Uncovering the fungus responsible for basal stem and root rot of false indigo in the United States: pathogen identification, new disease description, and genome analyses

Authors: Harrigian, Fiona; Leblanc, Nicholas; Eriksen, Renee; BUSH, ELIZABETH - Virginia Tech; RODRIGUEZ-SALAMANCA, LINA - Virginia Tech; Salgado-Salazar, Catalina

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/29/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: The fungal genus Calonectria includes many destructive plant pathogens world wide with more than 300 plant hosts including agricultural, horticultural, and forestry crops affected. This research focused on the molecular identification, pathogenicity and genome analysis of a Calonectria isolate recovered from ornamental blue false indigo (Baptisia australis) plants showing disease symptoms of crown and root rot in a commercial nursery in Virginia. This is the first report of this fungus causing a disease on this ornamental host. Resources generated will be useful for mycologists and plant pathologists in the development of quick and efficient assays for its detection, understanding pathogenicity, developing strategies to control its spread and to prevent the economic losses to nursery growers and the public.

Technical Abstract: Calonectria spp. are most well known as pathogens of Eucalyptus but also can infect other forestry crops, legumes like soybean and peanut, and ornamentals. Calonectria pathogens of ornamental plants are not well characterized or understood, though they have been widely documented as an issue in the ornamental industry. This study characterized Calonectria sp. 134-2022, originally isolated from diseased cuttings of the perennial ornamental legume Baptisia australis. Calonectria sp. 134-2022 was initially identified using multilocus sequencing and phylogenetics. In addition, a high-quality hybrid genome assembly was generated using Illumina and Nanopore sequencing and annotated to identify putative virulence and pathogenicity factors. Pathogenicity of Calonectria sp. 134-2022 was confirmed using Koch’s postulates in a series of controlled growth chamber experiments. Multilocus sequencing and phylogenetics identified the original fungal isolate from B. australis as Calonectria fujianensis, a member of the C. colhounii species complex. The genome assembly was 62.7 Mb and composed of 16 contigs, four of which were complete chromosomes. A total of 750 effectors were found in the genome, many sharing similar annotations of known cutinase and pectinase virulence factors in other Calonectria genomes. Inoculation of B. australis lead to symptoms of root and crown rot and foliar wilting. Recovered fungal isolates produced similar disease symptoms and were confirmed as the same organism based on DNA sequencing of two genetic markers. Characterization of this novel disease of B. australis advances our understanding of Calonectria spp. as an important but poorly studied group of plant pathogens.