Comparative genomics reveal processes implicated in host-specificity in species within the American clade of the Fusarium fujikuroi species complex

Abstract

Species in the Fusarium fujikuroi species complex (FFSC) comprise some of the most socio-economically important pathogens globally. Many of these fungi have genomic sequence data available, with some even assembled to chromosome level. In this study, we investigated the molecular basis of host-specificity by comparing the genomes of species associated with Pinus species (i.e., F. circinatum FSP34, F. pininemorale CMW 25243 and F. fracticaudum CMW 25245) and members of Poaceae (i.e., F. temperatum CMW 40964, F. subglutinans NRRL 22016 and F. konzum NRRL 11616). Genes common and unique to the two sets of species were identified and subjected to functional annotation. A total of 11 850 genes were shared amongst the six species, while 72 and 47 genes were unique to the respective sets of genomes. These two sets were enriched for genes implicated in carbohydrate and protein metabolism. Phylogenetic analysis of the unique genes suggested various evolutionary origins, indicating that they were acquired over time from numerous sources. This study found that the frequency distribution of unique genes differed significantly between telomeric and non-telomeric regions and that some tended to cluster together or were located close to another cluster. An instance of chromosome length polymorphism was found for chromosome 12. Chromosome 12 of F. temperatum CMW 40964 was larger than that of F. circinatum FSP34 and possessed more unique genes, which are potentially involved in niche-specificity amongst Fusarium species associated with Poaceae. These findings demonstrate the different molecular mechanisms employed by these Fusarium species to infect, inhabit and cause disease on their respective plant hosts.