Marine Genomics 20 (2015) 17–18
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/Technical resources
Draft genome sequence of Pseudomonas oleovorans strain MGY01 isolated from deep sea water Runping Wang a,b, Chong Ren c, Nan Huang c, Yang Liu d, Runying Zeng a,e,⁎ a
China Shool of Marine Sciences, Ningbo University, Ningbo 315211, China State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, SOA, Xiamen 361005, China China Shipbuilding Industry Corporation (CSIC), No. 710 Institute, China d Central Laboratory of Fujian Academy of Agricultural Sciences, Fujian 350003, China e Collaborative Innovation Center of Deep Sea Biology, Hangzhou 310058, China b c
a r t i c l e
i n f o
Article history: Received 11 October 2014 Received in revised form 25 November 2014 Accepted 8 December 2014 Available online 17 December 2014 Keywords: Pseudomonas oleovorans Marine bacteria Malachite green-degrading Genome sequence
a b s t r a c t Pseudomonas oleovorans MGY01 isolated from the deep-sea water of the South China Sea could effectively degrade malachite green. The draft genome of P. oleovorans MGY01 was sequenced and analyzed to gain insights into its efficient metabolic pathway for degrading malachite green. The data obtained revealed 109 Contigs (N50; 128,269 bp) with whole genome size of 5,201,892 bp. The draft genome sequence of strain MGY01 will be helpful in studying the genetic pathways involved in the degradation of malachite green. © 2014 Elsevier B.V. All rights reserved.
1. Introduction Malachite green (MG) is a synthetic triarylmethane dye (C23H26N2CI) and often used in textile manufacturing for coloring silk, jute, leather, cotton, paper. In aquaculture industry it is used as an anti-fungal and antiparasitic agent, which is absorbed in fish and accumulated, is harmful to the ecosystem and human health (Shivaji et al., 2004). Although some species of the genus Pseudomonas have been reported to decolorize triphenylmethane dyes (Chen et al., 2007, Kalyani et al., 2012; Li et al., 2009), no P. oleovorans have been reported. In this study, a MGdegrading strain was isolated from consortium that had been enriched in deep sea water of the South China Sea (21°03′298″E, 118°23′170″N, 1981 m depth) for one year, and was identified as P. oleovorans. This strain has been deposited in the Marine Culture Collection of China (accession number: MCCC 1A10591). The 16S rRNA sequence of MGY01 available in GenBank database (accession number: KF992130) showed 98.55% identity with that of P. oleovorans subsp. lubricantis RS1T (accession number: DQ842018). The genome of MGY01 was sequenced using the Illumina/Solexa MiSeq technology at the Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China). A library with a fragment length of 500 bp was constructed, and a total of 2,978,149 paired-end reads of 300 bp ⁎ Corresponding author at: China Shool of Marine Sciences, Ningbo University, Ningbo 315211, China. Tel./fax: +86 592 2195323. E-mail address: [email protected] (R. Zeng).
http://dx.doi.org/10.1016/j.margen.2014.12.003 1874-7787/© 2014 Elsevier B.V. All rights reserved.
were generated. Approximately 2,961,814 high-quality reads, which provided a 258-fold depth of coverage were assembled with SOAPdenovo version 1.05 (Li et al., 2008). Protein-coding sequences were predicted by Glimmer software version 3.0 (Delcher et al., 2007) and annotated using BLAST searches of nonredundant protein sequences from the NCBI, Swiss-Prot and TrEMBL, COG (Tatusov et al., 2001) and KEGG (Kanehisa et al., 2004) databases. Ribosomal RNA genes were detected using RNAmmer software version 1.2 (Lagesen et al., 2007); transfer RNA genes were detected using tRNAscan-SE (Lowe and Eddy, 1997) (Table 1). In the whole genome, 3669 genes (76.2%) that encode knownfunction proteins and 1020 (21.2%) genes were considered to encode hypothetical proteins. Of the total, 128 (2.7%) genes have no database match. There are 191 genes related to stress response and 72 related Table 1 General features of P. oleovorans MGY01 draft genome. P. oleovorans MGY01 Assembly size (bp) Gene/genome (%) GC content (%) Predicted ORFs Contigs Contig N50 (bp) tRNA rRNA
5,201,892 87.4 64.93 4817 109 128,269 84 2
18
R. Wang et al. / Marine Genomics 20 (2015) 17–18
Fig. 1. Subsystem category distribution of Pnn oleovorans MGY01 (based on RAST annotation server).
Development Program of China (863 program of China; 2012AA092101, 2012AA092103).
Table 2 Genes of P. oleovorans MGY01 participated in degrading MG.
Orf 00245 Orf 00538 Orf 04039
start
Stop
Length(AA)
Description
amount
264829 571597 4344854
265560 572802 4346920
243 401 688
Laccase Catalase Catalase–Peroxidase
1 1 1
to metabolism of aromatic compounds when the contigs were submitted to RAST annotation server (Aziz et al. 2008) (Fig. 1), which may be responsible for the strain MGY01 inhabiting an extreme environment and degrading MG. P. oleovorans MGY01 contains several genes involved in the polycyclic aromatic hydrocarbon degradation, such as ferredoxin component, 3-ketoacyl-CoA thiolase, short-chain dehydrogenase, 4-hydroxy-2-oxovalerate aldolase, dihydrodiol dehydrogenase, 4hydroxyphenylpyruvate dioxygenase and 4,5-DOPA dioxygenase extradiol et al. (Kim et al. 2008). They may be responsible for the degradation of triarylmethane. Of which, there are 3 enzymes most likely related to decolorization MG: laccase, catalase and catalase/peroxidase HPI (Table. 2) (Kalyani et al., 2012; Muhammad et al. 2012). Especially, the laccase has been used for the removal of MG from aqueous solution in previous reports (Kumar et al., 2012; Sinirlioglu et al. 2013). 2. Nucleotide sequence accession number This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JNHE00000000. Acknowledgments This work was financially supported by the China Ocean Mineral Resources R&D Association (DY125-15-T-06), and Hi-Tech Research and
References Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., et al., 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9–75. Chen, C.C., Liao, H.J., Cheng, C.Y., Yen, C.Y., Chung, Y.C., 2007. Biodegradation of crystal violet by Pseudomonas putida. Biotechnol. Lett. 29, 391–396. Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679. Kalyani, D.C., Telke, A.A., Surwase, S.N., et al., 2012. Ecolorization and detoxification of triphenylmethane dye malachite green (MG) by Pseudomonas aeruginosa NCIM 2074 and its enzyme system. Clean Techn. Environ. Policy 14, 989–1001. Kanehisa, M., Goto, S., Kawashima, S., et al., 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280. Kim, S.J., Kweon, O., Jones, R.C., et al., 2008. Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19, 859–881. Kumar, V.V., Sathyaselvabala, V., Premkumar, M.P., et al., 2012. Biochemical characterization of three phrase partitioned laccase and its application in decolorization and degradation of synthetic dyes. J. Mol. Catal. B Enzym. 74, 63–72. Lagesen, K., Hallin, P., Rodland, E.A., et al., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Li, R., Li, Y., Kristiansen, K., et al., 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714. Li, L.T., Qing, H., Xin, Y., Gui, H.F., et al., 2009. Isolation of a malachite green-degrading Pseudomonas sp. MDB-1 strain and cloning of the tmr 2 gene. Biodegradation 20, 769–776. 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, 955–964. Muhammad, A., Rauf, S., Salman, A., 2012. Survey of recent trends in biochemically assisted degradation of dyes. Chem. Eng. J. 209, 520–530. Shivaji, S., Ranjana, S., Roy, D., 2004. Toxicological effects of malachite green. Aquat. Toxicol. 66, 319–329. Sinirlioglu, Z.A., Sinirlioglu, D., Akbas, F., 2013. Preparation and characterization of stable cross-linked enzyme aggregates of novel laccase enzyme from Shewanella putrefaciens and using malachite green decolorization. Bioresour. Technol. 146, 807–811. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., et al., 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22–28.
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/Technical resources
Draft genome sequence of Pseudomonas oleovorans strain MGY01 isolated from deep sea water Runping Wang a,b, Chong Ren c, Nan Huang c, Yang Liu d, Runying Zeng a,e,⁎ a
China Shool of Marine Sciences, Ningbo University, Ningbo 315211, China State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, SOA, Xiamen 361005, China China Shipbuilding Industry Corporation (CSIC), No. 710 Institute, China d Central Laboratory of Fujian Academy of Agricultural Sciences, Fujian 350003, China e Collaborative Innovation Center of Deep Sea Biology, Hangzhou 310058, China b c
a r t i c l e
i n f o
Article history: Received 11 October 2014 Received in revised form 25 November 2014 Accepted 8 December 2014 Available online 17 December 2014 Keywords: Pseudomonas oleovorans Marine bacteria Malachite green-degrading Genome sequence
a b s t r a c t Pseudomonas oleovorans MGY01 isolated from the deep-sea water of the South China Sea could effectively degrade malachite green. The draft genome of P. oleovorans MGY01 was sequenced and analyzed to gain insights into its efficient metabolic pathway for degrading malachite green. The data obtained revealed 109 Contigs (N50; 128,269 bp) with whole genome size of 5,201,892 bp. The draft genome sequence of strain MGY01 will be helpful in studying the genetic pathways involved in the degradation of malachite green. © 2014 Elsevier B.V. All rights reserved.
1. Introduction Malachite green (MG) is a synthetic triarylmethane dye (C23H26N2CI) and often used in textile manufacturing for coloring silk, jute, leather, cotton, paper. In aquaculture industry it is used as an anti-fungal and antiparasitic agent, which is absorbed in fish and accumulated, is harmful to the ecosystem and human health (Shivaji et al., 2004). Although some species of the genus Pseudomonas have been reported to decolorize triphenylmethane dyes (Chen et al., 2007, Kalyani et al., 2012; Li et al., 2009), no P. oleovorans have been reported. In this study, a MGdegrading strain was isolated from consortium that had been enriched in deep sea water of the South China Sea (21°03′298″E, 118°23′170″N, 1981 m depth) for one year, and was identified as P. oleovorans. This strain has been deposited in the Marine Culture Collection of China (accession number: MCCC 1A10591). The 16S rRNA sequence of MGY01 available in GenBank database (accession number: KF992130) showed 98.55% identity with that of P. oleovorans subsp. lubricantis RS1T (accession number: DQ842018). The genome of MGY01 was sequenced using the Illumina/Solexa MiSeq technology at the Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China). A library with a fragment length of 500 bp was constructed, and a total of 2,978,149 paired-end reads of 300 bp ⁎ Corresponding author at: China Shool of Marine Sciences, Ningbo University, Ningbo 315211, China. Tel./fax: +86 592 2195323. E-mail address: [email protected] (R. Zeng).
http://dx.doi.org/10.1016/j.margen.2014.12.003 1874-7787/© 2014 Elsevier B.V. All rights reserved.
were generated. Approximately 2,961,814 high-quality reads, which provided a 258-fold depth of coverage were assembled with SOAPdenovo version 1.05 (Li et al., 2008). Protein-coding sequences were predicted by Glimmer software version 3.0 (Delcher et al., 2007) and annotated using BLAST searches of nonredundant protein sequences from the NCBI, Swiss-Prot and TrEMBL, COG (Tatusov et al., 2001) and KEGG (Kanehisa et al., 2004) databases. Ribosomal RNA genes were detected using RNAmmer software version 1.2 (Lagesen et al., 2007); transfer RNA genes were detected using tRNAscan-SE (Lowe and Eddy, 1997) (Table 1). In the whole genome, 3669 genes (76.2%) that encode knownfunction proteins and 1020 (21.2%) genes were considered to encode hypothetical proteins. Of the total, 128 (2.7%) genes have no database match. There are 191 genes related to stress response and 72 related Table 1 General features of P. oleovorans MGY01 draft genome. P. oleovorans MGY01 Assembly size (bp) Gene/genome (%) GC content (%) Predicted ORFs Contigs Contig N50 (bp) tRNA rRNA
5,201,892 87.4 64.93 4817 109 128,269 84 2
18
R. Wang et al. / Marine Genomics 20 (2015) 17–18
Fig. 1. Subsystem category distribution of Pnn oleovorans MGY01 (based on RAST annotation server).
Development Program of China (863 program of China; 2012AA092101, 2012AA092103).
Table 2 Genes of P. oleovorans MGY01 participated in degrading MG.
Orf 00245 Orf 00538 Orf 04039
start
Stop
Length(AA)
Description
amount
264829 571597 4344854
265560 572802 4346920
243 401 688
Laccase Catalase Catalase–Peroxidase
1 1 1
to metabolism of aromatic compounds when the contigs were submitted to RAST annotation server (Aziz et al. 2008) (Fig. 1), which may be responsible for the strain MGY01 inhabiting an extreme environment and degrading MG. P. oleovorans MGY01 contains several genes involved in the polycyclic aromatic hydrocarbon degradation, such as ferredoxin component, 3-ketoacyl-CoA thiolase, short-chain dehydrogenase, 4-hydroxy-2-oxovalerate aldolase, dihydrodiol dehydrogenase, 4hydroxyphenylpyruvate dioxygenase and 4,5-DOPA dioxygenase extradiol et al. (Kim et al. 2008). They may be responsible for the degradation of triarylmethane. Of which, there are 3 enzymes most likely related to decolorization MG: laccase, catalase and catalase/peroxidase HPI (Table. 2) (Kalyani et al., 2012; Muhammad et al. 2012). Especially, the laccase has been used for the removal of MG from aqueous solution in previous reports (Kumar et al., 2012; Sinirlioglu et al. 2013). 2. Nucleotide sequence accession number This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JNHE00000000. Acknowledgments This work was financially supported by the China Ocean Mineral Resources R&D Association (DY125-15-T-06), and Hi-Tech Research and
References Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., et al., 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9–75. Chen, C.C., Liao, H.J., Cheng, C.Y., Yen, C.Y., Chung, Y.C., 2007. Biodegradation of crystal violet by Pseudomonas putida. Biotechnol. Lett. 29, 391–396. Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679. Kalyani, D.C., Telke, A.A., Surwase, S.N., et al., 2012. Ecolorization and detoxification of triphenylmethane dye malachite green (MG) by Pseudomonas aeruginosa NCIM 2074 and its enzyme system. Clean Techn. Environ. Policy 14, 989–1001. Kanehisa, M., Goto, S., Kawashima, S., et al., 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280. Kim, S.J., Kweon, O., Jones, R.C., et al., 2008. Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19, 859–881. Kumar, V.V., Sathyaselvabala, V., Premkumar, M.P., et al., 2012. Biochemical characterization of three phrase partitioned laccase and its application in decolorization and degradation of synthetic dyes. J. Mol. Catal. B Enzym. 74, 63–72. Lagesen, K., Hallin, P., Rodland, E.A., et al., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Li, R., Li, Y., Kristiansen, K., et al., 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714. Li, L.T., Qing, H., Xin, Y., Gui, H.F., et al., 2009. Isolation of a malachite green-degrading Pseudomonas sp. MDB-1 strain and cloning of the tmr 2 gene. Biodegradation 20, 769–776. 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, 955–964. Muhammad, A., Rauf, S., Salman, A., 2012. Survey of recent trends in biochemically assisted degradation of dyes. Chem. Eng. J. 209, 520–530. Shivaji, S., Ranjana, S., Roy, D., 2004. Toxicological effects of malachite green. Aquat. Toxicol. 66, 319–329. Sinirlioglu, Z.A., Sinirlioglu, D., Akbas, F., 2013. Preparation and characterization of stable cross-linked enzyme aggregates of novel laccase enzyme from Shewanella putrefaciens and using malachite green decolorization. Bioresour. Technol. 146, 807–811. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., et al., 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22–28.
