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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 #358327

Research Project: Molecular Genetic Tools Advancing the Application of Biotechnology for Crop Improvement

Location: Crop Improvement and Genetics Research

Title: Draft genome sequence of serratia sp. 1D1416

item Alabed, Diaa
item HUO, NAXIN - University Of California, Davis
item Gu, Yong
item McCue, Kent
item Thomson, James - Jim

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2018
Publication Date: 1/17/2019
Citation: Alabed, D.F., Huo, N., Gu, Y.Q., McCue, K.F., Thomson, J.G. 2019. Draft genome sequence of serratia sp. 1D1416. Microbiology Resource Announcements. 8(3):e01354-18.

Interpretive Summary: This work reports the draft genome of Serratia euonymus. The assembled genome contains a complete circular chromosome composed of 5,613,923 bp and a small circular fragment 36,168 bp. The strain was discovered in a mixed culture from a gall isolated from the evergreen shrub Japanese spindle (Euonymus japonicus).

Technical Abstract: Published ‘unusual’ Serratia spp. include Serratia ficaria, Serratia fonticola, Serratia odorifera, Serratia plymuthica and Serratia rubidaea. Serratia ficaria was the first non-pathogen microbe associated with plant growth and was characterized in 1979 as an important part of the fig tree ecosystem. Others like Serratia plymuthica, S. liquefaciens and S. rubidaea have been observed as part of the rhizosphere microbiome and may have antibacterial and or antifungal properties. Serratia euonymus appears to have low-level resistance to tetracycline but is susceptible to chloramphenicol, kanamycin and gentamycin. This is a typical feature of Serratia spp. and may include the entire genus Serratia. Here we present the genome of the novel Serratia euonymus isolated from a mixed culture along with an Agrobacterium tumefaciens microbe isolated from Euonymus japonicus gall. Genomic DNA isolated was used for PacBio sequencing to generate of a complete circular chromosome composed of 5,577,755 bp with a GC content of 59.6% and a circular fragment composed of 36,168 bp with a GC content of 60.5%. No autonomous replication genes were detected on this circular fragment and was therefore deemed to be a novel plasmid. Overall coverage was approximately 110X. A unique cluster of opine genes were detected within the circular chromosome and used to develop primers to identify the genome. Automated annotation was performed by the Rapid Annotation Using Subsystem Technology (RAST) Pipeline was used for annotation of the genome. Serratia euonymus contains 5,234 predicted coding sequences, 570 subsystems and 118 predicted RNAs.