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Title: Sarcococca blight: Use of whole genome sequencing as a strategy for fungal disease diagnosis

item Wight-Malapi, Martha
item SALGADO-SALAZAR, CATALINA - Rutgers University
item Demers, Jill
item CLEMENTS, DAVID - Collaborator
item RANE, KAREN - University Of Maryland
item Crouch, Jo Anne

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/29/2016
Publication Date: 6/14/2016
Citation: Wight-Malapi, M., Salgado-Salazar, C., Demers, J.E., Clements, D., Rane, K., Crouch, J. 2016. Sarcococca blight: Use of whole genome sequencing as a strategy for fungal disease diagnosis. Plant Disease. 100(6):1093-1100.

Interpretive Summary: Each year, fungal diseases cause billions of dollars of damage to crop plants worldwide. Fast and accurate identification of disease-causing fungi - before the fungi can spread and infect new plants - is the first step used to reduce crop losses. In this research, we used a new technology, called next-generation genome sequencing, to identify the fungus causing a new disease of ornamental sarcococca plants. Although this technology is commonly used to identify plant viruses, human pathogens, and to diagnose human genetic disorders, this is the first time a fungal pathogen diagnosis has been made using next-generation genome sequencing. Use of this technology showed us that the sarcococca disease was caused by the same fungus that causes boxwood blight disease. The fungi infecting sarcococca and boxwood had almost identical DNA fingerprints, even though they came from different plants. This research is important in that it shows that this state-of-the-art technology can be used to quickly identify fungi. It also shows that the boxwood blight fungus is able to infect plants other than boxwood. This information will be important to researchers, diagnostic laboratories, nursery managers and regulatory agencies looking for ways to diagnose and control these and other plant diseases.

Technical Abstract: Early and accurate diagnosis of new plant pathogens is vital for the rapid implementation of effective mitigation strategies and appropriate regulatory responses. Most commonly, pathogen identification relies on morphology and DNA marker analysis. However, for new diseases, these approaches may not be sufficient for precise diagnosis. In this study, we used whole genome sequencing (WGS) to identify the causal agent of a new disease affecting Sarcococca hookeriana (sarcococca). Blight symptoms were observed on sarcococca and adjacent Buxus sempervirens (boxwood) plants in Maryland during 2014. Symptoms on sarcococca were novel, and included twig dieback and dark lesions on leaves and stems. Calonectria sp. was isolated from both hosts and used to fulfill Koch’s postulates, but morphology and marker sequence data precluded species-level identification. A 51.4-Mb WGS was generated for the two isolates, and identified both as C. pseudonaviculata. A single nucleotide polymorphism at a non-coding site differentiated between the two host isolates. These results indicate that the same C. pseudonaviculata genotype has the ability to induce disease on both plant species. This study marks the first application of WGS for fungal plant pathogen diagnosis and demonstrates the power of this approach to rapidly identify causal agents of new diseases.