Genomic and Transcriptomic Analyses Reveal Mechanisms Associated with Pathogenesis of <i>Fusarium annulatum</i> and <i>F. commune</i> in Nursery-Grown Conifer Seedlings

In this study, we used coniferous and non-coniferous hosts to assess pathogenicity of a <i>Fusarium annulatum</i> isolate derived from southwestern white pine (<i>Pinus strobiformis</i>), along with <i>F. commune</i> isolates derived from coniferous and herbaceous, non-conifer hosts. All isolates of both <i>Fusarium</i> spp. were found to be pathogenic to conifer hosts. For the tested non-coniferous hosts, <i>F. commune</i> isolates were found pathogenic to both rice and tomato, while <i>F. annulatum</i> was only found pathogenic to rice. To investigate the molecular basis of pathogenicity, we identified differentially expressed pathogenicity-/virulence-associated genes by inoculating loblolly pine (<i>P. taeda</i>) seedlings with isolates of conifer-derived <i>F. commune</i> (collected from ponderosa pine [<i>P. ponderosa</i>]) and <i>F. annulatum</i> (collected from southwestern white pine), which were all previously confirmed pathogenic to loblolly pine in our assays. Seedlings were harvested at 12-, 24-, and 48-hours post-inoculation for transcriptomic analyses to identify pathogen genes associated with early infection of the host. Among the upregulated in planta (UIP) genes, we identified putative pathogenicity-/virulence-associated genes including secreted effectors, secondary metabolite gene clusters involved in mycotoxin biosynthesis, and carbohydrate-active enzymes. To identify putative conifer pathogenicity profiles of these potential conifer pathogens, we compared these UIP genes with the predicted proteomes of 17 conifer-associated <i>Fusarium</i> spp. isolates. While these putative pathogenicity profiles did not definitively correspond with pathogenicity on coniferous versus herbaceous hosts, but rather aligned with <i>Fusarium</i> species complexes. A subset of these shared UIP genes may aid in the development of detection methods for conifer-specific pathogens based on <i>Fusarium</i> species complexes.