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United States Department of Agriculture

Agricultural Research Service

Research Project: Enhanced Alfalfa Germplasm and Genomic Resources for Yield, Quality, and Environmental Protection

Location: Plant Science Research

Title: Complete genome sequence of Clavibacter michiganensis subsp. insidiosus

item Lu, You
item Samac, Deborah - Debby
item Ishimaru, Carol
item Glazebrook, Jane

Submitted to: American Phytopathological Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/12/2014
Publication Date: 8/9/2014
Citation: Lu, Y., Samac, D.A., Ishimaru, C.A., Glazebrook, J. 2014. Complete genome sequence of Clavibacter michiganensis subsp. insidiosus. American Phytopathological Society Annual Meeting. August 9-13, 2014, Minneapolis, MN. Available:

Interpretive Summary:

Technical Abstract: Clavibacter michiganensis subsp. insidiosus (Cmi) causes bacterial wilt disease of alfalfa (Medicago sativa L.) and can also infect the model legume plant M. truncatula. The virulence mechanisms of Cmi are yet to be identified, hampered by the lack of efficient mutagenesis tools as well as by the lack of a reference genome sequence. Here we describe use of Illumina sequencing to obtain the complete genome sequence of one Cmi field isolate from Minnesota, Cmi R1-1. Cmi R1-1 has a genome average G+C content of 73%, which is similar to other sequenced subspecies of C. michiganensis. The genome of Cmi R1-1 is comprised of one presumably circular chromosome of 3,206 kbp and two circular plasmids, pCI1 and pCI2, of 48 kbp and 153 kbp, respectively. pCI2 appears to be required for virulence, as sequencing of an avirulent strain, Cmi ATCC10253, revealed the loss of this plasmid. Cmi R1-1 has 23 copies of the repetitive insertion element IS1122 in the chromosome and two copies on each of the plasmids. Whole genome rearrangement events compared to C. michiganensis subsp. michiganensis were detected at four of the IS1122 loci. A total of 3,355 genes are predicted from the genome of Cmi R1-1. Reciprocal BLAST analysis between subspecies of C. michiganensis reveals that many genes are unique to Cmi. These Cmi unique genes are candidates for identifying virulence factors contributing to colonization and symptom development of Cmi infecting alfalfa.

Last Modified: 06/25/2017
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