Sclerotinia is one of the most economically devastating fungal genera in agriculture, yet its taxonomy remains surprisingly unsettled. A new review published in IMA Fungus traces the complex taxonomic history of this plant-pathogenic genus and offers recommendations for how future research should incorporate molecular data to finally clarify species boundaries. The stakes are high: the best-known species, Sclerotinia sclerotiorum, is estimated to cause annual losses exceeding 200 million dollars in the United States alone, and severe outbreaks can push those figures far higher. In 2009, Sclerotinia on soybean incurred an estimated cost of 560,149,000 dollars. Considering that these numbers are neither global nor recent, the real economic impact of diseases caused by this fungus is certainly much greater.
Sclerotinia sclerotiorum infects over 425 host plants and has a near-worldwide distribution, which makes estimating the true economic cost complicated, if not near impossible. The genus also contains at least two other significant plant pathogens, S. minor and S. trifoliorum, which contribute to agricultural losses. Beyond agriculture, Sclerotinia and related genera in the family Sclerotiniaceae present an intriguing case study for host generalism—the ability of a pathogen to infect multiple plant species. This trait, shared with the well-known generalist Botrytis cinerea, offers an opportunity for molecular and genomic investigations to uncover insights into pathogenicity. Some key pathogenicity genes within Sclerotiniaceae have already been explored using comparative genetics, but this only scratches the surface of what could be learned from these pathogens.
The taxonomic history of Sclerotinia is complex and spans nearly two centuries. The oldest name for S. sclerotiorum is Peziza sclerotiorum, described in 1837 by Libert, who noted that its apothecia resembled ascomycetous cup fungi classified in Peziza. Thirty-three years later, Fuckel renamed the species in honor of Libert as Sclerotinia libertiana when he introduced the genus Sclerotinia. De Bary later considered S. libertiana illegitimate and provided the new name Sclerotinia sclerotiorum as a result. Whetzel’s 1945 work represented a convergence point for the histories of S. sclerotiorum, the genus Sclerotinia, and the family Sclerotiniaceae. He proposed major changes to the group when introducing the family, designating Sclerotinia as its type and proposing 12 species within the genus, with S. sclerotiorum as the generic type.
However, this classification was later challenged. Korf and Dumont introduced the genus Whetzelinia in 1972 and renamed S. sclerotiorum as Whetzelinia sclerotiorum, arguing that S. candolleana—which Honey had considered the type of Sclerotinia—should have remained in the genus. Buchwald and Neergaard subsequently proposed conserving Sclerotinia with S. sclerotiorum as the type species, a move approved by the Special Committee on Fungi and Lichens in 1978. This resulted in the classification still in use today, with S. sclerotiorum as the type species of Sclerotinia, which in turn is the type genus of Sclerotiniaceae.
The higher-order taxonomy of Sclerotiniaceae has also been marked by historical instability. Whetzel originally classified the family in the class Discomycetes, which contained all apothecia-producing fungi. Over time, it became clear that Discomycetes belonged to several unrelated lineages, leading to these fungi being reassigned to various taxonomic groups. The order Helotiales, which includes Sclerotiniaceae, was eventually moved to the class Leotiomycetes. Since then, the higher-level taxonomy of Sclerotiniaceae has remained consistent, with its position in Ascomycota, Pezizomycotina, Leotiomycetes, and Helotiales unchanged. Some publications still incorrectly list Sclerotinia species as Discomycetes, likely because the most cited review of S. sclerotiorum lists it in this class.
A significant change came when Holst-Jensen and colleagues split Sclerotiniaceae into two distinct families in 1997. Historically, all stromatic, stipitate discomycetes were grouped into Sclerotiniaceae, but several studies showed that the sclerotial and substratal stromatal taxa likely represented separate lineages. A phylogenetic evaluation supported this two-lineage hypothesis, triggering the formation of Rutstroemiaceae and the subsequent division of genera between the two families. When the family was first described, it included 15 genera. Two additional genera were subsequently described by Kohn in 1979. Following the introduction of Rutstroemiaceae, Sclerotiniaceae retained nine genera and gained five new ones, while several genera were reclassified into Rutstroemiaceae.
Recent phylogenetic studies have offered the most up-to-date insights into the classification of Sclerotiniaceae within Leotiomycetes. Ekanayaka and colleagues produced a maximum-likelihood tree from 482 strains representing 187 Leotiomycetes species based on sequence data from five regions, including the internal transcribed spacer rDNA region (ITS), the 28S nuclear ribosomal large subunit, the 18S nuclear ribosomal small subunit, and partial gene regions of rpb2 and tef1-α. They observed a Sclerotiniales clade that included six families. Johnston and colleagues used three approaches: a phylogenomic tree based on 3,156 single-copy genes from 51 species, a 15-gene phylogeny of 259 selected species, and an ITS phylogeny that included taxa not represented in the other analyses. They identified a sclerotinioid clade comprising four strongly supported subclades. The two studies identified 36 genera as belonging to Sclerotiniaceae, with 26 placed there by both publications. However, six genera showed conflicting placements, and the broad structure of the sclerotinioid clade remains broadly similar but not identical between the studies.
Turning to the genus itself, species delineation in Sclerotinia has been the subject of much debate. Before 1979, 279 Sclerotinia species had been described. Their taxonomy was revised by Kohn, who accepted only three species: S. sclerotiorum, S. minor, and S. trifoliorum. Wherever possible, Kohn examined specimens and their published protologues, which led to the synonymization of 21 names with the three accepted species. Two hundred and ten names were removed from Sclerotinia and transferred to other genera. While evaluating these 279 names, she also introduced two new genera, Dumontinia and Elliottinia, to accommodate Sclerotinia tuberosa and Sclerotinia kerneri respectively. No living type material was available for the three species she accepted, leading to the lectotypification of S. sclerotiorum and the neotypification of S. minor and S. trifoliorum.
Kohn’s monograph was also valuable for its extensive review of the morphological characters informative in delimiting Sclerotinia species. Whetzel’s initial description of the genus was limited to species that produce definite, tuberoid sclerotia, have single-celled, hyaline ascospores, and lack a functional conidial state. Kohn further restricted the genus by including only those species in which the cells of the outer excipulum of the apothecium are globose and oriented perpendicularly to the apothecial surface. She distinguished between the three accepted species based on characteristics of their ascospores, apothecia, and sclerotia in agar culture. S. trifoliorum is the only species that exhibits ascospore dimorphism, with a segregation of large and small ascospores typically observed in a 4:4 ratio. Ascospores of S. sclerotiorum contain two nuclei, whereas those of S. minor and S. trifoliorum contain four. S. sclerotiorum and S. trifoliorum typically produce small numbers of large sclerotia on the growing tips of hyphae at the colony periphery, whereas S. minor forms many smaller sclerotia that develop laterally on hyphae dispersed throughout the colony.
Since Kohn’s monograph, 13 new Sclerotinia species have been described, including S. antarctica, S. asari, S. atrostipitata, S. cirsii-spinosissimi, S. ginseng, S. glacialis, S. himalayensis, S. nivalis, S. pseudoplatani, S. subarctica, S. tetraspora, S. trillii, and S. verrucispora. Most of these were described based solely on morphology, and many lack DNA sequence data or living strains deposited in culture collections. The review evaluates each of these species in detail. S. cirsii-spinosissimi has been transferred to Botrytis based on morphological characters and ITS sequence analysis, which showed 98.3 to 98.7 percent BLAST similarity with many Botrytis cinerea sequences. S. pseudoplatani is unlikely to belong in Sclerotinia, as there is no evidence that it meets the morphological criteria of the genus. S. subarctica has been widely used as a provisional name but was never formally described, meaning a valid species description is needed to ensure nomenclatural stability. Excluding S. cirsii-spinosissimi and S. pseudoplatani reduces the total number of possible Sclerotinia species to 14.
The review highlights two major limitations currently hindering the application of phylogenetic approaches in Sclerotinia: the lack of a reliable DNA barcode with sufficient resolution to distinguish among species, and the absence of ex-type cultures with associated molecular data. Although the ITS region is the formal DNA barcode for fungi, its limited variability across Sclerotiniaceae may compromise its effectiveness for species-level resolution in Sclerotinia. Compounding this issue is the scarcity of viable type strains. Although Kohn re-typified the three core species, these are non-living fungarium specimens, restricting their use in molecular analyses. The practical challenges associated with recovering DNA from aged, non-living material or destructively sampling type vouchers present significant technical and ethical obstacles. The stabilization of names through epitypification therefore represents a critical step, as it ensures that species are anchored to well-characterised, publicly accessible living cultures.
Genomic resources represent a largely untapped opportunity for resolving these taxonomic issues. As of August 2025, more than 160 Sclerotiniaceae genomes covering nine genera are publicly available through NCBI, although Botrytis is overrepresented, with 92 genome sequences. Although some genomes have been used to investigate the biology and pathogenicity of S. sclerotiorum, they remain underutilised for taxonomic purposes. Genome-scale data could be readily incorporated into multilocus phylogenies and phylogenomic analyses, accelerating efforts to clarify species boundaries and uncover cryptic diversity. The situation closely parallels the former state of Ceratocystis, a genus that also encompassed diverse but morphologically similar taxa until multigene phylogenies prompted its reclassification into multiple genera. As with Ceratocystis, the development of a robust phylogenetic framework for Sclerotinia would clarify generic and species boundaries across the group.
Despite its economic importance and long history of study, the taxonomy of Sclerotinia remains largely unresolved. However, incorporating molecular data offers a clear path forward. Establishing a robust taxonomic framework supported by validated reference strains and informative DNA barcode markers will allow clarification of the currently tenuous identities of some newly described species, such as S. trillii and S. glacialis, and will refine species limits within the core taxa. A clearer understanding of the taxonomic relationships among Sclerotinia species will also facilitate research into areas such as pathogenicity and population genetics, which may ultimately contribute to improved management of the devastating diseases caused by these pathogens. The ongoing ambiguity surrounding Sclerotinia borealis exemplifies how unresolved classifications continue to undermine taxonomic clarity, and the review charts a course toward a clearer understanding of taxonomic relationships among Sclerotinia species that will benefit researchers across multiple disciplines.
Subject of Research: Advancing the taxonomy of Sclerotinia (Helotiales, Sclerotiniaceae): a review and recommendations for an important plant-pathogenic genus
Article Title: Advancing the taxonomy of Sclerotinia ( Helotiales , Sclerotiniaceae ): a review and recommendations for an important plant-pathogenic genus
Article References: Thomas, C., Wilken, P. M., Coetzee, M. P. A., & Visagie, C. M. (2026). Advancing the taxonomy of Sclerotinia (Helotiales, Sclerotiniaceae): a review and recommendations for an important plant-pathogenic genus. IMA Fungus, 17, Article e175737. https://doi.org/10.3897/imafungus.17.175737
Image Credits: AI Generated
DOI: 10.3897/imafungus.17.175737
Keywords: Advancing, taxonomy, Sclerotinia, Helotiales, Sclerotiniaceae, review, recommendations, important, plant-pathogenic, genus, scientific research
News Source: Roger Howard. (October 19, 2026). Sclerotinia: the fungal genus that still puzzles taxonomists. Scienmag.
