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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Research Project #441826

Research Project: Omics-Based Approach to Detection, Identification, and Systematics of Plant Pathogenic Phytoplasmas and Spiroplasmas

Location: Molecular Plant Pathology Laboratory

Project Number: 8042-22000-320-000-D
Project Type: In-House Appropriated

Start Date: Feb 26, 2022
End Date: Feb 26, 2027

Objective 1: Enhance understanding of the genetic diversity of plant pathogenic mollicutes (phytoplasmas and spiroplasmas) and their interactions with host plants through genomic, transcriptomic, and metabolomic studies. (NP303, C1, PS1A, PS1B) Objective 2: Identify molecular markers involved in pathogen genetic diversity, niche adaptation, and pathogenicity. (NP303, C1, PS1A, PS1B) Sub-objective 2.A: Identify genus-, species-, and lineage-specific multi-locus genomic markers of diverse phytoplasmas associated with diseases of domestic and international importance. Sub-objective 2.B: Explore and evaluate redox, hormonal, and metabolic markers of pathogenesis for earlier detection and enhanced identification of diverse mollicutes. Objective 3: Devise new and improved diagnostic tools for the detection and identification of exotic, emerging, and evolving phytoplasmas. (NP303, C1, PS1A, PS1B) Sub-objective 3.A: Devise rapid and sensitive phytoplasma detection and identification protocols based on pathogen species- and lineage-specific genomic markers. Sub-objective 3.B: Devise biosensors for early disease diagnosis based on host redox, hormonal, and metabolic signals. Objective 4: Expand multi-locus and whole-genome sequence information-based classification and systematics of phytoplasmas and spiroplasmas. (NP303, C1, PS1A, PS1B) Sub-objective 4.A: Construct a multi-locus sequence typing (MLST)-based phytoplasma classification scheme and establish a whole-genome sequence information-based operational metrics for phytoplasma species delineation. Sub-objective 4.B: Identify genomic features correlated with divergent evolutionary trajectories of plant pathogenic spiroplasmas at differing levels of taxonomic rank.

The proposed project unites physiology, molecular biology, and genomics in synergistic multidisciplinary research. The goal is to discover and utilize new knowledge to devise and develop new, improved technologies to detect, identify, and classify wall-less bacteria (mollicutes), (noncultivable) phytoplasmas and (cultivable) spiroplasmas that cause economically important plant diseases. The project will discover gene markers of previously unknown phytoplasmas; new strains will be incorporated into our classification scheme, forming new phylogenetic groups, and we will describe/name the new taxa. Small genomes, and evolutionary loss of metabolic functions, make mollicutes ideal models for comparative genomics. Comparative genomics will elucidate genotypic events in the evolution of phytoplasmas and spiroplasmas, and will help establish molecular markers at differing levels of taxonomic rank. Spiroplasma genus-universal and species-specific gene markers will be identified to facilitate spiroplasma identification, and established spiroplasma species will serve as models to distinguish putative species and genera of phytoplasmas. Investigation of physiological and metabolic signals, and gene pathways regulating the oxidative (redox) and hormonal status, will open new avenues for early phytoplasma disease diagnosis - possibly before symptoms appear - and for control of redox sensitive plant pathogenic mollicutes. We will devise a scheme of combined rRNA-ribosomal protein-secY gene sequences to classify closely related phytoplasma strains, and will expand our online program for computer-assisted phytoplasma classification to accommodate automated analysis of diverse functional classes of genes. The new knowledge gained and technologies and tools devised will advance fundamental science, strengthen applied research, enhance disease management, and improve implementation of quarantine regulations worldwide.