctatus allows for the recognition of two additional species

Buyck, Bart; Henkel, Terry W.; Hofstetter, Valérie

doi:10.3897/mycokeys.49.32034

Cited by 7 publications

(2 citation statements)

References 29 publications

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“…Although the study of fungal diversity has been biased toward Northern Hemisphere temperate ecosystems, there have been major efforts to reconcile the gap in knowledge regarding tropical and Southern Hemisphere fungi, with major foci of activity in the eastern paleotropics (Luo et al, 2016; Vadthanarat et al, 2018, 2019; Sukarno et al, 2019), Central and South America (Kuhar et al, 2017; Accioly et al, 2018; Kaishian and Weir, 2018; Ovrebo et al, 2019), Africa (Castellano et al, 2016; Buyck et al, 2018, 2019; Jami et al, 2018), and Australia (Midgley et al, 2018; Davoodian et al, 2019; Ji et al, 2019; Khmelnitsky et al, 2019).…”

Section: Figurementioning

confidence: 99%

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Continental‐scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria

et al. 2020

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Due to their fundamentally microscopic nature and their usually ephemeral reproductive structures (e.g., mushrooms, apothecia, etc.), the identification of fungi has historically been exceptionally difficult, relying on often artificial groupings based on limited morphological features. The advent and maturation of molecular approaches has revolutionized mycology; in the past two decades, a significant number of new orders, classes, and even phyla have been described (

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Section: Figurementioning

confidence: 99%

“…, Africa (Castellano et al, 2016;Buyck et al, 2018Buyck et al, , 2019Jami et al, 2018), and Australia (Midgley et al, 2018;Davoodian et al, 2019;Ji et al, 2019;Khmelnitsky et al, 2019).…”

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Continental‐scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria

et al. 2020

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The unbearable lightness of sequenced-based identification

Hofstetter

Buyck

Eyssartier³

et al. 2019

Fungal Diversity

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Using the basic GenBank local alignment search tool program (BLAST) to identify fungi collected in a recently protected beech forest at Montricher (Switzerland), the number of ITS sequences associated to the wrong taxon name appears to be around 30%, even higher than previously estimated. Such results rely on the in-depth re-examination of BLAST results for the most interesting species that were collected, viz. first records for Switzerland, rare or patrimonial species and problematic species (when BLAST top scores were equally high for different species), all belonging to Agaricomycotina. This paper dissects for the first time a number of sequence-based identifications, thereby showing in every detail-particularly to the user community of taxonomic information-why sequence-based identification in the context of a fungal inventory can easily go wrong. Our first conclusion is that in-depth examination of BLAST results is too time consuming to be considered as a routine approach for future inventories: we spent two months on verification of approx. 20 identifications. Apart from the fact that poor taxon coverage in public depositories remains the principal impediment for successful species identification, it can be deplored that even very recent fungal sequence deposits in GenBank involve an uncomfortably high number of misidentifications or errors with associated metadata. While checking the original publications associated with top score sequences for the few examples that were here reexamined , a positive consequence is that we uncovered over 80 type sequences that were not annotated as types in GenBank. Advantages and pitfalls of sequence-based identification are discussed, particularly in the light of undertaking fungal inventories. Recommendations are made to avoid or reduce some of the major problems with sequence-based identification. Nevertheless, the prospects for a more reliable sequence-based identification of fungi remain quite dim, unless authors are ready to check and update the metadata associated with previously deposited sequences in their publications.

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Notes, outline and divergence times of Basidiomycota

et al. 2019

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The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

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Epitypification of the Central African Cantharellus densifolius and C. luteopunctatus allows for the recognition of two additional species

Cited by 7 publications

References 29 publications

Continental‐scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria

Continental‐scale metagenomics, BLAST searches, and herbarium specimens: The Australian Microbiome Initiative and the National Herbarium of Victoria

The unbearable lightness of sequenced-based identification

Notes, outline and divergence times of Basidiomycota

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