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.

Molecular Diagnosis and Vegetative Compatibility Group Analysis of Fusarium Wilt of Banana in Nepal

“…Apart from races, Foc has been also grouped based on vegetative compatibility (VCGs). So far, 24 VCGs have been identified, but there is solid evidence that other VCGs also exists [ 9 ]. By far, TR4, which belongs to VCG 01213/16, is the most aggressive strain causing FWB.…”

A deep genetic analysis of banana Fusarium wilt pathogens of Cuba in a Latin American and Caribbean diversity landscape

“…However, these analyses focused on Southeast Asia, which is the center of origin of Musa , but thus far there is no information about these species in the LAC context. Previous studies used DNA fingerprinting (Bentley et al ., 1998), multigene phylogeny (Fourie et al ., 2009; Maryani et al ., 2019; Magdama et al ., 2020), DArTseq (Mostert et al ., 2022), or whole-genome sequence comparisons (Garcia-Bastidas et al ., 2020; Acuña et al ., 2021; Leiva et al ., 2022; Reyes-Herrera et al ., 2022), but included only a limited number of isolates from Latin America or only focused on individual countries (Magdama et al ., 2020; Batista et al ., 2022). Hence, no conclusions could yet be drawn on the phylogeography of FWB-causing fungi in LAC.…”

“…This illustrates that there is no strict correlation between VCGs and races in the FWB-banana pathosystem (Ordóñez et al ., 2015). Nevertheless, VCGs (up to 24) have been used to gain insight into the dissemination and evolution of the causal agents of FWB (Fourie et al ., 2009; Ordóñez et al ., 2015; Mostert et al ., 2022), although they do not provide a measure of genetic distance between phenotypes (Bentley et al ., 1998; Fourie et al ., 2009). Thus, neither VCGs nor physiological races have contributed to a thorough understanding of the phylogeny and dissemination of the causal fungi of FWB (Dita et al ., 2020).…”

“…Previously, phylogenetic analyses revealed that Foc is polyphyletic and divided over the three recognized FOSC clades, which can be further divided into eight to 10 individual genetic lineages (Bentley et al ., 1998; O’Donnell et al ., 1998; Groenewald et al ., 2006; Fourie et al ., 2009; Mostert et al ., 2017; Ordoñez, 2018). High-resolution genotyping-by-sequencing analyses using Diversity Array Technology (DArTseq; Cruz et al ., 2013, Kilian et al ., 2003) is a genome-wide method that validated and extended these findings (Ordóñez et al ., 2015; Mostert et al ., 2022) It has also been used to study genetic diversity and resistance mapping in many crop species, such as cassava, chickpea, pea, tea, and wheat (Sohail et al ., 2015; Malebe et al ., 2019; Adu et al ., 2021; Sampaio et al ., 2021; Ahmed et al ., 2021) as well as in banana (Amorim et al ., 2009; Risterucci et al ., 2009; Sardos et al ., 2016; Ahmad et al ., 2020) and their pathogens (Sharma et al ., 2014; Ordóñez et al ., 2015; Mostert et al ., 2022).…”

Diagnostics of Fusarium wilt in banana: Current status and challenges

“…Vegetative compatibility was first reported in 1985 and is based on the ability of genetically similar filamentous fungi to naturally anastomose (merge their mycelium) and form stable heterokaryons (Glass et al., 2000; Maymon et al., 2020; Puhalla, 1985). At least 24 different VCGs have been recognized in Foc and novel VCGs continue to be identified (Katan, 1999; Mostert et al., 2022).…”