ABSTRACT
Bacillus paralicheniformis MDJK30 was isolated from the rhizosphere of a peony. It could control the pathogen of peony root rot. Here, we report the complete genome sequence of B. paralicheniformis MDJK30. Eleven secondary metabolism gene clusters were predicted.
GENOME ANNOUNCEMENT
The Bacillus genus comprises typical species of plant growth-promoting rhizobacteria (PGPRs) that are able to suppress some plant pathogens by producing antagonistic substances. For instance, B. subtilis RB14-CS can inhibit the plant pathogen Rhizoctonia solani by exerting iturin A (1). The difficidin (2), bacilysin (3), and surfactin (4) produced by B. amyloliquefaciens are considered to be beneficial compounds against plant pathogens. B. paralicheniformis is a Gram-positive species of the Bacillus genus. Rubén Palacio-Rodríguez et al. reported that B. paralicheniformis LBEndo1 can promote the growth of Arabidopsis thaliana (5). B. paralicheniformis MDJK30 was isolated from the rhizosphere of peony in Shandong, China. It has the ability to suppress Fusarium solani, which can cause root rot in peonies.
The whole genome of B. paralicheniformis MDJK30 was sequenced using the Illumina MiSeq and PacBio RS II platforms. We obtained 5,106,074 high-quality reads through the Illumina MiSeq platform and 996,186 reads through the PacBio RS II platform. The coverage of the sequence reached 263×. All reads produced with the Illumina MiSeq were de novo assembled using Newbler version 2.8 (20110517_1502) (6), and those produced with the PacBio RS II were assembled with FALCON-integrate version 0.3.0. The annotation of the complete genome sequence was conducted using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok). The clustered regularly interspaced short palindromic repeats (CRISPRs) were predicted with the CRISPR recognition tool (CRT) (7). The PHAge search tool (PHAST) was utilized to find the prophages (8). The analysis of carbohydrate-active enzymes was carried out using the Carbohydrate-Active enZYmes database (9). Genomic islands were predicted using IslandViewer (10). The secondary metabolisms were predicted with antiSMASH (11) version 3.0.5 (http://antismash.secondarymetabolites.org).
The circular chromosome of B. paralicheniformis MDJK30 consists of 4,352,468 bp, and the G+C content is 45.94%. A total of 4,363 genes were annotated, including 4,134 coding genes, 110 RNA genes, and 119 pseudogenes. The RNA genes were composed of 24 rRNAs, 81 tRNAs, and 5 ncRNAs. Two CRISPRs and one prophage were discovered. The analysis of the genome showed that 166 genes were related to code carbohydrate-active enzymes, 71 genes coding auxiliary activities, 39 genes related to carbohydrate-binding modules, 9 genes coding carbohydrate esterases, 34 genes relevant to glycoside hydrolases, 5 genes coding glycosyl transferases, and 25 genes coding polysaccharide lyases. A total of 22 genomic islands were predicted, and 220 annotated genes were found in them. Eleven gene clusters related to secondary metabolism were predicted. The gene cluster (BLMD_02100-BLMD_02320) was 100% similar to that of lichenysin biosynthesis genes. The gene cluster (BLMD_12845-BLMD_13070) was 100% similar to that of bacitracin biosynthesis genes. These two gene clusters both belonged to nonribosomal peptide synthetases. The other gene clusters might be related to the production of new antimicrobial compounds. The complete genome of B. paralicheniformis MDJK30 will be helpful for studying the mechanisms of plant growth promotion and biocontrol at the molecular level.
Accession number(s).
The genomic sequence of B. paralicheniformis MDJK30 has been deposited at GenBank under the accession number CP020352.
ACKNOWLEDGMENTS
We thank everyone who contributed to this report. This work was supported by the Key Agricultural Application Technology Innovation Program of Shandong Province “Development and Application on New-Type Bio-Fertilizer of Famous Flower” (2014GNC113006), the Science and Technology Major Projects of Shandong Province (2015ZDXX0502B02), the National Science and Technology Pillar Program of China (2014BAD16B02), the National Natural Science Foundation of China (31600090; 31100005), the Key Technical Project of Shandong Yancao Co. Ltd. (KN238-201602), and the China Postdoctoral Science Foundation (2015M582121).
Footnotes
Citation Wang Y, Liu H, Liu K, Wang C, Ma H, Li Y, Hou Q, Liu F, Zhang T, Wang H, Wang B, Ma J, Ge R, Xu B, Yao G, Xu W, Fan L, Ding Y, Du B. 2017. Complete genome sequence of Bacillus paralicheniformis MDJK30, a plant growth-promoting rhizobacterium with antifungal activity. Genome Announc 5:e00577-17. https://doi.org/10.1128/genomeA.00577-17.
REFERENCES
- 1.Mizumoto S, Hirai M, Shoda M. 2007. Enhanced iturin A production by Bacillus subtilis and its effect on suppression of the plant pathogen Rhizoctonia solani. Appl Microbiol Biotechnol 75:1267–1274. doi: 10.1007/s00253-007-0973-1. [DOI] [PubMed] [Google Scholar]
- 2.Chen XH, Scholz R, Borriss M, Junge H, Mögel G, Kunz S, Borriss R. 2009. Difficidin and bacilysin produced by plant-associated Bacillus amyloliquefaciens are efficient in controlling fire blight disease. J Biotechnol 140:38–44. doi: 10.1016/j.jbiotec.2008.10.015. [DOI] [PubMed] [Google Scholar]
- 3.Wu L, Wu H, Chen L, Yu X, Borriss R, Gao X. 2015. Difficidin and bacilysin from Bacillus amyloliquefaciens FZB42 have antibacterial activity against Xanthomonas oryzae rice pathogens. Sci Rep 5:12975. doi: 10.1038/srep12975. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Zhao J, Cao L, Zhang C, Zhong L, Lu J, Lu Z. 2014. Differential proteomics analysis of Bacillus amyloliquefaciens and its genome-shuffled mutant for improving surfactin production. Int J Mol Sci 15:19847–19869. doi: 10.3390/ijms151119847. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Gagat P, Mackiewicz P. 2017. Cymbomonas tetramitiformis—a peculiar prasinophyte with a taste for bacteria sheds light on plastid evolution. Symbiosis 71:1–7. doi: 10.1007/s13199-016-0464-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Chaisson MJ, Pevzner PA. 2008. Short read fragment assembly of bacterial genomes. Genome Res 18:324–330. doi: 10.1101/gr.7088808. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. 2007. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209. doi: 10.1186/1471-2105-8-209. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: a fast phage search tool. Nucleic Acids Res 39:W347–W352. doi: 10.1093/nar/gkr485. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Lombard V, Golaconda Ramulu HG, Drula E, Coutinho PM, Henrissat B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495. doi: 10.1093/nar/gkt1178. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Langille MG, Brinkman FS. 2009. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25:664–665. doi: 10.1093/bioinformatics/btp030. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R. 2011. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346. doi: 10.1093/nar/gkr466. [DOI] [PMC free article] [PubMed] [Google Scholar]