search for


Draft genome sequence analysis of Paenibacillus polymyxa JE201, an antagonist of plant fungal pathogens
Korean J. Microbiol. 2021;57(4):295-296
Published online December 31, 2021
© 2021 The Microbiological Society of Korea.

Seongho Ahn*, Daseul Lee, Seunghwn Kim, and Chang-Muk Lee

Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju 55365, Republic of Korea
Correspondence to: E-mail:;
Tel.: +82-63-238-3076; Fax: +82-63-238-3076
Received December 6, 2021; Revised December 16, 2021; Accepted December 16, 2021.
Paenibacillus polymyxa JE201 was isolated from Chwinamul rhizosphere soil, and its antagonistic activity against fungal plant pathogens was evaluated. Here we present the draft genome sequence of JE201. The genome comprises 6,147,064 bp with GC content of 45.27% that includes 5,425 predicted protein-coding genes, 46 ribosomal RNAs, and 111 transfer RNAs. Analysis of the biosynthetic gene cluster for secondary metabolites showed that the JE201 contains 24 biosynthetic clusters.
Keywords : Paenibacillus polymyxa, antagonistic, antifungal, JE201, plant disease

Paenibacillus polymyxa, a Gram-positive endospore-forming bacterium, is considered to be a plant-growth-promoting rhizobacterium (PGPR) because several strain of thin species have been identified as environmentally friendly alternatives to agrochemicals improving crop yield and quality (Rybakova et al., 2015). Paenibacillus polymyxa JE201 was isolated from isolated from the rhizosphere soil in the natural habitat of Chwinamul in Jeongeup, Korea. The strain showed antagonistic activities against plant fungal pathogens (Ahn et al., 2021).

The genome of JE201 was sequenced using PacBio RS II and the Illumina HiSeq platform at Microgen Inc. The sequence generated by PacBio RS II was assembled de novo using RSHGAP assembly version 3.0, and HiSeq reads were subsequently used for error correction of the draft genome assemblies using Pilon version 1.21. Gene prediction and functional annotation were performed using the NCBI prokaryotic genomes annotation pipeline and Prokka (v 1.12b) server. The genes involved in secondary metabolite gene cluster were analyzed using anti-SMASH version 6.0.0.

The draft genome sequence revealed a total length of 6,147,064 bp comprising 3 contigs with the GC content of 45.27%. The annotation results indicated the presence of 5,425 coding sequences, 46 ribosomal RNAs, 111 transfer RNAs, and 119 pseudogenes (Table 1). The fraction of the genome related of COG categories amino acid transport and metabolism, transcription, and carbohydrate transport and metabolism were 5.55% (290 genes), 7.88% (412 genes), and 8.57% (448 genes), respectively.

Genomic features of Paenibacillus polymyxa JE201

Features Value
GenBank accession no. JAENEW000000000
No. of Contig 3
Genome Coverage (x) 151.52
Genome size (bp) 6,147,064
GC ratio (%) 45.27
Total genes 5,425
Protein-coding genes 5,145
rRNA (5S, 16S, 23S) 46 (16, 15, 15)
tRNA 111
Pseudogenes 119

Analysis of the biosynthetic gene cluster for secondary metabolites showed that the JE201 contains 24 biosynthetic clusters. Among them, for polymyxin synthesis gene cluster (K5E38_16785-16975), and fusaricidin synthetic gene cluster (K5E38_12810-12990) (Lie et al., 2017). Polymyxin (Hsu et al., 2017) and fusaricidin (Debois et al., 2013; Li and Chen, 2019) are the major antifungal compound in P. polymyxa. The draft genome sequence of JE201 provides further genetic insight into its strain-specific properties and its utility as a biological control.

Nucleotide sequence accession numbers

The draft genome sequence of P. polymyxa JE201 has been deposited to DDBJ/ENA/GenBank under the accession number JAINEW000000000, 16S rRNA accession number MK294313.1, and the strain has been deposited in the Korean Agricultural Culture Collection (KACC) under accession number KACC 81114BP.

적 요

식물병원균에 대해 강한 길항 작용을 나타내는 Paenibacillus polymyxa JE201은 정읍의 취나물 자생지에서 분리되었다. 본 연구에서 JE201 균주의 유전체 염기서열을 분석한 결과, 3개의 contig로 이루어졌으며, 6,147,064 bp, GC 함량은 45.27%로 구성되었으며, 5,425개의 단백질 암호화 유전자를 가졌으며, 46개의 rRNA와 111개의 tRNA 유전자를 포함하였다. JE201의 2차 대사물질에 대한 클러스터를 조사한 결과 총 24개의 클러스터가 있었다.


This study was carried out with the support of “Research Program for Agricultural Science & Technology Development (Project No PJ0142712021)” from the National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea.

Conflict of Interest

The authors have no conflict of interest to report.

  1. Ahn SH, Kim D, Park BY, Han JH, and Lee SY. 2021. Biological characterization of Paenibacillus polymyxa JE201 with antifungal activity against fungal leaf spot disease of aster scaber. Korean J. Org. Agric. 29, 257-273.
  2. Debois D, Ongena M, Cawoy H, and De Fauw E. 2013. MALADI-FTICR MS imaging as a powerful tool to identify Paenibacillus antibiotics involved in the inhibition of plant pathogenes. J Am. Soc. Mass. Spectrom. 24, 1202-1213.
  3. Hsu LH, Wang HF, Sun PL, Hu FR, and Chen YL. 2017. The antibiotic polymyxin B exhibites novel antifungal activity against Fusarium species. Int. J. Antimicrob. Agents 49, 740-748.
  4. Li Y and Chen S. 2019. Fusaricidin produced by Paenibacillus polymyxa WLY78 induces systemic resistance against fusarium wilt of cucumber. Int. J. Mol. Sci. 20, 5240.
    Pubmed KoreaMed CrossRef
  5. Liu H, Wang C, Li Y, Liu K, Hou Q, Xu W, Fan L, Zhao J, Gou J, and Du BDu B, et al. 2017. Complete genome sequence of Paenibacillus polymyxa YC0573, a plant growth-promoting rhizobacterium with antimicrobial activity. Genome Announc. 5, e01636-16.
    Pubmed KoreaMed CrossRef
  6. Rybakova D, Wetzlinger U, Müller H, and Berg G. 2015. Complete genome sequence of Paenibacillus polymyxa strain Sb3-1, a soilborne bacterium with antagonistic activity toward plant pathogens. Genome Announc. 3, e00052-15.
    Pubmed KoreaMed CrossRef

December 2021, 57 (4)
Full Text(PDF) Free

Social Network Service

Author ORCID Information

Funding Information
  • National Institute of Agricultural Sciences, Rural Development Administration