Investigating Species Differences in Fungal Plant Pathogens with a High-Density Inter-Species Genetic Map and a Draft Genome

Fusarium, a genus of ascomycete fungi, contains many important plant pathogens, some of which reduce crop yield and quality by producing contaminating mycotoxins. Among them, F. proliferatum (Fp) and F. fujikuroi (Ff) are closely related but have different host specificity and produce different mycotoxins. To explore the genetic bases behind these differences, we generated a genetic map from an inter-species cross between them and sequenced the Fp genome to compare with available Ff genomes. We sequenced the Fp parent from this cross to a depth of 50x and assembled a draft genome. This assembly has an N50 of over 824 kb and contains 241 supercontigs, with the largest one over 2.1 Mb and a combined length of 43.1 Mb. The assembly is predicted to contain over 14,000 genes, with 0.76% of the assembly masked by RepeatMasker. We constructed a high density genetic map of 12 linkage groups with genotype data from 6,381 high quality Genotyping-by-Sequencing markers and 253 progeny from the cross. We anchored 97.8% (42.2 Mb) of the total assembly onto the 12 linkage groups, corresponding to the 12 chromosomes present in each parent species. Despite the high similarity and colinearity of these two species’ genomes, we detected several divergent regions that might play important roles in the species’ phenotypic differentiation and plant pathogenicity. The genetic map and genome assembly also provide valuable resources for further studies on the genomics and biology of Fusarium fungi.