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ARS Home » Northeast Area » Frederick, Maryland » Foreign Disease-Weed Science Research » Research » Publications at this Location » Publication #409529
Research Project: Discovery and Development of Microbial-Based Biological Control Agents for Use Against Invasive Weeds in the United States

Location: Foreign Disease-Weed Science Research

Title: Genomic features of the host-specific fungal biocontrol agent Ramularia crupinae approved for the management of the federally noxious weed Crupina vulgaris.

Author
item Tancos, Matthew
item Fulcher, Michael

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/26/2023
Publication Date: 11/29/2023
Citation: Tancos, M.A., Fulcher, M.R. 2023. Genomic features of the host-specific fungal biocontrol agent Ramularia crupinae approved for the management of the federally noxious weed Crupina vulgaris. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-10-23-0138-SC.
DOI: https://doi.org/10.1094/PHYTOFR-10-23-0138-SC

Interpretive Summary: A reference genome for the host-specific fungal pathogen, Ramularia crupinae, was developed and compared with closely related fungal pathogen species. Ramularia crupinae was recently approved for the management of the foreign weed common crupina, which has invaded thousands of acres of grasslands in the western United States. Developing a high-quality genome and identifying unique proteins and toxins that aid infection are crucial to understanding how R. crupinae infects its weed host, while also providing genomic insights into this poorly studied fungal group.

Technical Abstract: Ramularia crupinae is a novel host-specific fungal pathogen of the invasive rangeland weed common crupina (Crupina vulgaris). The foliar and stem blighting pathogen was originally identified in France and has been approved by the United States Department of Agriculture – Animal and Plant Health Inspection Service as the first biological control agent for the management of common crupina in the western United States. In this study, a chromosome-level genome assembly of R. crupinae 00-010 was performed using PacBio sequencing technology. The assembly had a total size of 37.9 Mb distributed across 14 (telomere to telomere) chromosomes, with a GC content of 47.6%. The genome encoded 10,159 protein-coding genes with 890 predicted secreted proteins that comprised both unique and conserved canonical pathogen effectors. Genome comparisons with closely related pathogen species in the family Mycosphaerellaceae demonstrated family-wide orthologous effector groups and Ramularia specific orthogroups. This new reference sequence is a valuable genomic tool that will assist in characterizing Ramularia-Crupina interactions and increase our understanding of Ramularia pathogenicity on both crops and weeds.