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Title: Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and aggressiveness on Medicago truncatula

item LU, YOU - University Of Minnesota
item ISHIMARU, CAROL - University Of Minnesota
item GLAZEBROOK, JANE - University Of Minnesota
item Samac, Deborah - Debby

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/22/2017
Publication Date: 1/16/2018
Citation: Lu, Y., Ishimaru, C.A., Glazebrook, J., Samac, D.A. 2018. Comparative genomic analyses of Clavibacter michiganensis subsp. insidiosus and aggressiveness on Medicago truncatula. Phytopathology. 108:172-185.

Interpretive Summary: Bacterial wilt of alfalfa occurs throughout most alfalfa growing regions worldwide and for this reason the pathogen is considered a phytosanitary risk for international seed movement. Despite its importance in crop production, very little is known about the pathogen. To bridge this gap in knowledge, the complete genome sequence of three isolates the pathogen was compared to previously sequenced genomes of related bacteria causing disease in potato, tomato, and corn. The three isolates were also used to identify accessions of barrel medic that are susceptible or resistant to the disease. Genes unique to the alfalfa pathogen were identified in the chromosome and plasmids. The isolate causing the weakest disease symptoms was found to have lost 35,000 base pairs of chromosomal sequence as well as plasmid DNA. The information generated will be useful in developing specific assays for identifying highly virulent strains of the pathogen and for gaining an understanding of the mechanisms promoting disease. The plant accessions can be used for gaining an understanding of mechanisms of disease resistance. Improved assays and disease resistant germplasm will facilitate international seed movement and extend alfalfa stand life and productivity.

Technical Abstract: Clavibacter michiganensis is the most economically important gram-positive bacterial plant pathogen with subspecies that cause serious diseases of maize, wheat, tomato, potato, and alfalfa. Much less is known about pathogenesis involving gram-positive plant pathogens than is known for gram-negative bacteria. Comparative genome analyses of C. michiganensis subspecies affecting tomato, potato, and corn have provided insights on pathogenicity. In this study, we identified strains of C. michiganensis subsp. insidiosus with contrasting aggressiveness on three accessions of the model legume Medicago truncatula. We generated complete genome sequences for two strains and compared these to a previously sequenced strain and genome sequences of four other subspecies. The three C. michiganensis subsp. insidiosus strains varied in gene content due to genome rearrangements, most likely facilitated by insertion elements, and plasmid number, which varied from one to three depending on strain. The core C. michiganensis genome consisted of 1,930 genes, with 401 genes unique to C. michiganensis subsp. insidiosus. An operon for synthesis of the extracellular blue pigment indigoidine, enzymes for pectin degradation, and an operon for inositol metabolism are among the unique features. Secreted serine proteases belonging to both the pat-1 and ppa families were present but highly diverged from those in other subspecies.