Comparative analyses of Fusarium oxysporum f.sp. lactucae and other F. oxysporum f.spp. Genome sequencing and assembly

In this study we present the first genome and transcriptome analyses for Fusarium oxysporum f. sp. lactucae race 1 and race 4 (Fola1 and Fola4). Long-read genome sequencing of three Fola1 and three Fola4 isolates revealed key differences in putative effector complement between races and with other F. oxysporum f.spp. following mimp-based bioinformatic analyses. Notably, homologues of both SIX9 and SIX14 (multiple copies with sequence variants) were present in both Fola1 and Fola4 isolates but all Fola4 isolates also contained an additional single copy of SIX8 which varied in sequence for one isolate. RNAseq of lettuce inoculated with Fola1 and Fola4 isolates identified highly expressed effectors, some of which were homologues of those reported in other F. oxysporum f.spp. including several in F. oxysporum f.sp. apii. Although SIX8, SIX9 and SIX14 were all highly expressed in Fola4, of the two SIX genes present in Fola1 only SIX9 was expressed as further analysis revealed that copies of SIX14 were disrupted by insertion of a transposable element. In addition, Fola4 SIX8 was found to be divergently transcribed from a shared promoter with either PSE1 or PSL1 associated with each of the two different SIX8 variants. Evidence of two independent instances of HCT in different Fola4 isolates and the involvement of helitrons in genome rearrangement and gene expression is discussed.