Journal of Biotechnology 192 (2014) 85–86
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome Announcement
Complete genome sequence of the plant growth-promoting rhizobacterium Pseudomonas aurantiaca strain JD37夽 Qiuyue Jiang, Jing Xiao, Chenhao Zhou, Yonglin Mu # , Bin Xu, Qingling He, Ming Xiao ∗ Development Center of Plant Germplasm, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, PR China
a r t i c l e
i n f o
Article history: Received 2 October 2014 Accepted 13 October 2014 Available online 23 October 2014 Keywords: Pseudomonas aurantiaca JD37 Genome sequence Plant growth-promoting rhizobacteria Biological control
a b s t r a c t Pseudomonas aurantiaca Strain JD37, a Gram-negative bacterium isolated from potato rhizosphere soil (Shanghai, China), is a plant growth-promoting rhizobacterium. The JD37 genome consists of only one chromosome with no plasmids. Its genome contains genes involved plant growth promoting, biological control, and other function. Here, we present the complete genome sequence of P. aurantiaca JD37. As far as we know, this is the first whole-genome of this species. © 2014 Elsevier B.V. All rights reserved.
Pseudomonas aurantiaca is a Gram-negative, nonfluorescent rhizosphere soil bacterium which belongs to the group of the Pseudomonas bacteria (Esipov et al., 1975). These bacteria received attention for their ability to show potential for use as a bio-control agent against plant pathogenic microbes (Felker et al., 2005). A P. aurantiaca JD37 strain (accession no. GQ358919, 16S rDNA registered at GenBank) was isolated from potato rhizosphere soil, a suburb of Shanghai, China. The strain was found to effectively colonize the rhizosphere soil and internal roots of maize (Fang et al., 2013). Further analysis revealed that JD37 strain is not only able to promote the growth of maize, but also inhibit plant diseases (Fang et al., 2013), in agreement with previous reports (Felker et al., 2005; Evelin et al., 2008). Furthermore, a microbial fertilizer that comprises JD37 strain was prepared and the microbial fertilizer was shown to have a good effect on plant growth (Zhou, 2014). In order to obtain more information on the genetic equipment of this highly competitive bacterium in the rhizosphere, we sequenced the genome of P. aurantiaca JD37. The genome
夽 Nucleotide sequence accession number: The complete nucleotide genome sequence of JD37 has been deposited in GenBank under accession number CP009290. The strain was deposited in China General Microbiological Culture Collection Center (CGMCC) under accession no.7099. ∗ Corresponding author at: Biology Department, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, PR China. Tel.: +86 021 64321022; fax: +86 021 65642468. E-mail address: [email protected] (M. Xiao). # Present address: Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, No. 320, YueYang Road, Shanghai 200031, PR China. http://dx.doi.org/10.1016/j.jbiotec.2014.10.021 0168-1656/© 2014 Elsevier B.V. All rights reserved.
was sequenced using Pacbio RS (Levene et al., 2003). After corrected, reads were assembled by Celera Assembler (Myers et al., 2000), which was bundled in Sprai. All reads were assembled to only one scaffold. The genome was submitted to the NCBI for automated annotation and gene prediction using the NCBI’s Prokaryotic Genomes Annotation Pipeline (http://www.ncbi. nlm.nih.gov/genome/annotation prok/) and using the annotation tools GeneMarkS+ (Besemer et al., 2001). tRNA and rRNA genes were identified by tRNAscan-SE (Lowe and Eddy, 1997) and RNA hmmer 3.0 (Huang et al., 2009), respectively. The open reading frames (ORFs) were predicted using Glimmer 3.02 (Delcher et al., 2007). The metabolic pathways were examined through KAAS (KEGG automatic annotation server) (Moriya et al., 2007). P. aurantiaca JD37 is composed of a single circular chromosome of 6,702,062 bp in length with an average GC content of 62.75%, and no plasmid is detected. There are 5.915 genes and 5.780 putative coding sequences (CDs), including 51 pseudogenes. The genome includes 67 tRNA genes and 16 rRNA genes (Table 1). Genes involved in the activation of nitrogen assimilation (glnG) and catalyzing the uridylylation or deuridylylation of the P II nitrogen regulatory protein (glnD), and protecting cells from the toxic effects of hydrogen peroxide (katE), were annotated in the sequence. They may play a key role in biological control. Moreover, cell division protein ZipA was found in the genome. ZipA is a probable receptor for the septal ring structure, it may be related to produce siderophores (Qu et al., 2004) which can not only promote plant absorption of iron ion, but form specific chelate to prevent pathogens as well. The genome also contains genes involved in regulation of intracellular pH, biofilm formation and hemin adsorption, degradation of
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Q. Jiang et al. / Journal of Biotechnology 192 (2014) 85–86
Table 1 Genome features of Pseudomonas aurantiaca JD37. Features
Value
Genome size (bp) GC content Plasmid Replicons Total genes tRNA genes rRNA genes CDs
6,702,062 62.75% 0 1 5915 67 16 5780
aberrant cytoplasmic and membrane proteins, and other functions that possible contribute bacterium to root colonization. A further and deep analysis of JD37 will provide more useful information on this bacterium’s lifestyle and the molecular mechanism with other microorganisms and plants. Acknowledgements We thank Dr. Zhangjun Fei and Dr. Wen Bo (Boyce Thompson Institute for Plant Research, Cornell University) for excellent work in the genome assembly and analysis. This work was supported by Natural Science Foundation of Shanghai (12ZR1422100), Shanghai Municipal Science and Technology Commission (11JC1409300) and Shanghai Municipal Education Commission (13ZZ102). References Besemer, J., Lomsadze, A., Borodovsky, M., 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implication for finding sequence motifs in regulatory regions. Nucleic Acids Res. 29 (12), 2607–2618.
Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23 (6), 673–679. Esipov, S.E., Adanin, V.M., Baskunov, B.P., Kiprianova, E.A., Garagulia, A.D., 1975. New antibiotically active fluoroglucide from Pseudomonas aurantiaca. Antibiotiki 20 (12), 1077–1081. Evelin, C., Marisa, R., Alberto, R.J., Susana, B.R., 2008. Improvement of growth, under field conditions, of wheat inoculated with Pseudomonas chlororaphis subsp. aurantiaca SR1. World J. Microbiol. Biotechnol. 24 (11), 2653–2658. Fang, R., Jia, L., Yao, S.S., Wang, Y.J., Wang, J., Zhou, C.H., Wang, H.J., Xiao, M., 2013. Promotion of plant growth, biological control and induced systemic resistance in mazie by Pseudomonas aurantiaca JD37. Ann. Microbiol. 63 (3), 1177–1185. Felker, P., Medina, D., Soulier, C., Velicce, G., Velarde, M., Gonzalez, C., 2005. A survey of environmental and biological factors (Azospirillum spp, Agrobacterium rhizogenes, Pseudomonas aurantiaca) for their influence in rooting cuttings of Prosopis alba clones. J Arid Environ. 61 (2), 227–247. Huang, Y., Gilna, P., Li, W.Z., 2009. Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25 (10), 1338–1340. Levene, M.J., Korlach, J., Turner, S.W., Foquet, M., Craighead, H.G., Webb, W.W., 2003. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299 (5607), 682–686. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (5), 955–964. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M., 2007. KASS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35 (Web Server issue), W182–W185. Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo, D.P., Flanigan, M.J., Kravitz, S.A., Mobarry, C.M., Reinert, K.H., Remington, K.A., Anson, E.L., Bolanos, R.A., Chou, H.H., Jordan, C.M., Halpern, A.L., Lonardi, S., Beasley, E.M., Brandon, R.C., Chen, L., Dunn, P.J., Lai, Z.W., Liang, Y., Nusskern, D.R., Zhan, M., Zhang, Q., Zheng, X.Q., Rubin, G.M., Adams, M.D., Venter, J.C., 2000. A whole-genome assembly of Drosophila. Science 287 (5461), 2196–2204. Qu, S.C., Zhang, Z., Qiao, Y.S., 2004. Advance of ZIP gene family related to iron transporter in plant. Acta Bot. Boreal. Occident. Sinica 24 (7), 1348–1354. Zhou, C.H., (Master dissertation) 2014. The Development and Application of JD37 Biofertilizer in Green Vegetables Production. Shanghai Normal University, Shanghai (in Chinese with English abstract).
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome Announcement
Complete genome sequence of the plant growth-promoting rhizobacterium Pseudomonas aurantiaca strain JD37夽 Qiuyue Jiang, Jing Xiao, Chenhao Zhou, Yonglin Mu # , Bin Xu, Qingling He, Ming Xiao ∗ Development Center of Plant Germplasm, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, PR China
a r t i c l e
i n f o
Article history: Received 2 October 2014 Accepted 13 October 2014 Available online 23 October 2014 Keywords: Pseudomonas aurantiaca JD37 Genome sequence Plant growth-promoting rhizobacteria Biological control
a b s t r a c t Pseudomonas aurantiaca Strain JD37, a Gram-negative bacterium isolated from potato rhizosphere soil (Shanghai, China), is a plant growth-promoting rhizobacterium. The JD37 genome consists of only one chromosome with no plasmids. Its genome contains genes involved plant growth promoting, biological control, and other function. Here, we present the complete genome sequence of P. aurantiaca JD37. As far as we know, this is the first whole-genome of this species. © 2014 Elsevier B.V. All rights reserved.
Pseudomonas aurantiaca is a Gram-negative, nonfluorescent rhizosphere soil bacterium which belongs to the group of the Pseudomonas bacteria (Esipov et al., 1975). These bacteria received attention for their ability to show potential for use as a bio-control agent against plant pathogenic microbes (Felker et al., 2005). A P. aurantiaca JD37 strain (accession no. GQ358919, 16S rDNA registered at GenBank) was isolated from potato rhizosphere soil, a suburb of Shanghai, China. The strain was found to effectively colonize the rhizosphere soil and internal roots of maize (Fang et al., 2013). Further analysis revealed that JD37 strain is not only able to promote the growth of maize, but also inhibit plant diseases (Fang et al., 2013), in agreement with previous reports (Felker et al., 2005; Evelin et al., 2008). Furthermore, a microbial fertilizer that comprises JD37 strain was prepared and the microbial fertilizer was shown to have a good effect on plant growth (Zhou, 2014). In order to obtain more information on the genetic equipment of this highly competitive bacterium in the rhizosphere, we sequenced the genome of P. aurantiaca JD37. The genome
夽 Nucleotide sequence accession number: The complete nucleotide genome sequence of JD37 has been deposited in GenBank under accession number CP009290. The strain was deposited in China General Microbiological Culture Collection Center (CGMCC) under accession no.7099. ∗ Corresponding author at: Biology Department, College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, PR China. Tel.: +86 021 64321022; fax: +86 021 65642468. E-mail address: [email protected] (M. Xiao). # Present address: Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, No. 320, YueYang Road, Shanghai 200031, PR China. http://dx.doi.org/10.1016/j.jbiotec.2014.10.021 0168-1656/© 2014 Elsevier B.V. All rights reserved.
was sequenced using Pacbio RS (Levene et al., 2003). After corrected, reads were assembled by Celera Assembler (Myers et al., 2000), which was bundled in Sprai. All reads were assembled to only one scaffold. The genome was submitted to the NCBI for automated annotation and gene prediction using the NCBI’s Prokaryotic Genomes Annotation Pipeline (http://www.ncbi. nlm.nih.gov/genome/annotation prok/) and using the annotation tools GeneMarkS+ (Besemer et al., 2001). tRNA and rRNA genes were identified by tRNAscan-SE (Lowe and Eddy, 1997) and RNA hmmer 3.0 (Huang et al., 2009), respectively. The open reading frames (ORFs) were predicted using Glimmer 3.02 (Delcher et al., 2007). The metabolic pathways were examined through KAAS (KEGG automatic annotation server) (Moriya et al., 2007). P. aurantiaca JD37 is composed of a single circular chromosome of 6,702,062 bp in length with an average GC content of 62.75%, and no plasmid is detected. There are 5.915 genes and 5.780 putative coding sequences (CDs), including 51 pseudogenes. The genome includes 67 tRNA genes and 16 rRNA genes (Table 1). Genes involved in the activation of nitrogen assimilation (glnG) and catalyzing the uridylylation or deuridylylation of the P II nitrogen regulatory protein (glnD), and protecting cells from the toxic effects of hydrogen peroxide (katE), were annotated in the sequence. They may play a key role in biological control. Moreover, cell division protein ZipA was found in the genome. ZipA is a probable receptor for the septal ring structure, it may be related to produce siderophores (Qu et al., 2004) which can not only promote plant absorption of iron ion, but form specific chelate to prevent pathogens as well. The genome also contains genes involved in regulation of intracellular pH, biofilm formation and hemin adsorption, degradation of
86
Q. Jiang et al. / Journal of Biotechnology 192 (2014) 85–86
Table 1 Genome features of Pseudomonas aurantiaca JD37. Features
Value
Genome size (bp) GC content Plasmid Replicons Total genes tRNA genes rRNA genes CDs
6,702,062 62.75% 0 1 5915 67 16 5780
aberrant cytoplasmic and membrane proteins, and other functions that possible contribute bacterium to root colonization. A further and deep analysis of JD37 will provide more useful information on this bacterium’s lifestyle and the molecular mechanism with other microorganisms and plants. Acknowledgements We thank Dr. Zhangjun Fei and Dr. Wen Bo (Boyce Thompson Institute for Plant Research, Cornell University) for excellent work in the genome assembly and analysis. This work was supported by Natural Science Foundation of Shanghai (12ZR1422100), Shanghai Municipal Science and Technology Commission (11JC1409300) and Shanghai Municipal Education Commission (13ZZ102). References Besemer, J., Lomsadze, A., Borodovsky, M., 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implication for finding sequence motifs in regulatory regions. Nucleic Acids Res. 29 (12), 2607–2618.
Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23 (6), 673–679. Esipov, S.E., Adanin, V.M., Baskunov, B.P., Kiprianova, E.A., Garagulia, A.D., 1975. New antibiotically active fluoroglucide from Pseudomonas aurantiaca. Antibiotiki 20 (12), 1077–1081. Evelin, C., Marisa, R., Alberto, R.J., Susana, B.R., 2008. Improvement of growth, under field conditions, of wheat inoculated with Pseudomonas chlororaphis subsp. aurantiaca SR1. World J. Microbiol. Biotechnol. 24 (11), 2653–2658. Fang, R., Jia, L., Yao, S.S., Wang, Y.J., Wang, J., Zhou, C.H., Wang, H.J., Xiao, M., 2013. Promotion of plant growth, biological control and induced systemic resistance in mazie by Pseudomonas aurantiaca JD37. Ann. Microbiol. 63 (3), 1177–1185. Felker, P., Medina, D., Soulier, C., Velicce, G., Velarde, M., Gonzalez, C., 2005. A survey of environmental and biological factors (Azospirillum spp, Agrobacterium rhizogenes, Pseudomonas aurantiaca) for their influence in rooting cuttings of Prosopis alba clones. J Arid Environ. 61 (2), 227–247. Huang, Y., Gilna, P., Li, W.Z., 2009. Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics 25 (10), 1338–1340. Levene, M.J., Korlach, J., Turner, S.W., Foquet, M., Craighead, H.G., Webb, W.W., 2003. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299 (5607), 682–686. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (5), 955–964. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M., 2007. KASS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35 (Web Server issue), W182–W185. Myers, E.W., Sutton, G.G., Delcher, A.L., Dew, I.M., Fasulo, D.P., Flanigan, M.J., Kravitz, S.A., Mobarry, C.M., Reinert, K.H., Remington, K.A., Anson, E.L., Bolanos, R.A., Chou, H.H., Jordan, C.M., Halpern, A.L., Lonardi, S., Beasley, E.M., Brandon, R.C., Chen, L., Dunn, P.J., Lai, Z.W., Liang, Y., Nusskern, D.R., Zhan, M., Zhang, Q., Zheng, X.Q., Rubin, G.M., Adams, M.D., Venter, J.C., 2000. A whole-genome assembly of Drosophila. Science 287 (5461), 2196–2204. Qu, S.C., Zhang, Z., Qiao, Y.S., 2004. Advance of ZIP gene family related to iron transporter in plant. Acta Bot. Boreal. Occident. Sinica 24 (7), 1348–1354. Zhou, C.H., (Master dissertation) 2014. The Development and Application of JD37 Biofertilizer in Green Vegetables Production. Shanghai Normal University, Shanghai (in Chinese with English abstract).
