Burkholderia cepacia is widely distributed in diverse ecological niches such as the soil, water, marine, rhizosphere, and plants. Although some strains of B. cepacia are known to opportunistic pathogens to immunocompromised patients, this species has attracted considerable commercial interest in field of agriculture since it showed potent plant growth-promoting activity and inhibition of fungal disease in several different plants (Zhao et al., 2014; Jung et al., 2018). Burkholderia cepacia strain JK11 was isolated from plant lily bulbs at a garden plot in Wanju, Korea (35°54'00.0"N 127°13'12.0"E) on 4 July, 2019. The strain JK11 showed the several plant growth promoting characteristics, such as antifungal activity, siderophore production, and phosphate solubilizing activity (Supplementary data Fig. S1).

Genomic DNA of strain JK11 was prepared using the Maxwell® RSC Tissue DNA Kit (Promega) and used for both Illumina and PacBio sequencing. Briefly, Illumina libraries were prepared with the TruSeq Nano DNA Kit (Illumina) and sequenced on an Illumina NovaX at Macrogen Inc. For PacBio sequencing, genomic DNA was sheared and ligated to SMRTbell adapters using the PacBio SMRTbell prep kit. The library was sequenced using the PacBio Sequel IIe sequencing platform at Macrogen Inc. De novo assembly of the PacBio reads was performed using the Microbial Assembly application of SMRT Link 13.0 based on the Hierarchical Genome Assembly Process (HGAP) version 4 (Chin et al., 2013). A total of 5,322,824 filtered reads (803,195,061 bp) were assembled using Microbial Assembly in SMRT tools. After assembly, Illumina reads were applied for accurate genome sequencing using Pilon 1.21 (Walker et al., 2014). Then, the consensus sequence with depth of coverage data was generated by mapping the Illumina reads against the assembled contigs (N50 of 3,787,680 and depth of 37x). The assembled data revealed that the JK11 genome consisted of three circular chromosomes and a plasmid. The size and G + C content of the total genome were 8,970,404 bp and 66.4%, respectively (Table 1). The average nucleotide identity (ANI) analysis (Figueras et al., 2014) using BLASTn indicated that B. cepacia strain BC16 (GCA_009586235) was the nearest neighbor of strain JK11 with an ANI value of > 0.99. Gene prediction and annotation with NCBI’s PGAP 6.6 (Tatusova et al., 2016) indicated that the JK11 genome included 8,111 protein-coding genes.

Table 1

Genome features of Burkholderia cepacia JK11

Genome features	Value
Total genome size (bp)	8,970,404
Chromosome I	3,826,233
Chromosome II	3,787,680
Chromosome III	1,328,515
Plasmid	27,976
G + C content (%)	66.4
Total number of genes	8,203
Protein-coding genes	8,111
tRNA genes	70
rRNA genes	18
ncRNA genes	3
tmRNA	1
GenBank accession number	CP158564–CP158567

The antiSMASH 7.0 (Blin et al., 2023) analysis indicated that the genome of JK11 contains several secondary metabolite biosynthetic gene clusters associated with the biosynthesis of ornibactin C8 (siderophore) from Burkholderia cenocepacia J2315 (100% similarity), pyochelin (siderophore) from Burkholderia cepacia ATCC 25416 (100% similarity), and pyrrolnitrin (antibiotic) from Pseudomonas chlororaphis (100% similarity), and lomofungin (antibiotic) from Streptomyces lomondensis (27% similarity). Our report will provide a feasible genetic resource to understand the plant growth-promoting activity of B. cepacia.

Strain and nucleotide sequence accession numbers

Burkholderia cepacia JK11 has been deposited at the Korean Collection for Type Cultures (KCTC) under the preservation number of KCTC14199BP. The complete genome sequence of B. cepacia JK11 has been deposited in the NCBI GenBank under accession number CP158564-CP158567. The associated Bioproject, Biosample, and SRA accession numbers are PRJNA 792752, SAMN24462211, and SRR29484633, respectively.

Burkholderia cepacia JK11 균주는 한국의 백합 구근에서 분리된 호기성 그람 음성 박테리아이다. JK11균주의 전체 유전체는 3개의 원형 염색체와 1개의 플라스미드로 구성되었으며, 총 8,970,404 bp의 길이와 66.4%의 G + C 함량을 가지고 있다. JK11유전체는 8,111개의 단백질 암호화 유전자, 18개의 rRNA, 70개의 tRNA, 3개의 ncRNA, 1개의 tmRNA유전자를 가지고 있다. 특히 유전체 기반의 antiSMASH 분석 결과 JK11유전체에는 식물의 생장 촉진과 병원균으로부터의 방어에 필수적인 이차대사산물 생산을 위한 생합성 유전자가 포함되어있는 것을 확인하였다.

This research was supported by “Regional Innovation Strategy (RIS)” through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (MOE) (2023RIS-008).

The authors have no conflicts of interest to this research.