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Complete genome sequence of Pseudomonas sp. BC42, an antagonistic bacterium against Colletotrichum orbiculare
Korean J. Microbiol. 2023;59(2):151-153
Published online June 30, 2023
© 2023 The Microbiological Society of Korea.

Jiwon Kim1,2, Ho-Jong Ju2, and Mee Kyung Sang1*

1Division of Agricultural Microbiology, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
2Department of Agricultural Biology, College of Agricultural & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
Correspondence to: *E-mail:; Tel.: +82-63-238-3055; Fax: +82-63-238-3834
Received March 24, 2023; Revised May 4, 2023; Accepted May 16, 2023.
Pseudomonas sp. BC42, a potential biocontrol candidate against a fungal plant pathogen, Colletotrichum orbiculare, was isolated from the rhizosphere soil of pepper in Buyeo. Strain BC42 contains a single circular 6,876,563 bp chromosome with 63.6% G + C contents. The chromosome contains 6,089 protein-coding sequences and 80 tRNA and 19 rRNA genes. Additionally, genes associated with antagonism to various plant pathogens, including 2,4-diacetylphloroglucinol and rhizoxin A, were identified.
Keywords : Pseudomonas sp., antagonistic, genome

Pseudomonas spp. are aerobic, Gram-negative bacteria, and has been known to have various beneficial traits for the plant, such as promoting growth, producing antagonistic metabolites against phytopathogens, and inducing systemic resistance (Weller, 2007; Takeuchi et al., 2015). Strain BC42 was isolated from the rhizosphere soil in the natural habitat of pepper in Buyeo, Korea. Pseudomonas sp. BC42 could secrete extracellular antifungal metabolites against C. orbiculare according to the previous study. The result of treatment with an extract of BC42 significantly reduced appressorium formation, mycelial growth, and sporulation of C. orbiculare, compared to the control. Additionally, the lower anthracnose lesions appeared on the cucumber leaves after the extract was sprayed on them compared to the control. These results suggest that the metabolite derived from Pseudomonas sp. BC42 can be used as a control agent against cucumber anthracnose for eco-friendly agriculture (Kim et al., 2022).

The whole genome of BC42 was sequenced using the Pacbio Sequel system and the Illumina HiSeqXten platform at Macrogen Inc. The PacBio reads were assembled, and the Illumina reads were used for the error correction of the genome assembly using Pilon (version 1.21). The genome of BC42 comprises a single circular chromosome of 6,876,563 bp with a G + C content of 63.6% and contains 6,089 predicted coding sequences (CDSs), 80 transfer RNAs (tRNA), and 19 ribosomal RNA (rRNA) (Table 1). The genome was functionally annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016). The clusters of orthologous groups (COG) functional annotation analysis was performed using EggNOG mapper v2, which predicted that 5,829 (95.7% of total predicted CDS) genes were composed of 22 COG categories (Fig. 1A). OrthoANI values were calculated and UPGMA and heatmap were generated using the OrthoANI algorithm version v0.93.1 (Lee et al., 2016) from available genomes of Pseudomonas species. The OrthoANI values, which shared an average nucleotide identity (ANI), between Pseudomonas saponiphila DSM97 and the BC42 genome sequences were found to be 94.81% (Fig. 1B).

Genome features of Pseudomonas sp. BC42
Genome features Chromosome
Genome size (bp) 6,876,563
Number of contig 1
Genome coverage 100
G + C ratio (%) 63.6
Protein-coding genes (CDSs) 6,089
tRNA genes 72
rRNA genes (5S, 16S, 23S) 7, 6, 6

Fig. 1. EggNog analysis of the Pseudomonas sp. BC42 (A) and genetic similarity test of strain BC42 (B). The letter (T) means type strain of the species.

Pseudomonas spp. are known to produce various secondary antibiotic metabolites, such as phenazine-1-carboxylic acid (PCA), 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (Prn), and pyolureorin (Plt) (Shtark et al., 2003; Weller, 2007). The genes involved in the secondary metabolite gene cluster were analyzed using anti-SMASH version 6.0.0 (Blin et al., 2021). Strain BC42 codes for genes related to disease suppressive secondary metabolites, such as DAPG (L1O02_RS01230-L1O02_RS01420), and rhizoxin A (L1O02_RS15740-L1O02_RS15900) with 100% similarity. DAPG is known as an antibiotic metabolite produced by the genus Pseudomonas, with broad-spectrum antibiotic activity against bacteria to fungi. Rhizoxin shows antifungal activity against Pythium ultimum and Fusarium oxysporum (Takeuchi et al., 2015).

The genome analysis of Pseudomonas sp. BC42 revealed the presence of genes involved in the production of various secondary metabolites with antifungal activity, such as DAPG and rhizoxin A. The results will provide provides insight into the antifungal activity of Pseudomonas sp. BC42 and its potential use as a control agent against fungal plant pathogens.

Nucleotide sequence accession numbers

The complete sequence of Pseudomonas sp. BC42 has been deposited to Genbank under the accession number CP091067. The strain has been deposited in the Korean Agricultural Culture Collection (KACC) under accession number KACC 92342P.

적 요

식물 병원성 곰팡이 Colletotrichum orbiculare에 대한 항균활성이 있는 Pseudomonas sp. BC42 균주를 고추의 토양 근권에서 분리하였다. BC42 균주는 6,876,563 bp 길이의 단일 환형 염색체를 가지며 G + C 함량은 63.6%였다. 균주의 유전체로부터 6,089개의 단백질 암호화 염기서열과, 80개의 tRNA 그리고 19개의 rRNA 유전자가 확인되었다. 유전체 분석 결과를 통해 BC42 균주에서 식물병원균에 대해 길항효과가 알려진 DAPG와 rhizoxin A 등 유전자가 확인되었으며, Pseudomonas sp. BC42의 식물병원균 억제 기작을 이해할 수 있는 기반자료로 활용될 수 있을 것이다.


This study was carried out with the support of “Research program for Agricultural Science & Technology Development (Project No PJ01497802)” from the National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea. This study was supported by 2020–2023 collaborative research program between university and Rural Development Administration, Republic of Korea.

Conflict of Interest

The authors have no conflict of interest to report.

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September 2023, 59 (3)