Abstract
A high-quality draft genome sequence of a multi-antibiotic resistant strain, Paenibacillus strain LK1 isolated from the rhizosphere of Auricularia auricular is described. Strain LK1 produced several types of phytohormones, which included Indole-3-acetic acid (IAA) and Zeatin. Phylogenetic analysis of the 16S rRNA gene of strain LK1 showed a close relationship to P. taichungensis and P. pabuli (99% gene sequence similarity). The genome size of strain LK1 was estimated to be 7.16 Mb that consisted of 82 contigs contained in 49 scaffolds. The G + C content of the genome was 45.63% and it encoded 6499 genes, 115 pseudo genes, 8 rRNAs, 33 tRNAs, and 4 ncRNAs, based on the Prokaryotic Genome Annotation Pipeline (PGAP). Further analysis of the genome of strain LK1 identified 16 genes encoding monooxygenase and six genes encoding cytochrome P450, which may be potentially involved in zeatin biosynthesis. The draft whole genome sequence and annotation of strain LK1 has been deposited at DDBJ/EMBL/GenBank under the accession number (PEII00000000).
References
Colston SM, Fullmer MS, Beka L et al (2014) Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. MBio 5(6):e02136. https://doi.org/10.1128/mBio.02136-14
Delcher AL, Bratke KA, Powers EC et al (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6):673–679. https://doi.org/10.1093/bioinformatics/btm009
Grady EN, MacDonald J, Liu L et al (2016) Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 15:203. https://doi.org/10.1186/s12934-016-0603-7
Hinsch J, Vrabka J, Oeser B et al (2015) De novo biosynthesis of cytokinins in the biotrophic fungus Claviceps purpurea. Environ Microbiol 17(8):2935–2951. https://doi.org/10.1111/1462-2920.12838
Keshishian EA, Rashotte AM (2015) Plant cytokinin signalling. Essays Biochem 58:13–27. https://doi.org/10.1042/bse0580013
Liang TW, Wang SL (2015) Recent advances in exopolysaccharides from Paenibacillus spp.: production, isolation, structure, and bioactivities. Mar Drugs 13:1847–1863. https://doi.org/10.3390/md13041847
Luo R, Liu B, Xie Y et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18. https://doi.org/10.1186/2047-217X-1-18
Richter M, Rosselló-Móra R, Glöckner FO et al (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32(6):929–931. https://doi.org/10.1093/bioinformatics/btv681
Rybakova D, Cernava T, Köberl M et al (2016) Endophytes-assisted biocontrol: novel insights in ecology and the mode of action of Paenibacillus. Plant Soil 405:125–140. https://doi.org/10.1007/s11104-015-2526-1
Soussi A, Ferjani R, Marasco R et al (2016) Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential. Plant Soil 405(1–2):357–370
Sun Z, Liu K, Zhang J et al (2017) IAA producing Bacillus altitudinis alleviates iron stress in Triticum aestivum L. seedling by both bioleaching of iron and up-regulation of genes encoding ferritins. Plant Soil 419(1–2):1–11. https://doi.org/10.1007/s11104-017-3218-9
Xie J, Shi H, Du Z et al (2016) Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species. Sci Rep 6:21329. https://doi.org/10.1038/srep21329
Acknowledgements
This work was partially supported by a grant from Zhoukou Normal University (no. ZKNU2015107) and a grant from the Education Department of Henan Province (no. 17A180017).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
We declare no conflict of interest with respect to this paper.
Additional information
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PEII00000000. The version described in this paper is version PEII00000000.1.
Rights and permissions
About this article
Cite this article
Liu, K., He, L., Li, S. et al. Draft genome sequence of Paenibacillus strain LK1, a phytohormone producing bacterium. 3 Biotech 8, 85 (2018). https://doi.org/10.1007/s13205-017-1042-9
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s13205-017-1042-9