15 Oct Fusarium

Fusarium Link, Mag. Gesell. naturf. Freunde, Berlin 3(1-2): 10 (1809)

Fusarium is a genus with 20 monophyletic species complexes (Rana et al. 2017). Species formerly belonged to F. solani species complex were transferred to genus Neocosmospora based on sexual morph characters and molecular phylogeny (Lombard et al. 2015; Sandoval-Denis & Crous (2018). Fusarium species are saprobes, parasites, endophytes, soil-borne or isolated from water (Rana et al. 2017). Species of Fusarium are economically important fungi as they are responsible for blights, cankers, rots, and wilts of horticultural, ornamental and forest crops in both agricultural and natural ecosystems, worldwide, and also human infections (Rana et al. 2017; Varela et al. 2013; Peraldi et al. 2013; Al-Hatmi et al. 2019; Maryani et al. 2019a, b). In nature, sexual morphs of Fusarium occur less commonly than the asexual morphs (Gräfenhan et al. 2011; Rossman et al. 1999).

 Classification – Sordariomycetes, Hypocreomycetidae, Hypocreales, Nectriaceae

Type species – Fusarium sambucinum Fuckel, Hedwigia 2: 135.1863.

Distribution – Worldwide

Disease symptoms – blights, cankers, rots, and wilts

Plant pathogenic species of this genus have the capability to change their lifestyle to saprotrophic and can survive for long periods as chlamydospores in host tissues. Fusarium species damage their hosts by systemically colonizing and occluding the host xylem (Ploetz et al. 2003).

Hosts – Known from many host plant families.

Morphological based identification and diversity

Fusarium was also known from the sexual morphic fungus name Gibberella, which was suppressed in favour of Fusarium by Rossman et al. (2013). Currently, 1,552 Fusarium epithets are listed in Index Fungorum (2019). Variation and mutation in culture and lack of clear morphological characters for separating species are the main problems which make the species concept of Fusarium much broader (Geiser et al. 2004). It leads to the incorrect and confusing application of species names to toxigenic and pathogenic isolates (Geiser et al. 2004). Species boundaries have been inferred using multi-gene phylogenetic methods, reflecting the species diversity more than morphological treatments (Aoki and O’Donnell 1999; Geiser et al. 2004; O’Donnell 2000; O’Donnell et al. 1998a, b; Ward et al. 2002). A combined phylogenetic analysis of LSU, ITS, RPB2 and new phylogenetic marker acl1 by Gräfenhan et al. (2011), revealed that the early concept of Fusarium is not monophyletic. Fusarium sensu Wollenweber divided into two large groups, basal ‘Fusarium-like clades’, and the other one terminal ‘Fusarium clade’ in the Nectriaceae (Gräfenhan et al. 2011).

Fig. Sexual morph of a Fusarium sp. a Herbarium material. b Ascomata on the host. c Section of ascomata. d Section of the ostiolar region. e Peridium in face view. f–h Asci (h in Melzer’s reagent). i, j Ascospores. k Germinating ascospore. l, m Colony on MEA. Scale bars: c = 100 µm, d = 50 µm, e–k = 20 µm.

Molecular based identification and diversity

ITS and LSU are least informative in species-level identification of Fusarium (O’Donnell et al. 2008a; Hyde et al. 2014). Moreover, non-orthologous copies of the ITS2, which can lead to wrong phylogenetic inferences, can be detected in many species of Fusarium (Geiser et al. 2004; O’Donnell et al. 1998). Generally, for the species-level identification of fungi intron-rich regions of protein-coding genes are used as the markers (Geiser et al. 2004). The translation elongation factor 1-a (tef1), which lacks non-orthologous copies of the gene, is highly informative at the species level in Fusarium (Geiser et al. 2004). RPB1 and RPB2 are also very informative gene regions for species identification of Fusarium (O’Donnell et al. 2013; Hyde et al. 2014). Lombard et al. (2018) observed that tef1 and RPB2 genes provide better resolution of the species in the F. oxysporum complex than cmdA and tub2.

Recommended genetic markers (genus level) – ATP citrate lyase (acl1), tef1 and ITS

Recommended genetic markers (species level) – calmodulin-encoding gene (cmdA), tub2, tef1, RPB1 and RPB2

Accepted number of species: There are 1552 species epithets in Index Fungorum (2019) under this genus. More than 175 species have DNA sequence data.

References: Booth 1971, Rossman et al. 1999 (morphology), Rana et al. 2017, Gräfenhan et al. 2011; Laurence et al 2014; Lombard et al. 2018, 2019; Maryani et al. 2019a, b; Wang et al. 2019; Nalim et al. 2011(morphology, phylogeny).

Table Details of the Fusarium isolates used in the phylogenetic analyses. Ex-type (ex-epitype) strains are in bold and marked with an asterisk* and voucher strains are in bold.

Fig. Phylogram generated from RAxML analysis based on combined RPB1, RPB2 and tef1 sequences of accepted species of Fusarium. Related sequences were obtained from GenBank. One hundred sixty-five taxa are included in the analyses, which comprise 3980 characters including gaps. Single gene analyses were carried out and compared with each species, to compare the topology of the tree and clade stability. The tree was rooted in Fusicolla aquaeductuum (NRRL 20696). Tree topology of the ML analysis was similar to the BYPP. The best scoring RAxML tree with a final likelihood value of -63956.723151 is presented. The matrix had 2254 distinct alignment patterns, with 25.13% of undetermined characters or gaps. Estimated base frequencies were as follows; A = 0.257298, C = 0.251723, G = 0.248896, T = 0.242083; substitution rates AC = 1.366599, AG = 4.760724, AT = 1.266971, CG = 0.903914, CT = 9.564945, GT = 1.000000; gamma distribution shape parameter α = 1.089091. RAxML and maximum parsimony bootstrap support value ≥70% are shown near the nodes. The scale bar indicates 0.07 changes. The ex-type strains are in bold.