Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

By Henrik R. Nilsson, R. Henrik Nilsson, Erik Kristiansson, Martin Ryberg, N. Hallenberg, Karl-Henrik Larsson. Evolutionary bioinformatics online, 2008

871 citations recorded by the source corpus.

The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequence-based mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra- and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3% threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITS-based species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names.

Subfields: Cell Biology, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/af9fe71d4e3eb3eed3574db83875ac8295765836

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cell Biology

In Molecular Biology

In Plant Science

Citations in the corpus

Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics (2021, methodology): “Given that fixed thresholds to dot exist between species, but stem branch length depends on the time since divergence (Nilsson et al. 2008; Collins and Cruickshank 2013; Leavitt et al. 2016a; Lücking et al. 2020a), the barcoding gap approach is generally inferior to quantitative species delimitation”
Hidden fungi, emergent properties: endophytes and microbiomes. (2011, background): “The internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA) is likely to become the official barcoding region for fungi (107), but other regions, such as CO1 (cytochrome c oxidase subunit I) and multilocus barcodes, are still being investigated (131, 141).”
454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. (2009, result): “In the present pyrosequencing experiment, and as reported in other studies (Liu et al., 2008; Nilsson et al., 2009), an average length of 252 bp for the ITS-1 sequences is long and sufficiently polymorphic to allow the identification of the majority of fungal OTUs at the species’ or genus levels.”
Do mycorrhizal symbioses cause rarity in orchids? (2011, background): “However, different groups of fungi show different levels of sequence divergence between species, suggesting that these arbitrary thresholds only have a limited applicability (Nilsson et al. 2008).”
FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild (2016, background): “Guild assignments of OTUs that matched to 93% sequence similarity to a reference sequence were kept, as this conservatively reflects the genus boundaries with the ITS gene region for many fungi (Nilsson et al., 2008).”
Chronic nitrogen additions fundamentally restructure the soil fungal community in a temperate forest (2016, background): “High-throughput bioinformatics, particularly denoising (Gaspar and Thomas, 2013), sequence clustering (Nilsson et al., 2008, 2011), and the subsequent choice of a representative sequence used as a comparison with public databases, may cause one of several minor variants to be chosen as the true…”
Ice nucleation activity in the widespread soil fungus Mortierella alpina (2015, positive): “Indeed, the identity level between the ITS regions of different M. alpina isolates ranges from 94-100% (Ho and Chen, 2008), almost twice the value of 3.24% suggested for intraspecific variability within the zygomycotic fungi by Nilsson and Kristiansson (2008).”
Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces (2015, methodology): “A cut-off level of 97% identity is often used to define species or OTUs (operational taxonomic units) in mycology (Nilsson et al. 2008; Yamamoto and Bibby 2014).”
Next‐generation sequencing technologies for environmental DNA research (2012, background): “Received 15 October 2011; revision received 11 February 2012; accepted 14 February 2012”
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi (2012, background): “This finding confirms the fact that fungal diversity remains poorly sampledwithDNA sequences for these lineages (43, 48).”
The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors (2009, methodology): “…in molecular techniques, appropriate DNA databases (Koljalg et al. 2005) and powerful in silico capacities of data compilation and analysis (Nilsson et al. 2005, 2008), identification of taxa in fungal ecology could be easily expanded from traditional molecular methods to high-throughput…”