New endemic Fusarium species hitch-hiking with pathogenic Fusarium strains causing Panama disease in small-holder banana plots in Indonesia.

Fusarium species are well known for their abundance, diversity and cosmopolitan life style. Many members of the genus Fusarium are associated with plant hosts, either as plant pathogens, secondary invaders, saprotrophs, and/or endophytes. We previously studied the diversity of Fusarium species in the Fusarium oxysporum species complex (FOSC) associated with Fusarium wilt of banana in Indonesia. In that study, several Fusarium species not belonging to the FOSC were found to be associated with Fusarium wilt of banana. These Fusarium isolates belonged to three Fusarium species complexes, which included the Fusarium fujikuroi species complex (FFSC), Fusarium incarnatum-equiseti species complex (FIESC) and the Fusarium sambucinum species complex (FSSC). Using a multi-gene phylogeny that included partial fragments of the beta-tubulin (tub), calmodulin (cmdA), translation elongation factor 1-alpha (tef1), the internal transcribed spacer region of the rDNA (ITS), the large subunit of the rDNA (LSU), plus the RNA polymerase II large subunit (rpb1) and second largest subunit (rpb2) genes, we were able to identify and characterise several of these as new Fusarium species in the respective species complexes identified in this study.

Phylogeny and genetic diversity of the banana Fusarium wilt pathogen Fusarium oxysporum f. sp. cubense in the Indonesian centre of origin.

Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt or Panama disease on banana, is one of the major constraints in banana production worldwide. Indonesia is the centre of origin for wild and cultivated bananas, which likely co-evolved with Foc. This study explored the widest possible genetic diversity of Foc by sampling across Indonesia at 34 geographically and environmentally different locations in 15 provinces at six islands. This resulted in a comprehensive collection of ∼200 isolates from 40 different local banana varieties. Isolates were identified and assessed using sequence analysis of the translation elongation factor-1alpha (tef1), the RNA polymerase II largest subunit (rpb1), and the RNA polymerase II second largest subunit (rpb2). Phylogenetic analyses of these genes allowed the identification of 180 isolates of Fusarium oxysporum f. sp. cubense (Foc), and 20 isolates of the Fusarium fujikuroi species complex (FFSC), the Fusarium incarnatum-equiseti species complex (FIESC), and the Fusarium sambucinum species complex (FSSC). Further analyses, incorporating a worldwide collection of Foc strains, revealed nine independent genetic lineages for Foc, and one novel clade in the Fusarium oxysporum species complex (FOSC). Selected isolates from each lineage were tested on the banana varieties Gros Michel and Cavendish to characterise their pathogenicity profiles. More than 65 % of the isolates were diagnosed as Tropical Race 4 (Foc-TR4) due to their pathogenicity to Cavendish banana, which supports the hypothesis that Foc-TR4 is of Indonesian origin. Nine independent genetic lineages for Foc are formally described in this study. This biodiversity has not been studied since the initial description of Foc in 1919. This study provides a detailed overview of the complexity of Fusarium wilt on banana and its diversity and distribution across Indonesia.