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The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402. Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid
  • Marjolein Hooykaas,
  • Paul Hooykaas
Marjolein Hooykaas
Leiden University
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Paul Hooykaas
Leiden University
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Abstract

We report here the complete genome sequence of the Rhizobium rhizogenes (formerly Agrobacterium rhizogenes) strain LBA9402 (NCPPB1855rifR), a pathogenic strain causing hairy root disease. In order to assemble a complete genome we obtained short-reads from Illumina sequencing as well as long-reads from Oxford Nanopore Technology sequencing. The genome consists of a 3,958,212 bp chromosome, a 2,005,144 bp chromid (secondary chromosome) and a 252,168 bp Ri plasmid (pRi1855), respectively. The primary chromosome was very similar to that of the avirulent biocontrol strain K84, but the chromid showed a 724 kbp deletion accompanied by a large 1.8 Mbp inversion revealing the dynamic nature of these secondary chromosomes. The sequence of the agropine Ri plasmid was compared to other types of Ri and Ti plasmids. Thus we identified the genes responsible for agropine catabolism, but also a unique segment adjacent to the TL-region that has the signature of a new opine catabolic gene cluster including the three genes that together encode an opine dehydrogenase. Our sequence analysis also revealed a novel gene at the very right end of the TL-DNA, which is unique for the agropine Ri plasmid. The protein encoded by this gene was most related to the succinamopine synthases of chrysopine and agropine Ti plasmids and thus may be involved in synthesis of the unknown opine that can be degraded by the adjacent catabolic cluster. The available sequence will facilitate the use of R. rhizogenes and especially LBA9402 in both the laboratory and for biotechnological purposes.

Peer review status:ACCEPTED

04 Jan 2021Submitted to MicrobiologyOpen
05 Jan 2021Submission Checks Completed
05 Jan 2021Assigned to Editor
12 Jan 2021Reviewer(s) Assigned
15 Feb 2021Review(s) Completed, Editorial Evaluation Pending
15 Feb 2021Editorial Decision: Revise Major
24 Feb 20211st Revision Received
25 Feb 2021Submission Checks Completed
25 Feb 2021Assigned to Editor
25 Feb 2021Review(s) Completed, Editorial Evaluation Pending
25 Feb 2021Reviewer(s) Assigned
27 Feb 2021Editorial Decision: Accept