Genomic and transcriptomic comparisons of the twig blight pathogen, Passalora sequoiae with Mycosphaereallaceae foliar and conifer pathogens

Authors: DOBBS, JOHN - Colorado State University; CABALLERO, JORGE - Colorado State University; ATA, JESSA - Colorado State University; Babiker, Ebrahiem; Copes, Warren; STEWART, JANE - Colorado State University

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/6/2023
Publication Date: 4/5/2024
Citation: Dobbs, J.T., Caballero, J.R., Ata, J.P., Babiker, E.M., Copes, W.E., Stewart, J.E. 2024. Genomic and transcriptomic comparisons of the twig blight pathogen, Passalora sequoiae with Mycosphaereallaceae foliar and conifer pathogens. Phytopathology. 114:732-742. https://doi.org/10.1094/PHYTO-08-23-0271-R.
DOI: https://doi.org/10.1094/PHYTO-08-23-0271-R

Interpretive Summary: Passalora sequoiae is a fungus that causes severe needle blight on Leyland cypress trees that are sold in the Christmas tree and ornamental landscape tree markets. Fungicide sprays are the main control approach. The current fungicide spray programs are expensive and adequately effective only when disease pressure is low to moderate. A molecular approach was taken to develop new innovative disease control approaches. Whole genome and transcriptome analyses were conducted to better understand the mechanisms of pathogen virulence and host resistance. Relevant genes, gene clusters and enzymes were identified that were unique to P. sequoiae or common to related Mycosphaereallaceae needle blight and twig canker plant pathogens. This research is an important step to building genomic resources for a serious plant pathogen on Leyland Cypress and to develop valuable information for breeding Leyland cypress cultivars with resistance to the needle blight disease.

Technical Abstract: Passalora sequoiae is a foliar pathogen to conifer tree species. In this study, we conducted whole genome and transcriptome analyses on isolates of P. sequoiae collected from symptomatic Leyland Cypress leaves from a Christmas tree farm in Mississippi. The objectives for this research were to elucidate the pathogenicity mechanisms of P. sequoiae by characterizing the genome and transcriptome and possibly identify unique and shared predicted genes in comparison with non-conifer/canker and foliar pathogens in the Mycosphaereallaceae family. P. sequoiae was found to be similar to other foliar Mycosphaerellaceae pathogens and likely represents a hemibiotrophic lifestyle based on comparisons across pathogens. The genome and in planta transcriptome highlighted some unique features of P. sequoiae: the significant presence of chitin synthases and fructose degrading carbohydrate degrading enzymes, transAT-PKS genes, and antibiotic gene clusters that were unique to P. sequoiae compared to the other Mycosphaereallaceae species genomes. Several transcripts, which were highly expressed in planta, were identified as effectors, yet the functions were not characterized. These targets provide amble resources to continue to characterize pathogen-conifer host interactions in conifer foliar pathogens. Further, this research helps build genomic resources for an important plant pathogen on Leyland Cypress that will further our ability to develop novel management practices that could begin with breeding for resistance.