Fusarium fujikuroi, a member of the Asian clade of the Fusarium fujikuroi species complex (FFC) causes 'bakanae' (foolish seedlings) disease of rice due to its exceptional ability to produce the plant hormones gibberellins. The disease was first described over 100 years ago in Japan, but in the last decades, bakanae has emerged as a problem in other rice-growing areas of the world such as Italy, France and California. The most evident symptom of this disease is yellowing and abnormal elongation of infected seedlings and subsequent loss of grain production.The genomes of 10 strains (including one F. oxysporum strain as outgroup) isolated from infected rice plants in different geographic regions were sequenced to determine the diversity of genome structure, distribution of mating types, the ability to produce secondary metabolites (SMs) and to study a potential correlation between virulence on rice and the ability to produce gibberellins and/or mycotoxins such as fumonisins, fusarins, fusaric acid and beauvericin. Furthermore, genome-wide transcriptome analysis was performed using an in planta RNA-sequencing approach.