Improved genome ofAgrobacterium radiobactertype strain provides new taxonomic insight intoAgrobacteriumgenomospecies 4

Abstract

The reportedAgrobacterium radiobacterDSM 30174Tgenome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced theAgrobacterium radiobactertype strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome ofAgrobacterium tumefaciensB6T, enabling for the first time, a proper comparative genomics of these contentiousAgrobacteriumspecies. We provide concrete evidence that the previously reportedAgrobacterium radiobactertype strain genome (Accession Number:ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose thatAgrobacterium tumefaciensbe reclassified asAgrobacterium radiobactersubsp.tumefaciensand thatAgrobacterium radiobacterretains it species status with the proposed name ofAgrobacterium radiobactersubsp.radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of bothAgrobacterium radiobacterandAgrobacterium tumefaciensinto a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates thatAgrobacterium radiobacterNCPPB3001 is sufficiently divergent fromAgrobacterium tumefaciensto propose two independent sub-clades. Third,Agrobacterium tumefaciensdemonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively thanAgrobacterium radiobacter.