Whole-genome sequencing and comparative genomic analysis of Agrobacterium fabrum L-11 causing crown gall disease in blueberry.

BACKGROUND AND AIMS: Crown gall caused by Agrobacterium fabrum is a significant bacterial disease affecting blueberry production worldwide. However, the lack of whole-genome information for this pathogen impedes genetic and molecular analysis of its pathogenic mechanisms.

METHOD AND RESULTS: To address this knowledge gap, A. fabrum L-11 was isolated from blueberry-growing areas in Qujing City, Yunnan Province, and its genome was sequenced using the Oxford Nanopore platform. Additionally, a comparative genome analysis was conducted with strains of A. radiobacter K84, A. fabrum 1D132, and A. fabrum C58 to understand its pathogenic mechanism, evolutionary path, and virulence factors. The complete genome of A. fabrum L-11 is 5.70 Mb with a GC content of 59.0%, consisting of a 2.93 Mb linear chromosome, a 2.02 Mb circular chromosome, and four large plasmids ranging from 0.12 to 0.232 Mb (total plasmid content 0.743 Mb), an exceptional feature among Agrobacterium strains. The genome includes 5,385 genes, comprising 5,245 protein-coding sequences (CDS) and 140 RNA genes (54 tRNAs, 12 rRNAs, and 74 other non-coding RNAs). Functional annotation revealed significant enrichment in multiple metabolic pathways such as ABC transporters, amino acid biosynthesis, and carbon metabolism. The genome encodes a broad range of carbohydrate-active enzymes (CAZymes), including glycoside hydrolases and glycosyl transferases, indicating advanced capabilities in carbohydrate metabolism. A comparative genome study showed that A. fabrum L-11 differs from other strains in terms of virulence factors, GC content, chromosomal number, and plasmid count. Virulence factor analysis identified 1,071 potential virulence-related genes, including those associated with secretion systems, ABC transporters, and lipopolysaccharide production. With notable differences in opine usage compared to other strains, the Ti plasmid analysis revealed essential genes involved in virulence and tumor formation.

CONCLUSION: Agrobacterium fabrum L-11's comprehensive genome analysis offers valuable new insights into its metabolic abilities, pathogenicity mechanisms, and evolutionary links with other Agrobacterium species. This genetic information will serve as a foundation for research on host-pathogen interactions and assist in developing biocontrol strategies for crown gall disease in blueberries, leading to more effective disease management.