Uncovering the Fungus Responsible for Stem and Root Rot of False Indigo: Pathogen Identification, New Disease Description, and Genome Analyses

<i>Calonectria</i> spp. can cause destructive diseases on forestry crops, legumes like soybean and peanut, and ornamentals. Species of <i>Calonectria</i> affecting ornamental plants are not well characterized or understood, although they have been widely documented as an issue in the ornamental industry. This research focused on the molecular identification, pathogenicity validation, and genome analysis of a <i>Calonectria</i> sp. isolate recovered from ornamental blue false indigo (<i>Baptisia australis</i>) plants showing disease symptoms of crown and root rot in a commercial nursery in Virginia. The fungus on <i>B. australis</i> was identified as <i>C. fujianensis</i> (Nectriaceae, Hypocreales), a member of the <i>C. colhounii</i> species complex, using multilocus sequencing. Pathogenicity tests were fulfilled by inoculating <i>C. fujianensis</i> conidia on <i>B. australis</i> seedlings, confirming a causal relationship between this pathogen and the disease symptoms observed. A 62.7 Mb high-quality hybrid genome assembly generated using Illumina and Nanopore data was obtained, contained in 16 contigs, 4 of which were complete chromosomes. A total of 750 effectors were found in the genome, similar to cutinase and pectinase virulence factors described from other <i>Calonectria</i> species' genomes. Characterization of this novel disease of <i>B. australis</i> advances our understanding of <i>Calonectria</i> as an important but poorly studied group of plant pathogens.