Kassaye Belay (he/him/his)
School of Plant and Environmental Sciences and Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, U.S.A
Blacksburg, VA, USA
Sahar Abdelrazek
Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Devin Bily
VDACS Office of Plant Industry
Richmond, Virginia, United States
Tashi Gyatso
Virginia Department of Agriculture and Consumer Services
Richmond, Virginia, United States
Farhat Avin, n/a
Researcher
Otis L. Floyd Nursery Research Center, Tennessee State University,
McMinnville, Tennessee, United States
Prabha Liyanapathiranage, PhD
State Plant Pathologist
Tennessee Department of Agriculture
Nashville, Tennessee, United States
Lina Rodriguez Salamanca
School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A.
Blacksburg, Virginia, United States
Fulya Baysal-Gurel, n/a
Associate Professor
Tennessee State University, Otis L. Floyd Nursery Research Center, Department of Agriculture Sciences and Engineering
McMinnville, TN, USA
Boris A. Vinatzer
Professor
School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061
Blacksburg, Virginia, United States
Vascular streak dieback (VSD), caused by Ceratobasidium theobromae (Ct), is a fungal disease, primarily affecting cacao in Southeast Asia. In the Mid-Atlantic U.S., a closely related species, Ceratobasidium sp. (Csp) was recently detected in multiple woody ornamental species with VSD-like symptoms. This is concerning since woody ornamentals play a crucial role in the landscaping industry, habitat restoration, and ecological conservation. Because Csp is fastidious, culture-independent metagenomic sequencing was used to assess the genetic diversity of Csp and to determine its evolutionary relationships with Ct. Sequencing was conducted using the PromethION long-read platform on 113 samples of vascular tissue of symptomatic plants that had tested positive for Csp by PCR or of mycelium growing out from symptomatic tissue of 25 species collected in four states. After removing plant sequences, Csp was identified with an abundance ranging from 0.08% to 86%. Genome assembly resulted in 17 high-quality genomes with an average size of 34 Mb. A core genome phylogeny revealed that the Csp sequences have limited genetic variation and are closely related to, but distinct from, Southeast Asian Ct sequences, which suggests recent introduction into the U.S. Comparative pangenome analysis identified genes with putative roles in host specificity and environmental adaptation. This study shows the potential of metagenomics to obtain whole genomes of fastidious fungal pathogens and gain insights into biology and evolution of emerging pathogens even when obtaining pure cultures is impossible.