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Complete genome sequence of Bacillus velezensis JBCS608 isolated from rhizosphere soil
Korean J. Microbiol. 2024;60(2):98-100
Published online June 30, 2024
© 2024 The Microbiological Society of Korea.

Swarnalee Dutta1, Jun An Kang1, and Yong Hoon Lee1,2*

1Division of Biotechnology, Jeonbuk National University, Iksan 54596, Republic of Korea
2Advanced Institute of Environment and Bioscience, Plant Medical Research Center and Institute of Bio-industry, Jeonbuk National University, Iksan 54596, Republic of Korea
Correspondence to: *E-mail:;
Tel.: +82-63-850-0841; Fax: +82-63-850-0834
Received March 22, 2024; Revised April 18, 2024; Accepted April 19, 2024.
Bacillus velezensis JBCS608 isolated from rhizosphere soil suppressed bacterial grain rot of rice and promoted growth of rice plants. The genome of strain JBCS608 comprises of 4,027,436 bp with GC content of 46.5%, which includes 3,823 protein-coding genes, 27 rRNAs, and 86 tRNAs. The genome of strain JBCS608 contains genes for production of secondary metabolites that are essential for the activities in protection and growth promotion of plants.
Keywords : bacterial grain rot, PGPR, rhizosphere, plant disease

Many members of Bacillus velezensis were grouped with Bacillus subtilis and Bacillus amyloliquefaciens because they shared a 99% DNA–DNA percentage phylogenetic similarity (Dunlap et al., 2016; Adeniji et al., 2019). The pan-genomic assignments recently reclassified Bacillus velezensis from B. subtilis and B. amyloliquefaciens (Ruiz-García et al., 2005; Adeniji et al., 2019; Rabbee et al., 2023). Numerous strains belong to B. velezensis have been reported to suppress plant pathogens and promote plant growth (Rabbee et al., 2023; Xue et al., 2023). The strain JBCS608 isolated from the rhizosphere soil and identified as B. velezensis with 97.7% average nucleotide identity suppressed bacterial grain rot of rice with efficacy of around 69% and also promoted fresh weight (around 20%) of the plants. Here, we present a complete genome sequence of strain JBCS608 to reveal its underlying characteristics for the biocontrol and plant growth-promoting activities.

The strain JBCS608 was cultured on Luria-Bertani agar media at 30°C and total genomic DNA was extracted using the Wizard Genomic DNA purification kit (Promega). The genome of strain JBCS608 was sequenced by Macrogen Inc. using PacBio Sequel System and Illumina HiSeq platform. The long-read data sets, 5,444,120 reads with an average length of 9,337 bp, were used for de novo assembly using the Microbial Assembly Application (SMRTlink) and corrected by Pilon (Walker et al., 2014) to produce a chromosome with 4,027,436 bp and an N50 value of 4,027,436 with 100% coverage. Gene prediction and functional annotation was performed using the National Center for Biotechnology Information (NCBI)’s Prokaryotic Genome Annotation Pipeline 2.0 (PGAP) (Tatusova et al., 2016) and functionally categorized by the Rapid Annotations using Subsystems Technology (RAST) (Aziz et al., 2008). The genome of strain JBCS608 contains 46.5% GC content, a total of 3,889 coding sequences (CDSs) of which 3,823 are protein CDSs, 86 tRNAs, and 27 rRNAs (Table 1). A total of 289 genes are involved in amino acid transport and metabolism in the cell followed by genes related to transcription (252), carbohydrate transport and metabolism (216), inorganic ion transport (178), cell wall/membrane/envelope biogenesis (178), and energy production and conversion (168). The genome of strain JBCS608 contains genes for indole acetic acid production, phosphate solubilization, siderophore production, and phenazine biosynthesis that are essential for the activities in plant protection and growth promotion (Rabbee et al., 2023; Xue et al., 2023).

The features of Bacillus velezensis JBCS608 genome

Features Value
Genome size (bp) 4,027,436
G + C content % 46.5
Total genes 4,007
Protein-coding genes (CDS) 3,823
Pseudo genes 66
rRNA (5S, 16S, 23S) 27 (9, 9, 9)
tRNA 86
ncRNA 5
NCBI accession No. CP143266.1

The ‘antibiotics & Secondary Metabolite Analysis Shell’ (antiSMASH) v. 6 (Blin et al., 2021) predicted thirteen biosynthetic gene clusters for secondary metabolite in the genome of strain JBCS608. Among them, four non-ribosomal peptide synthetase (NRPS) clusters are predicted to encode for rhizocticin A, surfactin, fengycin, and bacillibactin. Two type III PKS (T3PKS) clusters were predicted to produce bacillaene and unidentified one. Two trans- acyl transferase-PKS clusters were identified to encode macrolactin H and difficidin. A PKS-like cluster encoding butirosin A/ butirosin B, a lanthipeptide Class II cluster, a cluster producing bacilysin, and two clusters producing terpene were detected. The results indicates that strain JBCS608 contains many gene clusters for secondary metabolite biosynthesis which are important for suppression of pathogens and plant growth promotion.

Overall, the genome sequence of strain JBCS608 will contribute to understand the mechanisms and characteristics for the suppression of bacterial grain rot and plant growth promotion.

Nucleotide sequence accession number

The complete genome sequence of Bacillus velezensis JBCS608 has been deposited in the NCBI GenBank database under accession number CP143266.1 and the strain has been deposited in the Korean Agricultural Culture Collection under the accession number KACC23673.

적 요

근권 토양에서 분리한 Bacillus velezensis JBCS608 균주는 세균벼알마름병의 발생을 억제하였고, 식물체의 생육을 촉진하였다. 본 연구에서는 JBCS608균주의 전체 염기서열을 해독하고 분석하였다. JBCS608균주의 게놈은 4,027,436 bp 염기로 구성되어 있는데 GC 함량은 46.5%였고, 3,823개의 단백질을 코딩하는 유전자와 86개의 tRNA 및 27개의 rRNA를 가지고 있었다. 게놈내에는 식물의 생육 촉진과 병원균으로부터의 보호에 중요한 대사물질 생산에 관여하는 유전자가 포함된 것을 확인하였다.


This research was supported by the Cooperative Research Program for Agriculture Science & Technology Development (PJ015566), Rural Development Administration, Republic of Korea.

Conflict of Interest

The authors declare that there is no conflict of interest.

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June 2024, 60 (2)
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  • Agriculture Science & Technology Development
  • Rural Development Administration