Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007 Brookings, South Dakota, United States
We recently published the first report of Fusarium luffae (FL) causing disease in soybean fields in the USA. The identified FL isolate SLSDF2 shows aggressive root rot and foliar wilt symptoms compared to established pathogenic Fusarium species on soybean. We hypothesize that SLSDF2’s highly virulent nature may be due to uncharacterized virulence effectors that are either newly evolved or capable of evading the soybean’s existing resistance mechanisms. To identify the genomic regions of SLSDF2 harboring unique effectors, we assemble a chromosome level genome of Fusarium luffae using Oxford Nanopore long-read technology as genome availability announcement, and compared our data to publicly available Fusarium oxysporum (Foxy) and Fusarium oxysporum f. sp. luffae (FoL) (both nonpathogenic on soybean) genome data. The de novo assembly of SLSDF2 produced 38.14 Mb genome with 8 contigs (N50: 6.89 Mb, BUSCO completeness score: 98.6%), 12,231 predicted genes, and 35 secondary metabolite clusters, significantly improving over existing assemblies. Comparative analysis with FL, Foxy, and FoL revealed enriched repetitive elements, an expanded effector repertoire, and only three highly divergent effector proteins. Our long-term aim is to functionally characterize the putative effectors and to timely identify cognitive resistance loci in soybean germplasm so that we can stay ahead in the host resistance race against this potentially emerging pathogen species.
