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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #386381

Research Project: Identification of Novel Management Strategies for Key Pests and Pathogens of Grapevine with Emphasis on the Xylella Fastidiosa Pathosystem

Location: Crop Diseases, Pests and Genetics Research

Title: Complete genome resources for Xylella fastidiosa strains AlmaEM3 and BB08-1 reveal prophage-associated structural variation among blueberry-infecting strains

item O'Leary, Michael
item ARIAS-GIRALDO, LUIS - Institute For Sustainable Agriculture
item Burbank, Lindsey
item DE LA FUENTE, LEONARDO - Auburn University
item LANDA, BLANCA - Institute For Sustainable Agriculture

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/22/2021
Publication Date: 3/9/2022
Citation: O'Leary, M.L., Arias-Giraldo, L., Burbank, L.P., De La Fuente, L., Landa, B. 2022. Complete genome resources for Xylella fastidiosa strains AlmaEM3 and BB08-1 reveal prophage-associated structural variation among blueberry-infecting strains. Phytopathology. 112(3):732-736.

Interpretive Summary: Xylella fastidiosa is a plant pathogenic bacteria that causes disease on numerous agricultural hosts, including almond, citrus, grape, and olive. Some strains of Xylella fastidiosa, belonging to subspecies fastidiosa and multiplex, cause blueberry leaf scorch disease in the Southeastern United States (i.e., Alabama, Florida, Georgia, and Louisiana). However, very few genomic resources are available for blueberry-infecting Xylella fastidiosa strains. The few existing genome assemblies are relatively low contiguity or quality, potentially impacting comparative studies among blueberry-infecting strains or between these strains and others that do not cause disease on blueberry. This report describes complete, high-quality genome assemblies for two blueberry-infecting Xylella fastidiosa subspecies multiplex strains, and identifies additional genetic variation that further distinguishes these two strains.

Technical Abstract: Xylella fastidiosa is a gram-negative plant pathogenic bacterium with wide distribution and host range. X. fastidiosa strains are separated into genetically distinct subspecies, and further categorized into sequence types (ST). Genetic characterization of X. fastidiosa strains infecting blueberry has implicated strains of subspecies multiplex, and recently subspecies fastidiosa, as capable of causing blueberry leaf scorch disease under field conditions; furthermore, several blueberry-infecting strains likely originated as inter-subspecific recombinants between subspecies fastidiosa and multiplex strains. To better elucidate the relationships among blueberry-infecting X. fastidiosa subsp. multiplex strains, we completed the genomes of an ST 42 strain, AlmaEM3, and an ST 43 strain, BB08-1, using a hybrid assembly approach. Comparison of these assemblies reveals a large (0.95 Mb) chromosomal inversion in BB08-1 relative to AlmaEM3 and the reference strain M12, likely resulting from recombination between prophage regions.