Crown gall disease caused by Agrobacterium tumefaciens is an important bacterial disease of blueberry affecting production worldwide. However, the lack of whole genome information for this important pathogen impedes genetic and molecular analysis of its pathogenic mechanism. Whole genome sequencing can reveal its function, provide a basis for studying its pathogenic mechanism, and further explore the relationship between pathogens and endophytic bacteria. In this study, the genome of A. tumefaciens L-11 isolated from the Yunnan Province was sequenced using Illumina sequencing and compared with other strains of A. tumefaciens 1D132, K84, and C58. The results showed the genome A. tumefaciens L-11 comprising a 2.9 Mb circular chromosome, a 2.02 Mb chain chromosome, 4 plasmids containing a 0.23 Mb Ti plasmid, GC content ratio of 59.0%, and a total size of 5.70 Mb. The genome was predicted to contain 5245 genes, 5377 CDS, 140 RNAs (54 tRNAs, 12 rRNAs, and 74 other RNAs), and no CRISPR structure was found. We gained insights into its evolutionary trajectory and virulence factors by performing a comparative genome analysis between A. tumefaciens L-11 and the other 3 strains. There were differences in chromosome number, plasmid number, GC content, and virulence factors between A. tumefaciens L-11 and other strains. These discoveries provide insight into the unique traits and evolutionary background of A. tumefaciens L-11. Crucially, the availability of this excellent genetic resource will act as a cornerstone for research into A. tumefaciens biology, molecular pathogenesis, and virulence. Furthermore, identifying any potential weaknesses in its genetic makeup will aid in developing more effective biocontrol strategies.
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