Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4

PeerJ

article

Han Ming Gan¹  Melvin V.L. Lee³  Michael A. Savka⁴ 

[1] Deakin Genomics Centre, Deakin University;Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University;School of Science, Monash University Malaysia;College of Science, The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology

关键词: Type strain;    Average nucleotide identity;    Phylogenomics;    Agrobacterium radiobacter;    Agrobacterium tumefaciens;    Lipopolysaccharide;    Agrobacterium;    Ti plasmid;   

DOI  :  10.7717/peerj.6366

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.

【 授权许可】

CC BY