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

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.