Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli,the causal agent of stem canker in prickly ash

Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash,an ecologically and economically important forest tree.However,the genome lack of F.zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker.In this study,we sequence,assemble,and annotate a relatively high-quality genome of F.zanthoxyli with a size of 43.39 Mb,containing 55 contigs and encoding 11,316 putative genes.Furthermore,279 tRNAs,64 5s rRNAs,5 18s rRNAs,7 28s rRNAs,2 sRNAs,21 snRNAs and 2,491 repetitive elements known as direct repeats(DRs)were predicted in the genome of F.zanthoxyli.Pathogenicity-related factors are predicted,comprising 495 CAZymes,217 effectors,156 CYP450s,and 202 enzymes associated with secondary metabolism.Besides,a comparative genomics analysis along with 25 other fungal species from eight classes of Ascomycota and Basidiomycota revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1～88.4 million years ago(MYA).Additionally,a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F.zanthoxyli originated approximately 34.6～26.9 MYA,and events of gene expansion and contraction within them were also unveiled.Among the investigated fungal genomes,3,929 ortholog families were found to be present in all 12 Fusarium species.Interestingly,with a mere 24 gene families,encompassing 59 genes,were identified as exclusive to F.zanthoxyli,representing a modest 0.24%of its gene families.The contracted gene families in F.zanthoxyli was the most across all the 12 species with the number of 4,002,while a comparatively fewer gene families underwent expansion with the number of 278.Finally,utilizing conserved domain prediction,the results revealed that among the 59 unique genes of F.zanthoxyli,the most enriched domains were PnbA,Czco and ULP1.Among the 783 expanded genes,the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family.This study sheds light on the genetic basis of F.zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.