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      Corrections to recent changes in the taxonomy of the Sordariales

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      Mycological Progress
      Springer Science and Business Media LLC

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          Abstract

          The classification of taxa belonging to the Sordariales has been problematic over the years. With the beginning of the DNA era, ascospore morphology, which was the main criterium for the delimitation of taxa in the Sordariales, was demonstrated to not be useful for inferring taxonomic relationships especially at the genus level. In the past decades, the combination of both morphological and molecular data allowed the reclassification of these taxa. Recently, a study of some often overlooked Diaporthomycetidae and Sordariomycetidae included a new taxonomic classification for members of the Sordariales, many of which were based on nomenclatural errors or which lacked sufficient data to support their hypotheses. The authors did not contribute any new DNA sequences, but instead relied on datasets generated by previous authors in their published phylogenetic studies. Surprisingly, different results were obtained contradicting these previous studies and, in an act of taxonomic vandalism, five new families were introduced without performing further molecular analyses to verify the incongruencies with these previous studies. Three of these new families, which we consider doubtful, are Bombardiaceae, Lasiosphaeridaceae and Zygospermellaceae. The family Strattoniaceae is here considered superfluous since it was introduced to accommodate only a single genus and delimited based on a species that is not the type species of Strattonia. The Neoschizotheciaceae was erected based on the new genus Neoschizothecium, which was introduced to accommodate members of Schizothecium since Huang et al. (2021) considered Schizothecium as a synonym of Podospora after misinterpreting their type species as the same. However, Schizothecium and Podospora have been two independent genera based on two different type species for half a century, making Neoschizothecium and Neoschizotheciaceae superfluous. Moreover, they proposed 32 new combinations, 16 of which are now superfluous or doubtful. Most of these taxonomic errors could have been avoided if a proper literature review had been performed. Two examples are the new superfluous combinations of Triangularia tarvisina and Cladorrhinum olerum, because the former is considered conspecific with Triangularia setosa, and the latter conspecific with Cladorrhinum foecundissimum, the anamorph of Arnium olerum. The focus of the current review is to provide a scientifically responsible alternative to the erroneous novelties proposed at the family, genus and species level in the recent classification of Sordariales.

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          Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation

          Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100 000 fungal strains originally assigned to ca. 17 000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24 000 DNA barcode sequences of 12 000 ex-type and manually validated filamentous fungal strains of 7 300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, ∼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.
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            Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

            True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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              Bambusicolous fungi

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                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                Mycological Progress
                Mycol Progress
                Springer Science and Business Media LLC
                1617-416X
                1861-8952
                August 2022
                July 23 2022
                August 2022
                : 21
                : 8
                Article
                10.1007/s11557-022-01814-z
                1371f34a-daa4-4c4f-a4b1-b7d1fa93cb09
                © 2022

                https://creativecommons.org/licenses/by/4.0

                https://creativecommons.org/licenses/by/4.0

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