Expression profiles of nine Fusarium fujikuroi strains revealed common and different sets of up-regulated genes

We provide genome sequences of altogether 9 F. fujikuroi and one F. oxysporum (outgroup) strains, all isolated from rice plants in different geographical regions of the world, and searched for differences in genome structure, chromosome size, secondary metabolite production, virulence on rice, and in vitro and in planta transcriptome profiles. Despite their high relatedness on genome level, they differ significantly in their ability to infect rice, to form asexual spores (micro-and macroconidia), and to produce secondary metabolites. To gain insight into these differences, we compared the transcriptome of the ten strains in infected rice roots with that of liquid culture at low and high nitrogen (6 mM and 60 mM Gln) in vitro conditions by a RNA sequencing approach. Overall design: RNA-sequencing of 10 Fusarium strains; 3 conditions (rice roots 7 days post infection; synthetic liquid media with 6 mM or 60 mM glutamine after 3 days of cultivation) ,