Lifestyle, mating type and mitochondrial genome features of the plant pathogen Calonectria hawksworthii (Hypocreales, Nectriaceae) as revealed by genome analyses

Authors: Salgado-Salazar, Catalina; ROMBERG, MEGAN - Animal And Plant Health Inspection Service (APHIS); BLOMQUIST, CHERYL - California Department Of Food And Agriculture; NUNZIATA, SCHYLER - Animal And Plant Health Inspection Service (APHIS); CAI, WEILI - North Carolina State University; RIVERA, YAZMIN - Animal And Plant Health Inspection Service (APHIS)

Submitted to: Canadian Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/6/2022
Publication Date: 5/6/2022
Citation: Salgado-Salazar, C., Romberg, M., Blomquist, C., Nunziata, S., Cai, W., Rivera, Y. 2022. Lifestyle, mating type and mitochondrial genome features of the plant pathogen Calonectria hawksworthii (Hypocreales, Nectriaceae) as revealed by genome analyses. Canadian Journal of Plant Pathology. https://doi.org/10.1080/07060661.2022.2065534.
DOI: https://doi.org/10.1080/07060661.2022.2065534

Interpretive Summary: The genus Calonectria (family Nectriaceae) represents many destructive fungal plant pathogens with a worldwide distribution. Pathogenic species in this genus affect more than 335 plant including agricultural, horticultural and forestry crops. Given the importance of Calonectria as plant pathogen, relatively few completed genomes have been generated and analyzed for this group of fungi. This study generated and analyzed high quality genome sequences for a Calonectria hawksworthii isolate associated with avocado grafting seedlings in California found for the first time in the United States. This is the first genome to be completed for this species. This research will be useful for mycologists and plant pathologists to develop quick and efficient assays for its targeted detection, to understand pathogenicity and to develop strategies to control the spread and prevent the economic and societal losses associated with Calonectria diseases.

Technical Abstract: In June 2019, fungal necrotic spots were observed on the cotyledons of grafted avocado (Persea americana) grafting seedlings originating from a nursery in Ventura County, California. Morphology and comparison of DNA sequences from eight loci identified the fungal isolate as Calonectria hawksworthii, a species in the Nectriaceae not yet recorded in the U.S. Calonectria hawksworthii is a necrotrophic fungal pathogen in the C. cylindrospora species complex, and while most species in this group are found associated with Eucalyptus trees, the type host for C. hawksworthii was waterlilies (Nelumbo nucifera). In this study, the C. hawksworthii genome was sequenced using Illumina technologies. The draft assembly of 64.8 Mb contained 18,703 predicted gene models of which 70% could be assigned to a GO functional category. The mating type loci indicated this species is heterothallic. Approximately 3.79% of the draft genome consists of transposable elements (TE), and close to 36% of the predicted proteins were homologous to those known to be involved in pathogenicity in other fungal species. The C. hawksworthii genome displays elements typical of a necrotrophic lifestyle based on the composition of predicted genes encoding for carbohydrate-active enzymes, number of predicted secretory proteins including effectors, secondary metabolite biosynthesis clusters and cytochrome oxidase P450 (CYP) genes. The annotated mitochondrial genome was found to be 35.7 kb with very few intra or intergenic introns. This report constitutes the first draft genome of a Calonectria species belonging to the C. cylindrospora species complex, as well as the first report of C. hawksworthii species occurring in the United States on avocado. This study to increase our understanding of basic genetics, evolutionary mechanisms, and molecular physiology of necrotrophic and heterothallic Calonectria species and related plant pathogenic fungi.