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Background  Members of the  F. oxysporium  species complex (FOSC) in the f. sp.  apii  ( Foa ) are pathogenic on celery and those in f. sp.  coriandrii  ( Foci ) are pathogenic on coriander (=cilantro) . Foci  was first reported in California in 2005; a new and highly aggressive race 4 of  Foa  was observed in 2013 in California. Preliminary evidence indicated that  Foa  can also cause disease on coriander, albeit are less virulent than  Foci . Comparative genomics was used to investigate the evolutionary relationships between  Foa  race 4,  Foa  race 3, and the  Foci , which are all in FOSC Clade 2, and  Foa  race 2, which is in FOSC Clade 3.    Results  A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that  Foa  races 3 and 4 and the  Foci  are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the  Foci  versus  Foa  races 3 and 4 differ in multiple contigs. Based on significantly increased expression of  Foa  race 4 genes  in planta  vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either  Foa  race 2 or 4 and the  Foci  were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that  Foa  race 4 formed conidial anastomosis tubes (CATs) with  Foci .  Foa  race 4 and  Foa  race 2, which are in different somatic compatibility groups, did not form CATs with each other.    Conclusions  There was no evidence that  Foa  race 2 was involved in the recent evolution of  Foa  race 4;  Foa  race 2 and 4 are CAT-incompatible. Although  Foa  races 3 and 4 and the  Foci  are closely related, there is no evidence that either  Foci  contributed to the evolution of  Foa  race 4, or that  Foa  race 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 of  Foa  race 4 and the  Foci  and for their differences in host range.

bmc genomics

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii