Genomic differences between the newFusarium oxysporumf. sp.apii(Foa) race 4 on celery, the less virulentFoaraces 2 and 3, and the avirulent on celery f. sp.coriandrii

Background Members of theF. oxysporiumspecies complex (FOSC) in the f. sp.apii(Foa) are pathogenic on celery and those in f. sp.coriandrii(Foci) are pathogenic on coriander (=cilantro). Fociwas first reported in California in 2005; a new and highly aggressive race 4 ofFoawas observed in 2013 in California. Preliminary evidence indicated thatFoacan also cause disease on coriander, albeit are less virulent thanFoci. Comparative genomics was used to investigate the evolutionary relationships betweenFoarace 4,Foarace 3, and theFoci, which are all in FOSC Clade 2, andFoarace 2, which is in FOSC Clade 3. Results A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated thatFoaraces 3 and 4 and theFociare monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, theFociversusFoaraces 3 and 4 differ in multiple contigs. Based on significantly increased expression ofFoarace 4 genesin plantavs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of eitherFoarace 2 or 4 and theFociwere identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated thatFoarace 4 formed conidial anastomosis tubes (CATs) withFoci.Foarace 4 andFoarace 2, which are in different somatic compatibility groups, did not form CATs with each other. Conclusions There was no evidence thatFoarace 2 was involved in the recent evolution ofFoarace 4;Foarace 2 and 4 are CAT-incompatible. AlthoughFoaraces 3 and 4 and theFociare closely related, there is no evidence that eitherFocicontributed to the evolution ofFoarace 4, or thatFoarace 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes ofFoarace 4 and theFociand for their differences in host range.