Complete genome of Agrobacterium fabrum strain 1D1416

Authors: ALABED, DIA - Former ARS Employee; Huo, Naxin; Gu, Yong; Thomson, James - Jim

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2023
Publication Date: 6/20/2023
Citation: Alabed, D., Huo, N., Gu, Y.Q., Thomson, J.G. 2023. Complete genome of Agrobacterium fabrum strain 1D1416. Microbiology Resource Announcements. 12(7). https://doi.org/10.1128/mra.00264-23.
DOI: https://doi.org/10.1128/mra.00264-23

Interpretive Summary: This work reports the draft genome of Agrobacterium fabrum str. 1D1416. The assembled genome is composed of a 2,837,379 bp circular chromosome, 2,043,296 bp linear chromosome, 519,735 bp AT1 plasmid, 188,396 bp AT2 plasmid and a 196,706 bp Ti virulence plasmid. The wild non-disarmed strain produces gall-like structures in citrus tissue.

Technical Abstract: Here we present the novel genome from Agrobacterium fabrum str. 1D1416 obtained from Dr. Kado’s retired microbe collection at UC Davis. Strain 1D1416 was isolated from Euonymus japonicus and received by the Kado lab August 17th, 1979. The lyophilized strain was revived and grown in Luria Broth at 28-30oC shaking at 200 RPM. Characterization by the Kado lab indicates that the isolate was designated an agrobacterium based on a positive 3-keto-lactose test result. Further characterization by our lab demonstrated gall formation (pathogenicity) by 1D1416 to citrus tissue and the ability transfer a binary plasmid derived T-DNA producing DSRed expressing tissue. Binary plasmid and protocol used for citrus transformation previously published (1). The initial sequence was manually circularized via chimeric overlap of 28,929 bp for the circular chromosome and is composed of 2,837,379 bp with a GC content of 59.4%. The linear chromosome was determined to be 2,043,296 bp with a GC content of 59.3%. The AT1 plasmid composed of 589,645 bp with a GC content of 57.4%. The AT2 plasmid composed of 188,396 bp with a GC content of 58.1% and the virulence vector pTi-1D1416 composed of 196,706 bp with a GC content of 56.1%. One contig could not be aligned to the genome and was determined to be 10,295 bp with a GC content 59.7%. Assembled and raw read sequences were entered into the National Center for Biotechnology Information (NCBI) and BLAST was used for identification (http://blast.ncbi.nlm.nih.gov/). Automated annotation was performed by the Rapid Annotation Using Subsystem Technology (RAST) Pipeline for annotation of the genome (5; https://rast.nmpdr.org). Agrobacterium fabrum str. 1D1416 contains 5,761 predicted coding sequences, 595 subsystems and 65 predicted RNA-coding genes. The ability of 1D1416 to efficiently transform citrus makes it a novel tool for the improvement of citrus via biotechnology.