Bacillus velezensis possesses antagonistic activity against R. solanacearum and Fusarium oxysporum, causing wilt disease in cucumbers under laboratory conditions (Cao et al., 2018), accelerating the absorption of nutrients and increasing photosynthesis to growth plant promotion (Mosela et al., 2022), and is safe and environmentally friendly, has widely potential application in agriculture (Rabbee et al., 2023).

Therefore, the main objective of this study is to publish the draft genome of B. velezensis, which is valuable data for comparative genomic analyses to gain insights into gene groups connected to controling bacterial wilt disease caused by R. solanacearum on cucumbers.

Bacterial strains were isolated from the soil samples collected in Mekong, Vietnam, using colony morphology on LB medium. The resistance to R. solanacearum was investigated using the plate diffusion method. Strains with high resistance were tried to control bacterial wilt disease on cucumber plants in greenhouses. Strain DB2.1 had inhibitory effects on R. solanacearum on Petris, with a sterile ring diameter of 21.89 mm, and had the strongest inhibitory effects of controlling wilt disease caused by R. solanacearum on cucumbers under greenhouse conditions, with a lower illness rate than the control rate was 53.33%. The strain was identified as B. velezensis DB2.1 through 16S rRNA gene sequencing (Le et al., 2021) and selected for DNA extraction for genome sequencing. A DNA mini kit (Qiagen) was used for isolating bacterial genomic DNA. The genomic DNA of DB2.1 was sequenced at KTest Co., Ltd. using an Illumina Miniseq with NEBNext^® Ultra^TM II DNA Library Prep Kit 2x150 bp and assessed via capillary electrophoresis (Bioanalyzer, Agilent). Low-quality reads were filtered using Trimmomatic 0.36 and the filtered reads were assembled using Unicycler (version 0.4.4) with default metrics. A genome-wide phylogenetic tree was set up by autoMLST with genomes comparison from NCBI (Devi et al., 2019). AntiSMASH (Li et al., 2023), and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www.ncbi.nlm.nih.gov/protein/MCE49) were used for identifying the gene clusters.

The assembled genome of B. velezensis strain DB2.1 (with completeness of 99.41% and contamination of 0%) has an estimated 4,067,504 bp with a GC content of 46.25%. A total of 4,106 predicted genes, 72 pseudogenes, 84 RNA genes, 76 tRNAs, and 3 rRNAs were identified (Table 1).

Table 1

General feature of B. velezensis strain DB2.1 draft genome

Item	Description
Genome assembly data
Assembly method	Unicycler v.0.4.7
Genome coverage	110.0x
Genome feature
Genome size (bp)	4,067,504
Genes (total)	4,106
Genes (coding)	3,950
GC content (%)	46.25
Genes (RNA)	84
No. of rRNA	3
No. of tRNA	76
Pseudo genes	72

The gene sequence comparison of isolate strain DB2.1 using autoMLST on 87 house-keeping core genes, suggested a closer relationship with B. velezensis JS25R, B. velezensis NAU-B3, and B. velezensis YAU B9601-Y2, which are 99.0%, 98.9%, and 98.8% respectively. The genomic phylogenetic analysis indicates that B. velezensis strain DB2.1 belongs to the B. velezensis lineage (Fig. 1). B. velezensis strain DB2.1 is a safe, and effective biological control agent for use in agriculture (Mosela et al., 2022; Rabbee et al., 2023).

Fig. 1. A genome-wide phylogenetic tree using autoMLST.

Through the use of anti-SMASH genome analysis, four of the clusters have been clearly identified as being involved in the synthesis of difficidin, bacillibactin (Liu et al., 2023), surfactin, and fengycin (Chen et al., 2019) can counteract R. solanacearum. Using the NCBI Prokaryotic Genome Annotation Pipeline, ten gene clusters were found to be involved in acetolate biosynthesis (acetolactate synthase small subunit, acetolactate synthase large subunit, alpha-acetolactate decarboxylase, acetolactate synthase, and butanediol dehydrogenase [Liang et al., 2022]), and tryptophan biosynthesis (Substrate-specific component TrpP of tryptophan ECF transporter, Tryptophanyl-tRNA synthetase, Tryptophan synthase alpha, Tryptophan synthase beta, and Tryptophan RNA-binding attenuator protein [Cheng et al., 2024]) which are essential for producing the plant growth hormone; two gene clusters were found to be involved in Pathogenesis related protein biosynthesis (YdhK family protein, hypothetical protein [Köhl et al., 2019]) which induces systemic resistance plants.

Nucleotide sequence accession number

Data is available in GenBank with Bioproject PRJNA 789598 and accession number JAJUFA000000000.

The authors wish to thank National Center for Technological Progress – HCM Branch, Ho Chi Minh City, Viet Nam for support for this study.

There are no conflicts of interest to declare.

Data is available in GenBank with Bioproject PRJNA 789598 and accession number JAJUFA000000000.