Development of onion lines with robust resistance to Fusarium basal rot requires understanding of the interaction between the pathogens and their hosts. Fusarium spp. isolates ex. onion were sequenced with an aim to assemble lineage specific region in the F. oxysporum f. sp. cepae genome and identify putative effectors modulating host resistance. Inclusion of non-pathogenic isolates and closely related species aids identification of these lineage specific regions.