Persoonia 43, 2019: 1–47 ISSN (Online) 1878-9080 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE https://doi.org/10.3767/persoonia.2019.43.01 Epitypification of Fusarium oxysporum – clearing the taxonomic chaos L. Lombard1, M. Sandoval-Denis1,2, S.C. Lamprecht3, P.W. Crous1,2,4 Key words Abstract Fusarium oxysporum is the most economically important and commonly encountered species of Fusa­ rium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and non-pathogenic cryptic species strains. However, in its current concept F. oxysporum is a species complex consisting of numerous cryptic species. diversity Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the human and plant pathogens lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance species complex and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species subspecific classification recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species. Article info Received: 20 June 2018; Accepted: 19 October 2018; Published: 18 December 2018. INTRODUCTION species. These special forms were further expanded on by Gor- don (1965) to 66, most of which are still used in literature today. Fusarium oxysporum is the most economically important and The use of special forms or formae speciales as subspecific commonly encountered species of Fusarium. This soil-borne rank in F. oxysporum classification has become common prac- asexual fungus is known to harbour both pathogenic (plant, tice due to the broad morphological delineation of this species animal and human) and non-pathogenic strains (Leslie & Sum- (Leslie & Summerell 2006). This informal subspecific rank is merell 2006) and is also ranked fifth on a list of top 10 fungal defined based on the plant pathogenicity of the particular F. oxy­ pathogens based on scientific and economic importance (Dean sporum strain and excludes both clinical and non-pathogenic et al. 2012, Geiser et al. 2013). Historically, F. oxysporum has strains (Armstrong & Armstrong 1981, Gordon & Martyn 1997, been defined by the asexual phenotype as no sexual morph Kistler 1997, Baayen et al. 2000, Leslie & Summerell 2006). has yet been discovered, even though several studies have Therefore, F. oxysporum strains attacking the same plant host indicated the possible presence of a cryptic sexual cycle (Arie are generally considered to belong to the same special form. et al. 2000, Yun et al. 2000, Aoki et al. 2014, Gordon 2017). Although this homologous trait has led to erroneous assump- This is further supported by phylogenetic studies that place tions considering a specific special form to be phylogenetically F. oxysporum within the Gibberella Clade (Baayen et al. 2000, monophyletic, several studies (O’Donnell et al. 1998, 2004, O’Donnell et al. 2009, 2013). These studies also showed that 2009, O’Donnell & Cigelnik 1999, Baayen et al. 2000, Lievens F. oxysporum displays a complicated phylogenetic substruc- et al. 2009b, Van Dam et al. 2016) have highlighted the para- ture, indicative of multiple cryptic species within F. oxysporum and polyphyletic relationships within several F. oxysporum (Gordon & Martyn 1997, Laurence et al. 2014). As with other special forms, e.g., F. oxysporum f. sp. batatas, F. oxysporum Fusarium species complexes, the F. oxysporum species com- f. sp. cubense and F. oxysporum f. sp. vasinfectum. Addition- plex (FOSC) has suffered from multiple taxonomic/classification ally, several F. oxysporum special forms are able to infect and systems applied in the past. cause disease in more than one (sometimes unrelated) plant Diederich F.L. von Schlechtendal first introduced F. oxysporum hosts, whereas others are highly specialised to a specific plant in 1824, isolated from a rotten potato tuber (Solanum tubero­ host (Armstrong & Armstrong 1981, Gordon & Martyn 1997, sum) collected in Berlin, Germany. Wollenweber (1913) placed Kistler 1997, Baayen et al. 2000, Leslie & Summerell 2006, F. oxysporum within the section Elegans along with eight other Fourie et al. 2011). Fusarium species and numerous varieties and forms based Naming F. oxysporum special forms are not subject to the Inter- on similarity of the micro- and macroconidial morphology and national Code of Nomenclature for algae, fungi, and plants (ICN; dimensions. Snyder & Hansen (1940) later consolidated and McNeill et al. 2012, Thurland et al. 2018), and therefore no reduced all species within the section Elegans into F. oxysporum diagnosis (in Latin and/or English), nor the deposit of type ma- and designated 25 special forms (formae speciales) within this terial in a recognised repository is required. This decision was made due to the difficulty in accepting special forms within the 1 Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Code, even though these strains are of great importance to plant corresponding author e-mail: [email protected]. pathologists and breeders (Deighton et al. 1962, Gordon 1965, 2 Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, Armstrong & Armstrong 1981). Several studies on F. oxysporum University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa. indicate that between 70 to over 150 special forms are known 3 ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, in F. oxysporum (Booth 1971, Armstrong & Armstrong 1981, Western Cape, South Africa. 4 Wageningen University and Research Centre (WUR), Laboratory of Phyto- Kistler 1997, Baayen et al. 2000, Leslie & Summerell 2006, pathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands. Lievens et al. 2008, O’Donnell et al. 2009, Fourie et al. 2011, © 2018-2019 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. 2 Persoonia – Volume 43, 2019 Laurence et al. 2014, Gordon 2017). At present Index Fungo- detection methods have been developed to identify economi- rum (http://www.indexfungorum.org/) lists 124 special forms in cally important VCGs as diagnostic tool (Fernandez et al. 1998, F. oxysporum, whereas MycoBank (http://www.mycobank.org/) Pasquali et al. 2004a, c, Lievens et al. 2008), e.g., F. oxysporum list 127 special forms. Further careful scrutiny of literature re- f. sp. cubense TR4 VCG01213 (Dita et al. 2010). vealed that 144 special forms have been named until February Until recently, limited knowledge on the genetic premise for host 2018 (Table 1). Although the special forms concept of Snyder specificity in F. oxysporum was available (Gordon & Martyn & Hansen (1940) is still applied today, additional subspecific 1997, Kistler 1997, Baayen et al. 2000). However, the discovery classification systems for special forms of F. oxysporum have of a lineage-specific chromosome (or transposable/effector/ also been introduced, which include haplotypes, races and accessory chromosome) in F. oxysporum f. sp. lycopersici by vegetative compatibility groups (VCGs). Ma et al. (2010), in which the host specific virulence genes lie The haplotype subspecific classification system was introduced (Van der Does et al. 2008, Takken & Rep 2010, Ma et al. 2013), by Chang et al. (2006) and later expanded upon by O’Donnell has provided a new view into the evolution of pathogenicity in et al. (2008, 2009) to include strains from both the FOSC F. oxysporum. In vitro transfer of these accessory chromosomes and Neocosmospora (formerly the F. solani (FSSC) species into non-pathogenic F. oxysporum strains has converted the complex). This classification system is based on unique multi- latter strains into host-specific pathogens, providing evidence locus genotypes within the species complex, aimed to resolve that host-specific pathogenicity could be acquired through communication problems among public health and agricultural horizontal transfer of accessory chromosomes (Takken & Rep scientists (O’Donnell et al. 2008). Chang et al. (2006) proposed 2010, Ma et al. 2010, 2013, Van Dam et al. 2016, Van Dam & a standardised haplotype nomenclature system that depict Rep 2017). Therefore, the special form name can be linked to the species complex, species and genotype. O’Donnell et al. the accessory chromosome whereas race demarcation can be (2009) was able to identify 256 unique two-locus haplotypes linked to the specific virulence genes carried on these acces- sory chromosomes. from 850 isolates representing 68 special forms of F. oxysporum