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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(3): 306-308

https://doi.org/10.48022/mbl.2307.07013

Received: July 25, 2023; Accepted: August 9, 2023

Complete Genome Sequence of the Enterobacter asburiae IK3 Isolated from a Soybean (Glycine max) Rhizosphere

Sihyun Park1, GyuDae Lee2, Ikwhan Kim3, Yeongyu Jeong4, and Jae-Ho Shin1,2,3*

1Department of Integrative Biology, 2Department of Applied Biosciences, 3NGS Core Facility, Kyungpook National University, Daegu 41566, Republic of Korea
4Division of Agricultural Environment Research, Gyeongsangbuk-do Agricultural Research and Extension Services, Deagu 41404, Republic of Korea

Correspondence to :
Jae-Ho Shin,        jhshin@knu.ac.kr

Abstract

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This research presents the whole-genome sequence of Enterobacter asburiae strain IK3, which was isolated from the rhizosphere soil of soybean (Glycine max). The genome of the strain is composed of a single chromosome with 4 plasmids, total size of 5,084,040 bp, and the GC content is 55.5%.

Keywords: Enterobacter asburiae, whole genome sequencing, agriculture, genome, rhizosphere

Body

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This research presents the whole-genome sequence of Enterobacter asburiae strain IK3, which was isolated from the rhizosphere soil of soybean (Glycine max). The genome of the strain is composed of a single chromosome with 4 plasmids, total size of 5,084,040 bp, and the GC content is 55.5%.

The bacterium Enterobacter asburiae, in the Enterobacteriaceae family, is recognized for its potential in sustainable agriculture because of its multiple growthpromoting abilities. These include nitrogen fixation, phosphate solubilization, phytohormone production such as indole-3-acetic acid (IAA), siderophore production, and HCN production [1, 2].

The genome sequence of E. asburiae strain IK3 was procured after isolating it from the rhizosphere soil of a soybean plant. The sample was collected from a soybean field of Gyeongsangbuk-do Agricultural Research & Extension Services in Daegu, South Korea (35.9528°N, 128.5622°E). The isolation process involved serial dilution of 1 g of soil rhizosphere and then culturing the bacteria on lysogeny broth (LB) at 30℃ for 48 h. A single colony was isolated and cultivated in LB for 12 h prior to molecular identification.

Genomic DNA was extracted using the Wizard genomic DNA purification kit, following the guidelines provided by Promega, USA. The DNA's quantity and quality were measured using a Qubit 3.0 fluorometer (Thermo Fisher Scientific, USA) and a Nanopore One Spectrophotometer (Thermo Fisher Scientific), respectively. Whole genome sequencing was performed at NGS Core facility (Kyungpook National University, Daegu, Korea). Sequencing was performed through the following methods. The DNA was not pre-selected before the preparation of the sequencing library, which was made following the directions provided by Oxford Nanopore Technologies (ONT) for the use of the SQK-LSK109 ligation sequencing kit and the NEBNext companion module (New England BioLabs, USA). The library was then sequenced on the ONT MinION platform for 72 h using a FLO-MIN111 flow cell. The Guppy v4.4.1 software generated the FASTQ files, and sequences below Phred quality scores of 7 were removed from further analyses. This entire procedure yielded a total of 539,631,756 bp sequenced for E. asburiae IK3, made up of 101,826 reads, with the longest read being 214,335 bp. The raw coverage achieved was 106x.

The de novo assembly process began after basecalling with Guppy v4.4.1 software. Filtlong v0.2.1 software was used with default options to delete the bottom 5% of low quality reads (https://github.com/rrwick/Filtlong). We then assembled with Flye v2.9.1, optimizing parameters for high-quality ONT reads, and the resulting draft assembly was polished with Medaka v1.7.2 using the previously generated reads [4]. The genome was estimated to be around 5.1 mb in size, assembled into 5 contigs with a chromosome being 4,834,622 bp (CP129954.1) and 4 plasmids (CP129953.1, CP129955.1, CP129956.1 and CP129957.1) with lengths of 12,478 bp, 17,874 bp, 210,967 bp and 8,099 bp respectively (Table 1). Annotation was performed with NCBI PGAP. The genome contained 4,996 annotated genes, consisting of 4,740 protein-coding genes. The CGView was used to visualize the whole-genome sequence (Fig. 1) [5].

Table 1 . Genetic characteristics of E. asburiae strain IK3.

FeatureEnterobacter cloacae IK3
GenBank accessionNo. CP129953-CP129957
Genome size (bp)5,084,040 bp
Plasmid4
GC content (%)55.52%
total number of genes4,996
CDS (total)4,878
CDS (with protein)4,740
rRNA genes (5S, 16S, 23S)9, 8, 8 (5S, 16S, 23S)
tRNA genes83
ncRNAs genes10
Pseudo genes138


Figure 1.Genome map of the E. asburiae IK3 circular chromosome sequence, generated using the CGView visualization tool.

Data Availability

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The complete genome sequence data for E. asburiae IK3 have been submitted to the DDBJ/ENA/GenBank database with the accession number CP129953-CP129957.

Acknowledgments

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This research was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through the Crop Viruses and Pests Response Industry Technology Development Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (321097-3), and with the support of Korea Basic Science Institute (National research Facilities and Equipment center) grant funded by the Ministry of Education (2021R1A6C101A416).

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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  1. Jetiyanon K. 2015. Multiple mechanisms of Enterobacter asburiae strain RS83 for plant growth enhancement. Songklanakarin J. Sci. Technol. 37: 29-36.
  2. Saikia J, Kotoky R, Debnath R, Kumar N, Gogoi P, Yadav A, et al. 2023. De novo genomic analysis of Enterobacter asburiae EBRJ12, a plant growth-promoting rhizobacteria isolated from the rhizosphere of Phaseolus vulgaris L. J. Appl. Microbiol. 134: lxac090.
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  3. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. 2019. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37: 540-546.
    Pubmed CrossRef
  4. Stothard P, Grant JR, Van Domselaar G. 2019. Visualizing and comparing circular genomes using the CGView family of tools. Brief. Bioinformatics 20: 1576-1582.
    Pubmed KoreaMed CrossRef

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