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Fusarium oxysporum  is a globally distributed soilborne fungal pathogen causing root rots, bulb rots, crown rots and vascular wilts on a range of horticultural plants. Pathogenic  F. oxysporum  isolates are highly host specific and are classified as  formae speciales .  Narcissus  is an important ornamental crop and both the quality and yield of flowers and bulbs can be severely affected by a basal rot caused by  F. oxysporum  f. sp.  narcissi  (FON); 154  Fusarium  isolates were obtained from different locations and  Narcissus  cultivars in the United Kingdom, representing a valuable resource. A subset of 30  F. oxysporum  isolates were all found to be pathogenic and were therefore identified as FON. Molecular characterisation of isolates through sequencing of three housekeeping genes, suggested a monophyletic origin with little divergence. PCR detection of 14  Secreted in Xylem  ( SIX ) genes, previously shown to be associated with pathogenicity in other  F. oxysporum  f. spp., revealed different complements of  SIX7 ,  SIX9 ,  SIX10 ,  SIX12  and  SIX13  within FON isolates which may suggest a race structure.  SIX  gene sequences were unique to FON and  SIX10  was present in all isolates, allowing for molecular identification of FON for the first time. The genome of a highly pathogenic isolate was sequenced and lineage specific (LS) regions identified which harboured putative effectors including the  SIX  genes. Real-time RT-PCR, showed that  SIX  genes and selected putative effectors were expressed  in planta  with many significantly upregulated during infection. This is the first study to characterise molecular variation in FON and provide an analysis of the FON genome. Identification of expressed genes potentially associated with virulence provides the basis for future functional studies and new targets for molecular diagnostics.

Basal Rot of Narcissus: Understanding Pathogenicity in Fusarium oxysporum f. sp. narcissi