Insights gained into Vascular Streak Dieback, an Emerging Disease of Woody Ornamentals in the United States, using Metagenomic Sequencing

Summary Woody ornamentals are an integral part of home gardens and urban landscapes and are key to the economic vitality of the nursery industry. Movement of plants infected with emerging pathogens can quickly lead to wide geographic spread of new diseases impacting ecosystem health and leading to economic losses. Using metagenomic sequencing, we investigated the microbial species associated with vascular streak dieback (VSD), an emerging disease of woody ornamentals in the United States, analyzing 106 samples obtained from 34 different species in seven states. The fastidious fungal pathogen Ceratobasidium sp. ( Csp ), previously found to be associated with VSD, was the only putative pathogen consistently identified. Assembly of 17 high quality draft genomes followed by phylogenetic and pangenome analyses revealed Csp to form a tight genetic cluster closely related to, yet distinct in gene content, from genomes of Ceratobasidium theobromae , a pathogen of cacao, avocado, and cassava in Southeast Asia. These results reveal the unparalleled ability of metagenomics for identification and characterization of fastidious fungal pathogens and suggest the recent introduction of a single genetic lineage of Csp into the U.S., possibly from Southeast Asia, that is characterized by a wide host range and that quickly spread geographically.