A survey of boreal Entoloma with emphasis on the subgenus Rhodopolia

Kokkonen, Katri

doi:10.1007/s11557-015-1135-y

Cited by 21 publications

(32 citation statements)

References 21 publications

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“…However, DNA analyses of Favre's type specimens are rare and have only been used in a few studies. Altogether, the DNA sequences of eight type specimens (e.g., Cortinarius, Entoloma, Hebeloma , and Inocybe species) have been included recently in mycological surveys and phylogenetic analyses by Cripps et al ( 2010 ), Kokkonen and Vauras ( 2012 ), Kokkonen ( 2015 ), Eberhardt et al ( 2015 ), Liimatainen et al ( 2015 ), and Garnica et al ( 2016 ) (Table 6 ).…”

Section: Resultsmentioning

confidence: 99%

Ecology of Alpine Macrofungi - Combining Historical with Recent Data

et al. 2017

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Historical datasets of living communities are important because they can be used to document creeping shifts in species compositions. Such a historical data set exists for alpine fungi. From 1941 to 1953, the Swiss geologist Jules Favre visited yearly the region of the Swiss National Park and recorded the occurring fruiting bodies of fungi >1 mm (so-called “macrofungi”) in the alpine zone. Favre can be regarded as one of the pioneers of alpine fungal ecology not least because he noted location, elevation, geology, and associated plants during his numerous excursions. However, some relevant information is only available in his unpublished field-book. Overall, Favre listed 204 fungal species in 26 sampling sites, with 46 species being previously unknown. The analysis of his data revealed that the macrofungi recorded belong to two major ecological groups, either they are symbiotrophs and live in ectomycorrhizal associations with alpine plant hosts, or they are saprotrophs and decompose plant litter and soil organic matter. The most frequent fungi were members of Inocybe and Cortinarius, which form ectomycorrhizas with Dryas octopetala or the dwarf alpine Salix species. The scope of the present study was to combine Favre's historical dataset with more recent data, either with the “SwissFungi” database or with data from major studies of the French and German Alps, and with the data from novel high-throughput DNA sequencing techniques of soils from the Swiss Alps. Results of the latter application revealed, that problems associated with these new techniques are manifold and species determination remains often unclear. At this point, the fungal taxa collected by Favre and deposited as exsiccata at the “Conservatoire et Jardin Botaniques de la Ville de Genève” could be used as a reference sequence dataset for alpine fungal studies. In conclusion, it can be postulated that new improved databases are urgently necessary for the near future, particularly, with regard to investigating fungal communities from alpine regions using new techniques.

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Section: Resultsmentioning

confidence: 99%

Ecology of Alpine Macrofungi - Combining Historical with Recent Data

et al. 2017

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“…3. When blasting sequences for Entoloma, for example, one should be aware that, presently (late 2018), some 55 type sequences generated by Kokkonen (2015) are not yet visible in normal BLAST as part of the RefSeq Targeted Loci (RTL) database, but they are already visible when performing BLAST limited to 'sequences from type'. Therefore, there seems to be a considerable time of lapse between deposition of clearly annotated type sequences and their being prefixed as part of the RefSeq Targeted Loci (RTL) database.…”

Section: Poor Sequence Coverage Of Fungal Taxamentioning

confidence: 99%

“…1872, MB advocates the use of E. rhodopolium f. nidorosum (Fr.) Noordeloos 1989 as current name, while IF accepts E. nidorosum as the current name, being considered a distinct species following Kokkonen (2015). The latter paper neotypified E. rhodopolium with a sequenced specimen from Sweden, as both species are genetically sufficiently different to be accepted as separate species.…”

Section: The Rapidly Growing Challenge Of Updating Taxonomic Databasesmentioning

confidence: 99%

The unbearable lightness of sequenced-based identification

Hofstetter

Buyck

Eyssartier³

et al. 2019

Fungal Diversity

108

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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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“…Whether it is identical to E. rhodopolium in Europe and North America remain unclear. In fact, the ITS sequence of E. rhodopolium Tottori Er-1 is distinct from that of true E. rhodopolium that Kokkonen reported as a neotype 13 . Therefore, a molecular phylogenetic study is needed to classify Japanese E. rhodopolium and compare European and North American species.…”

Section: Introductionmentioning

confidence: 75%

“…Noordel. ex Kokkonen 13 , are morphologically diverse and abundant in Japan. However, the phylogenetic study has not yet been reported, although only E. rhodopolium Tottori Er-1 (Accession number in NCBI, AB301602) is registered as E. rhodopolium .…”

Section: Introductionmentioning

confidence: 99%

Molecular phylogenetic analysis of new Entoloma rhodopolium-related species in Japan and its identification method using PCR-RFLP

Kondo

Nakamura

Ishigaki

et al. 2017

Sci Rep

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Poisonous Entoloma rhodopolium and other similar species including edible E. sarcopum are morphologically diverse. People mistake poisonous species for edible species. Classification and the detection method of these species need to be defined. The morphological and phylogenetic studies have been reported in northern Europe. In Japan, the genetic study remains unsolved. Thus, phylogenetic analysis of E. rhodopolium was conducted using ITS and RPB2 sequences, and the result was compared with that of European species. Japanese E. rhodopolium was classified into three clades, none of which belonged to the true European E. rhodopolium and other known species. Three species were defined as new species. Entoloma rhodopolium clade-I (named E. lacus) was genetically close to but morphologically separated from E. majaloides. Clade-II (E. subrhodopolium) was classified to the same group as E. sinuatum and E. subsinuatum, but distinct from these species. Clade-III was segregated from known Entoloma species including E. lupinum, and named E. pseudorhodopolium. Based on the classification, a simple identification method PCR-RFLP was developed to discriminate between poisonous species and edible E. sarcopum, which is very similar in morphology. The study can help to clarify the taxonomy of complex E. rhodopolium-related species, and to prevent food poisoning.

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A survey of boreal Entoloma with emphasis on the subgenus Rhodopolia

Cited by 21 publications

References 21 publications

Ecology of Alpine Macrofungi - Combining Historical with Recent Data

Ecology of Alpine Macrofungi - Combining Historical with Recent Data

The unbearable lightness of sequenced-based identification

Molecular phylogenetic analysis of new Entoloma rhodopolium-related species in Japan and its identification method using PCR-RFLP

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