Phylogeny and origin of Fusarium oxysporum f. sp. vanillae in Indonesia

Abstract

Vanilla stem rot, caused by Fusarium oxysporum f. sp. vanillae (Fov), is the main constraint to increasing vanilla production in the major vanilla‐producing countries, including Indonesia. The current study investigated the origin of Fov in Indonesia using a multigene phylogenetic approach. Nineteen Fov isolates were selected to represent Indonesia, the Comoros, Mexico and Réunion Island. The translation elongation factor 1 alpha gene and the mitochondrial small subunit ribosomal RNA gene phylogenies resolved the Fov isolates into three distinct clades in both phylogenetic species of the F. oxysporum species complex, indicating a polyphyletic pattern of evolution. In addition, Fov isolates from Indonesia were also polyphyletic. These results suggest that the vanilla stem rot pathogen in Indonesia has a complex origin. The implications for disease management are discussed.

Phylogenetic position and nucleotide diversity of Fusarium oxysporum f. sp. vanillae worldwide based on translation elongation factor 1α sequences

“…Only four isolates from Mexico, reported by Pinaria et al . (), were grouped in clade III, which is congruent with their results. However, another three isolates from Mexico (JAGH2, Nay18 and Nay20) belong to clade II, along with an Indonesian isolate (IndonesiaWN1).…”

“…This is an important difference from the results of Pinaria et al . (), who reported that Mexican isolates were restricted to clade III; optimization of the pathogenicity trait shows that within this clade there are four different origins of the ability to infect vanilla.…”

Morphology, phylogeny and pathogenicity of Fusarium species from Sansevieria trifasciata in Malaysia

“…The mtSSU gene was the least informative for differentiation of isolates of F. concentricum , F. mangiferae , and F. proliferatum . This accorded with the preferred use of the gene in classification among F. oxysporum , compared to other species of the genus (O’Donnell et al , ; Mbofung et al , ; Pinaria et al , ). In the present study, within F. oxysporum , there were only two clades (I and IV) of mtSSU tree and two clades (III and VII) of IGS tree but all clades (I–VII) of TEF1‐α tree were equivalent with the inclusion of isolates in either two or all clades generated from the combined gene sequences.…”

“…The mtSSU , IGS, and TEF1‐α are preferred genes for identification and phylogenetic classification of Fusarium species (O’Donnell et al , , ; Mbofung et al , ; Nitschke et al , ; Wang et al , ; Pinaria et al , ). In the present study, all three genes were informative in classifying the isolates of F. oxysporum , F. pseudocircinatum , and F. solani .…”

“…This suggested that additional genes might be required for better resolution within the species. Nevertheless, the classification and naming system of formae speciales within Fusarium species has been challenged with the discovery of polyphyly and the wide host range of a forma specialis (Pinaria et al , ; Šišić et al , ). In addition, the nomenclature of formae speciales lack standardization and some formae speciales even have multiple names (Edel‐Hermann and Lecomte, ).…”