Population structure, genetic diversity and global migration of the banana Fusarium wilt pathogen, Fusarium oxysporum f. sp. cubense tropical race 4

Abstract

O_LIThe current epidemic of banana Fusarium wilt is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). Foc TR4 originates in Asia and was first reported in the early 1990s, whereafter it was restricted to five Asian countries and the Northern Territory of Australia for two decades. Since 2013, the fungus was detected in the Middle East, the Indian subcontinent, Africa and Latin America. Its recent spread may be caused by the expansion of Cavendish banana production and the movement of contaminated planting materials. C_LIO_LIWhole genome sequences of 119 Foc TR4 isolates were compared based on single nucleotide polymorphisms (SNPs) to assess the population structure, genetic diversity and relation among isolates from 20 countries to reveal the evolutionary origin and likely migration. C_LIO_LIFoc TR4 is a monophyletic lineage divided into four clusters. Two of the clusters included isolates mostly from eastern Indonesia and seem to be ancestral with many rare alleles and high genetic diversity supporting this region as centre of origin. The remaining clusters were less diverse and associated with pandemic expansion. C_LIO_LIKnowledge on Foc TR4 emergence and dispersal can be used to inform more effective biosecurity and management practice. C_LI