Complete genome sequence of Agrobacterium fabrum strain 1D159

Authors: HUO, NAXIN - University Of California, Davis; Gu, Yong; McCue, Kent; ALABED, DIAA - Former ARS Employee; Thomson, James - Jim

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/16/2019
Publication Date: 5/9/2019
Citation: Huo, N., Gu, Y.Q., McCue, K.F., Alabed, D., Thomson, J.G. 2019. Complete genome sequence of Agrobacterium fabrum strain 1D159. Microbiology Resource Announcements. 8(19):e00207-19. https://doi.org/10.1128/MRA.00207-19.
DOI: https://doi.org/10.1128/MRA.00207-19

Interpretive Summary: This work reports the draft genome of a unique strain of the microbial plant pathogen Agrobacterium tumefaciens that is commonly used for plant genetic engineering. The assembled genome is composed of two chromosomes of 2,861,352 bp and 2,058,040 bp, and two plasmids of 519,735 bp and 223,394 bp. The non-engineered strain is capable of producing small gall-like structures on citrus and has the ability to transform plant cells with DNA sequences containing the appropriate regulatory sequences. This 1D159 strain, originally isolated by researchers from the University of California, Davis may provide a basis for improving upon existing methodology for citrus genetic engineering.

Technical Abstract: Here we present the novel genome from Agrobacterium tumefaciens str. 1D159 obtained from Dr. Kobe’s microbe collection at UC Davis. This bacterium and has been deposited at ATCC as strain #27912. Strain 1D159 was obtained from soil around a gall-containing peach tree by the Kobe lab July 25th, 1969. Characterization of the 1D159 showed it to be pathogenic (gall forming) on sunflower. Further characterization by our lab demonstrated gall formation by 1D159 in citrus tissue and the ability transfer a binary plasmid derived T-DNA producing DSRed expressing in the tissue. The strain was grown in Luria Broth at 28-30oC shaking at 200 RPM. Genomic DNA isolated was used for PacBio sequencing to generate 4 polished contigs with N50 contig length of 2,890,282 bp and sum of contig lengths 5,726,826 bp. The linear DNA was manually circularized via chimeric overlap of 28,929 bp for the circular chromosome which has a final composition of 2,861,352 bp with a GC content of 59.6% (367 subsystems, 2,868 coding sequences and 50 rRNA genes). The linear chromosome was determined to be 2,058,040 bp with a GC content of 59.7% (157 subsystems, 1,896 coding sequences and 20 rRNA genes). The DNA was manually circularized via a chimeric overlap of 21,281 bp for the AT plasmid giving a composition of 519,735 bp with a GC content of 57.5% (43 subsystems, 676 coding sequences and 0 rRNA) and a chimeric overlap of 14,144 bp for the virulence vector pTi-1D159 providing a 223,394 bp with a GC content of 56.9% (21 subsystems, 239 coding sequences and 0 rRNA genes) final sequence.