A Polyphasic Approach Reveals Novel Genotypes and Updates the Genetic Structure of the Banana Fusarium Wilt Pathogen

Abstract

Fusarium oxysporum f. sp. cubense (Foc) is a soil-borne fungus that causes Fusarium wilt, a destructive plant disease that has resulted in devastating economic losses to banana production worldwide. The fungus has a complex evolutionary history and taxonomic repute and consists of three pathogenic races and at least 24 vegetative compatibility groups (VCGs). Surveys conducted in Asia, Africa, the Sultanate of Oman and Mauritius encountered isolates of F. oxysporum pathogenic to banana that were not compatible to any of the known Foc VCGs. Genetic relatedness between the undescribed and known Foc VCGs were determined using a multi-gene phylogeny and diversity array technology (DArT) sequencing. The presence of putative effector genes, the secreted in xylem (SIX) genes, were also determined. Fourteen novel Foc VCGs and 17 single-member VCGs were identified. The multi-gene tree was congruent with the DArT-seq phylogeny and divided the novel VCGs into three clades. Clustering analysis of the DArT-seq data supported the separation of Foc isolates into eight distinct clusters, with the suite of SIX genes mostly conserved within these clusters. Results from this study indicates that Foc is more diverse than hitherto assumed.

Keywords: banana Fusarium wilt; diversity array technology; phylogeny; secreted in xylem genes; vegetative compatibility.

Figure 1

Maximum parsimony tree inferred from the combined data sets of the rpb1, rpb2 and tef1 gene regions for Fusarium oxysporum f. sp. cubense isolates. Bootstrap values generated from the maximum parsimony, followed by maximum likelihood analysis (>60%), are shown at the internodes. Clade designation (A–E) is according to O’Donnell et al. [40], while the phylogenetic species boundary sensu Laurence et al. [23] is indicated (PS I and PS II). Culture collection number, Vegetative compatibility group (VCG) or single member VCG, are indicated on tips. Snapclust (SC) grouping is indicated in different colours. The tree is rooted with F. fujukuroi NRRL 13566.

Figure 2

Clustering analysis indicating Fusarium oxysporum f. sp. cubense (Foc) consists of eight distinct genetic clusters. (A) SplitsTree clustering network based on the distance between 83 Foc isolates as indicated by 5240 binary SNP markers. Different snapclust (SC) or discriminant analysis of principal component (DAPC) groups are shown by different colours, while individual isolates are indicated on each root tip. Foc clade identities as determined by O’Donnell et al. [40] are indicated on branches. (B) tion of the eight genetic on the plan DA1-DA2 (top) and DA1-DA3 (bottom). The percentages on each scatterplot indicate the inertia rate of each axis (which can be interpreted as the percentage of variation explained by the axis), while the SC groups are shown by different colours, and dots represent individual genotypes.

Figure 3

Maximum likelihood analysis of 83 Fusarium oxysporum f. sp. cubense isolates based on single nucleotide polymorphisms. Bootstrap values generated from the maximum likelihood analysis are shown at the internodes. Clade designation (A–C) according to O’Donnell et al. [40] and vegetative compatibility group (VCG) or single member VCG are indicated on nodes.