Cibaomyces and Cyptotrama, two new genera for Europe, and an emendation of Rhizomarasmius (Basidiomycota, Physalacriaceae)

Moreau, Pierre‐Arthur; Vilà, Jordi; Aime, M. Catherine; Antonín, Vladimír; Horak, Egon; Pérez-Butrόn, José Luis; Richard, Franck; Urban, Alexander; Welti, Stéphane; Vizzini, Alfredo

doi:10.1007/s11557-015-1024-4

Cited by 9 publications

(10 citation statements)

References 29 publications

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“…Sequence-based identification tends to propagate errors and even in the present study, several of our apparently straightforward identifications would clearly have resulted in deposits of wrong taxonomic names if these had not been re-examined (e.g. Cibaomyces glutinis, [''Cibaomyces glutinis Zhu L. Yang appeared to be common Rhizomarasmius setosus (= Marasmius setosus in the ARCS)'' section] in Moreau et al (2015), Lactarius helvus [''Lactarius helvus (Fr.) Fr.…”

Section: Reliability Of Publicly Deposited Barcode Sequencesmentioning

confidence: 78%

“…from France, including from a region near the Alps and thus not that far away from the Montricher forest. As these European specimens had been identified by a taxonomic expert in the group (Moreau et al 2015), there was little reason to doubt the correctness of the BLAST top hit on Cibaomyces glutinis.…”

Section: Molecular Delimitation and Identification Of The Otus (Or Tementioning

confidence: 99%

“…When reblasting these Asian type sequences, the only other sequence that comes close (at 95%) is KM588675, all other sequences were at 87% similarity and lower. The latter sequence (KM588675) was published in the same paper by Moreau et al (2015) but is associated in GenBank with data for a Canadian voucher specimen for Rhizomarasmius pyrrocephalus. From the discussion in the Moreau et al (2015) paper, it is clear that the latter sequence actually represents the French collection of Cibaomyces glutinis (as they interpret the 95% similarity with the Asian type sequence to intraspecific variation among European and Asian specimens).…”

Section: Molecular Delimitation and Identification Of The Otus (Or Tementioning

confidence: 99%

“…The latter sequence (KM588675) was published in the same paper by Moreau et al (2015) but is associated in GenBank with data for a Canadian voucher specimen for Rhizomarasmius pyrrocephalus. From the discussion in the Moreau et al (2015) paper, it is clear that the latter sequence actually represents the French collection of Cibaomyces glutinis (as they interpret the 95% similarity with the Asian type sequence to intraspecific variation among European and Asian specimens). Being unable to solve the problem, we then contacted the authors of the Moreau et al (2015) paper who kindly sent us their original sequence dataset.…”

Section: Molecular Delimitation and Identification Of The Otus (Or Tementioning

confidence: 99%

“…From the discussion in the Moreau et al (2015) paper, it is clear that the latter sequence actually represents the French collection of Cibaomyces glutinis (as they interpret the 95% similarity with the Asian type sequence to intraspecific variation among European and Asian specimens). Being unable to solve the problem, we then contacted the authors of the Moreau et al (2015) paper who kindly sent us their original sequence dataset. Comparison between the sequences deposited in GenBank and the original sequence dataset clearly showed that some kind of shift between taxon names and corresponding sequences must have occurred at the moment of deposit.…”

Section: Molecular Delimitation and Identification Of The Otus (Or Tementioning

confidence: 99%

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The unbearable lightness of sequenced-based identification

Hofstetter

Buyck

Eyssartier³

et al. 2019

Fungal Diversity

110

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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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Section: Reliability Of Publicly Deposited Barcode Sequencesmentioning

confidence: 78%

Section: Molecular Delimitation and Identification Of The Otus (Or Tementioning

confidence: 99%

Section: Molecular Delimitation and Identification Of The Otus (Or Tementioning

confidence: 99%

Section: Molecular Delimitation and Identification Of The Otus (Or Tementioning

confidence: 99%

Section: Molecular Delimitation and Identification Of The Otus (Or Tementioning

confidence: 99%

See 3 more Smart Citations

The unbearable lightness of sequenced-based identification

Hofstetter

Buyck

Eyssartier³

et al. 2019

Fungal Diversity

110

View full text Add to dashboard Cite

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Plunging hands into the mushroom jar: a phylogenetic framework for Lyophyllaceae (Agaricales, Basidiomycota)

Bellanger

Moreau

Corriol³

et al. 2015

Genetica

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During the last two decades, the unprecedented development of molecular phylogenetic tools has propelled an opportunity to revisit the fungal kingdom under an evolutionary perspective. Mycology has been profoundly changed but a sustained effort to elucidate large sections of the astonishing fungal diversity is still needed. Here we fill this gap in the case of Lyophyllaceae, a species-rich and ecologically diversified family of mushrooms. Assembly and genealogical concordance multigene phylogenetic analysis of a large dataset that includes original, vouchered material from expert field mycologists reveal the phylogenetic topology of the family, from higher (generic) to lower (species) levels. A comparative analysis of the most widely used phylogenetic markers in Fungi indicates that the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and portions of the genes for RNA polymerase II second largest subunit (RPB2) is the most performing combination to resolve the broadest range of taxa within Lyophyllaceae. Eleven distinct evolutionary lineages are identified, that display partial overlap with traditional genera as well as with the phylogenetic framework previously proposed for the family. Eighty phylogenetic species are delineated, which shed light on a large number of morphological concepts, including rare and poorly documented ones. Probing these novel phylogenetic species to the barcoding method of species limit delineation, indicates that the latter method fully resolves Lyophyllaceae species, except in one clade. This case study provides the first comprehensive phylogenetic overview of Lyophyllaceae, a necessary step towards a taxonomical, ecological and nomenclatural revision of this family of mushrooms. It also proposes a set of methodological guidelines that may be of relevance for future taxonomic works in other groups of Fungi.

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