The unbearable lightness of sequenced-based identification

Valérie Hofstetter,Sylvain Schnee,Katia Gindro,Bart Buyck,Guillaume Eyssartier

doi:10.1007/s13225-019-00428-3

Abstract

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 re-examined, 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.

Highlights

Until recently, fungi received very little attention in biology conservation (Griffith 2012; Heilmann-Clausen et al 2014) they play a key role in terrestrial ecosystems as decomposers of dead plant material, in carbon and nutrient recycling, and as symbionts of most terrestrialFungal Diversity (2019) 96:243–284 plants to which they provide nutrients and water
Such results rely on the in-depth re-examination of basic GenBank local alignment search tool program (BLAST) results for the most interesting species that were collected, viz. first records for Switzerland, rare or patrimonial species and problematic species, all belonging to Agaricomycotina
These collections were identified as Hydropus subalpinus and, our second BLAST search, performed in October 2018, identified our sequences with new GenBank deposits for Hydropus spp. with 98–99% of similarity for 100% of query coverage

Summary

Introduction

Fungi received very little attention in biology conservation (Griffith 2012; Heilmann-Clausen et al 2014) they play a key role in terrestrial ecosystems as decomposers of dead plant material, in carbon and nutrient recycling, and as symbionts of most terrestrialFungal Diversity (2019) 96:243–284 plants to which they provide nutrients and water (van der Heijden et al 2015). Because of the exponentially growing negative impact of human activities on natural habitats, many saprobic fungi on dead wood (Christensen et al 2005), as well as many ectomycorrhizal species (Di Marino et al 2009) are declining or even disappearing in Europe. The fungal kingdom is one of the most diverse groups of organisms composed of several millions of species (Blackwell 2011; Hibbett et al 2016; Scheffers et al 2012; Wijayawardene et al 2018). With merely 120,000 currently accepted species being named so far (Hawksworth and Lucking 2017), estimation of fungal biodiversity raises serious methodological problems, even when one restricts oneself to the ‘larger mushroom-forming fungi’ (principally Agaricomycotina), a group that has traditionally been well-studied in Europe. In Europe, this expertise has been steadily declining in professional circles (Buyck 1999; Samson 1995), and is mainly found among mycological societies and amateur mycologists, more and more referred to as ‘‘citizen scientists’’ (Shehan 2017)

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