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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #367387
Research Project: Molecular Genetic Tools Advancing the Application of Biotechnology for Crop Improvement

Location: Crop Improvement and Genetics Research

Title: Draft genome sequence of Agrobacterium tumefaciens strain 1D1526

Author
item HUO, NAXIN - University Of California, Davis
item Gu, Yong
item McCue, Kent
item ALABED, DIA - Former ARS Employee
item Thomson, James - Jim

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/16/2019
Publication Date: 11/7/2019
Citation: Huo, N., Gu, Y.Q., Mc Cue, K.F., Alabed, D., Thomson, J.G. 2019. Draft genome sequence of Agrobacterium tumefaciens strain 1D1526. Microbiology Resource Announcements. 8(45). https://doi.org/10.1128/MRA.01084-19.
DOI: https://doi.org/10.1128/MRA.01084-19

Interpretive Summary: This work reports the annotated genome sequence of Agrobacterium tumefaciens str. 1D1526. The assembled genome is composed of a circular chromosome, a linear chromosome, and an unincorporated 44,582 base pair sequence. The 1D1526 strain does not appear competent to form galls, consistent with the genome lacking the presence of disease-causing Ti virulence plasmid.

Technical Abstract: Here we present the novel genome from Agrobacterium tumefaciens strain 1D1526 obtained from the Kobe microbe collection at UC Davis. Strain 1D1526 was obtained from an apple tree gall on July 11th, 1982. There was no further characterization of 1D1526 by the Kobe lab to indicate whether it was pathogenic (crown gall disease forming) or not. To determine if Agrobacterium tumefaciens strain 1D1526 can cause crown gall disease, our lab co-cultivated the strain with citrus tissue; however, the tissue failed to produce galls. We sequenced and assembled the 1D1526 genome and entered it into the National Center for Biotechnology Information (NCBI) database. Automated annotation was performed by the Rapid Annotation Using Subsystem Technology (RAST) Pipeline for annotation of the genome. Agrobacterium tumefaciens str. 1D1526 contains 4,935 predicted coding sequences, 536 subsystems and 65 predicted RNA-coding genes as curated by SEED data (http://theSEED.org). Genomic comparisons with RAST show that the 1D1526 circular chromosome is closely related to Agrobacterium tumefaciens str. CCNWGS0286 genome while the 1D1526 linear chromosome is most closely related to Agrobacterium tumefaciens str. C58 genome. DNA matrix analysis of assembled contigs were also compared to the C58 circular and linear chromosome sequences (AE007869 and AE007870) with MacVector (version 17.0.0).