Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

Rosenblad, Magnus Alm; Martı́n, Marı́a P.; Tedersoo, Leho; Ryberg, Martin; Larsson, Ellen; Wurzbacher, Christian; Abarenkov, Kessy; Nilsson, R. Henrik

doi:10.3897/mycokeys.13.8579

Cited by 9 publications

(4 citation statements)

References 36 publications

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“…There is no shortage of potential complications that, if overlooked, could lead to needless and haphazard introduction of new species and genera in DFT and beyond. For instance, it is well known that some extant genera offer examples of very divergent ITS (or other ribosomal) regions (e.g., Basidiodendron , Oliveonia , and Cantharellus ; Feibelman et al 1994 ; Alm Rosenblad et al 2016 , 2022 ). When considered in isolation and out of context – in, say, a molecular ecology dataset – such sequences could be incorrectly interpreted to warrant new species and genus descriptions.…”

Section: Discussionmentioning

confidence: 99%

How, not if, is the question mycologists should be asking about DNA-based typification

Nilsson¹,

Ryberg²,

Wurzbacher³

et al. 2023

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Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community – that the current situation is satisfactory and that no change is needed to “the code” – and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.

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Section: Discussionmentioning

confidence: 99%

How, not if, is the question mycologists should be asking about DNA-based typification

Nilsson¹,

Ryberg²,

Wurzbacher³

et al. 2023

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“…Ambiguously aligned regions of the ITS alignment were highlighted and removed with the online version of GBlocks 0.91b (Castresana 2000) under the least stringent settings. Also removed was a 268-269 base pair insertion present in the ITS1 region of several taxa (Barge et al 2016, Rosenblad et al 2016.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

New reports, phylogenetic analysis, and a key to Lactarius Pers. in the Greater Yellowstone Ecosystem informed by molecular data

Barge¹,

Cripps²

2016

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The Greater Yellowstone Ecosystem (GYE), located in the Central Rocky Mountains of western North America, is one of the largest nearly intact temperate-zone ecosystems on Earth. Here, Lactarius is an important component of ectomycorrhizal communities in many habitat types, from low elevation riparian areas to high elevation conifer forests and alpine tundra. Molecular phylogenetic analyses of ITS and RPB2 gene sequences along with detailed morphological examination confirm at least 20 Lactarius species, as well as three varieties, and one unresolved species group in the GYE. Eight taxa are reported from the GYE for the first time, and nearly every major ectomycorrhizal host plant in the GYE appears to have at least one Lactarius species associated with it. Broad intercontinental distributions are suggested for alpine Salix and Betula associates, and for certain subalpine Picea and aspen (Populus spp.) associates. Some species appear to be restricted to western North America with Pinus, Pseudotsuga or Abies. The distribution and/or host affinities of others is not clear due in part to ambiguous host assignment, taxonomic problems or the relative rarity with which they have been reported. Key words

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“…The existence of introns in the 5′ end of the small subunit in certain Ascomycota lineages likely limits primer annealing and makes amplifying the ITS1 region challenging [ 29 , 30 ]. Similarly, the length heterogeneity of the ITS1 region complicates sequencing in genera like Cantharellus [ 31 ], Astraeus , Russula and Lactarius [ 32 ]. These challenges tend to undermine the utility of the ITS1 region.…”

Section: Introductionmentioning

confidence: 99%

Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

Wilson,

Eberhardt,

Nguyen

et al. 2023

JoF

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The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of “splitting” taxa into numerous taxonomic units produces greater barcode gaps when compared to “lumping”. The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.

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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

Cited by 9 publications

References 36 publications

How, not if, is the question mycologists should be asking about DNA-based typification

How, not if, is the question mycologists should be asking about DNA-based typification

New reports, phylogenetic analysis, and a key to Lactarius Pers. in the Greater Yellowstone Ecosystem informed by molecular data

Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

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Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

Cited by 9 publications

References 36 publications

﻿How, not if, is the question mycologists should be asking about DNA-based typification

﻿How, not if, is the question mycologists should be asking about DNA-based typification

New reports, phylogenetic analysis, and a key to Lactarius Pers. in the Greater Yellowstone Ecosystem informed by molecular data

Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

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Product

Resources

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How, not if, is the question mycologists should be asking about DNA-based typification

How, not if, is the question mycologists should be asking about DNA-based typification