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

Gan, Han Ming, Lee, Melvin VL and Savka, Michael A 2019, Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4, PeerJ, vol. 7, pp. 1-23, doi: 10.7717/peerj.6366.

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Title Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4
Author(s) Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Lee, Melvin VL
Savka, Michael A
Journal name PeerJ
Volume number 7
Article ID e6366
Start page 1
End page 23
Total pages 23
Publisher PeerJ Inc.
Place of publication Corte Madera, Calif.
Publication date 2019
ISSN 2167-8359
Keyword(s) Agrobacterium
Agrobacterium radiobacter
Agrobacterium tumefaciens
Average nucleotide identity
Lipopolysaccharide
Phylogenomics
Ti plasmid
Type strain
Summary 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.
Language eng
DOI 10.7717/peerj.6366
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2019, Gan et al.
Persistent URL http://hdl.handle.net/10536/DRO/DU:30119919

Document type: Journal Article
Collections: School of Life and Environmental Sciences
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