A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification

Harder, Christoffer Bugge; Læssøe, Thomas; Frøslev, Tobias Guldberg; Ekelund, Flemming; Rosendahl, Søren; Kjøller, Rasmus

doi:10.1016/j.funbio.2013.09.004

Cited by 41 publications

(65 citation statements)

References 73 publications

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“…However, in this study some of the morphotypes had identical sequences, although morphological differences were strong enough to keep them as separate species. Insufficiency of ITS sequences to separate fungal species has also been reported for other fungal species complexes 18, 19 . In contrast, intra-generic diversity of the ITS region of Diaporthe ( Phomopsis ) was high leading to the recognition of seven different species.…”

Section: Discussionmentioning

confidence: 69%

Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects

Singh

Sharma

Kumar

et al. 2017

Sci Rep

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Fungal endophytes were isolated from leaf, bark and stem of Tectona grandis Linn.f. sampled at four geographical locations in winter, summer and monsoon seasons. The recovered 5089 isolates were assigned to 45 distinct morphotypes based on morphology. The sequences of the internal transcribed spacers (ITS) of the nrDNA of some morphotypes were identical, but morphological differences were strong enough to consider these morphotypes as separate species. Forty-three morphotypes were assigned to ascomycotina and two to basidiomycotina. Ascomycotina was the predominating group with 99.7% of total isolates followed by basidiomycotina with only 0.3% of total isolates. Diaporthe (Phomopsis) species dominated the communities independently on tissue type, location or season. More than 60% of the examined tissue pieces were colonized by members of this species complex. While these endophytes are ubiquitous others were tissue or location specific. Tissue type had the strongest effect on the species evenness of the endophytic assemblage followed by geographical location and season. However, Shannon-Wiener index (H’) significantly (p ≤ 0.001) varied with all three factors i.e. season, location and tissue type. Leaves supported the highest diversity across all the seasons and locations. In conclusion, all the three factors together determined the structure of endophytic mycobiota assemblage of T. grandis.

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Section: Discussionmentioning

confidence: 69%

Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects

Singh

Sharma

Kumar

et al. 2017

Sci Rep

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“…) and there are cases where the ITS region shows larger within‐species variation, compared to between‐species distance, than single‐copy genes (Harder et al . ). Further studies are needed to determine how well suited the coalescence model is to model the evolution of the ITS region.…”

Section: The Probability Of Splitting Speciesmentioning

confidence: 97%

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi

Ryberg

2015

Molecular Ecology

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During the last couple of decades, an increasing number of studies use sequence clusters as units for taxonomic diversity. It is well known that such molecular operational taxonomic units (MOTUs) do not necessarily correspond to species, but they are treated as such when measuring diversity and testing theories. Here, I show that data from studies of molecular evolution and species diversification of fungi indicate that commonly used cutoffs are likely to lump species in many cases. At the same time, empirical studies show that the mean withinspecies variation is close to these cut-offs. That the within-species variation estimates are plausible is supported by coalescence modelling under a range of parameter settings. In addition, studies using crossing tests to delimit species show that there often is an overlap in within-and between-species distances. The available data therefore indicate that sequence clusters are likely to misrepresent species. However, to keep a biological relevance, MOTUs should be kept in close agreement with species. Studies using them should therefore asses how sensitive the results are to differences between MOTUs and species -something that is rarely done. An even better solution is to directly include the uncertainty in species delimitation in the analyses, but in many cases, we need to increase our knowledge of taxonomy and evolution to do this accurately. Even if the empirical data referred to here pertain to the "barcoding" region of rDNA in fungi, there is nothing indicating that the situation is substantially better for other taxa or genes.

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“…We thus aligned our ITS sequences with representative sequences from GenBank for sect. Purae benefitting from recently published phylogenetic studies (Harder et al 2010(Harder et al , 2013 and the authoritative but apparently problematic Mycena sequences from the Venice barcode project (Osmundson et al 2013). Our phylogenetic analyses (Fig.…”

Section: Mycenamentioning

confidence: 99%

The unbearable lightness of sequenced-based identification

Hofstetter

Buyck

Eyssartier³

et al. 2019

Fungal Diversity

109

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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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A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification

Cited by 41 publications

References 73 publications

Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects

Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi

The unbearable lightness of sequenced-based identification

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