For gene prediction, we generated transcriptome data from axenic culture and plant infections, resulting in a total of 21,781 genes, among which are eight presumptive effector genes (SIX1, SIX4, SIX8, SIX9, and FOA1-FOA4) that were previously known from Arabidopsis-infecting F. oxysporum16, as well as the homologous genes of FOA1 and FOA4, which were named FOA1b and FOA4b, respectively. This evidence concerns the gene SIX4 and infection.