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Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment
MARGEN-00325; No of Pages 3 Marine Genomics xxx (2015) xxx–xxx
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/Technical resource paper
Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment Hua-Qi Pan ⁎, Jiang-Chun Hu ⁎ Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
a r t i c l e
i n f o
Article history: Received 28 April 2015 Received in revised form 5 May 2015 Accepted 5 May 2015 Available online xxxx Keywords: Pseudomonas Deep-sea bacterium Antimicrobial activity Genome sequence
a b s t r a c t Pseudomonas sp. 10B238 was a putatively novel species of Pseudomonas, isolated from a deep-sea sediment of the South China Sea, which had the genetic potential to produce secondary metabolites related to nonribosomal peptides (NRPs), as well as showed moderate antimicrobial activities. Here we report a high quality draft genome of Pseudomonas sp. 10B238, which comprises 4,933,052 bp with the G + C content of 60.23%. A total of 11 potential secondary metabolite biosynthetic gene clusters were predicted, including a NRP for new peptide siderophore. And many anaerobic respiratory terminal enzymes were found for life in deep-sea environments. Our results may provide insights into biosynthetic pathway for antimicrobial bioactive compounds and be helpful to understand the physiological characteristic of this species. © 2015 Elsevier B.V. All rights reserved.
1. Introduction Marine microorganisms are an important source for the development of new antibiotics due to their vast majority and rich biodiversity as well as abundant and unique metabolites. Notably, it is likely that many of new species as novel taxon will be a promising source of new bioactive compounds (Goodfellow and Fiedler, 2010). Thus, we have focused on the isolation of novel marine bacteria from neglected ecological niches and extreme environments, and on screening for their capacity to produce new metabolites (Pan et al., 2015). Pseudomonas is one of the most diverse and prevalent genera that are present in all natural environments. A number of Pseudomonas strains are known biological control agents (BCAs) and plant growthpromoting rhizobacteria (PGPR) (Walsh et al., 2001). Such strains can produce a variety of secondary metabolites including siderophores and antibiotics which stimulate plant growth and/or suppress many phytopathogens, such as phenazine derivatives, pyoluteorin, pyrrolnitrin, 2,4-diacetylphloroglucinol, hydrogen cyanide, and so on (Haas et al., 1991; Shen et al., 2013). 2. Data description In the present study, a new strain Pseudomonas sp. 10B238 was isolated from a sediment collected at the depth of 1464 m from the South China Sea (6°59.980′ N 113°0.817′ E). And deposited at the China General Microbiological Culture Collection Center with the number CGMCC 115270. This strain had the genetic potential to produce ⁎ Corresponding authors. Tel.: +86 24 83970386; fax: +86 24 83970300. E-mail addresses: [email protected] (H.-Q. Pan), [email protected] (J.-C. Hu).
secondary metabolites related to nonribosomal peptides (NRPs), as well as showed moderate antimicrobial activities. Phylogenetic tree analysis of the 16S rRNA gene sequence (GenBank accession number: KP715167) clearly showed isolate 10B238 formed a distinct lineage clustered with the selected representatives of Pseudomonas (Fig. 1). The low DNA–DNA hybridization relatedness values (b50%) between strain 10B238 and the most closely related type strains of Pseudomonas xanthomarina KMM 1447T and Pseudomonas kunmingensis HL22-2T further demonstrated that the isolate represents a novel species of the genus Pseudomonas. In an effort to better understand the physiological characteristic and metabolic potential as well as to open up new opportunities in the functional genomics of this species, we report the draft genome sequence of Pseudomonas sp. 10B238. Pseudomonas sp. 10B238 was cultivated on tryptic soy broth (TSB), which contains: casein peptone (pancreatic) 17.0, soya peptone (papain digest.) 3.0, sodium chloride 5.0, dipotassium hydrogen phosphate 2.5, glucose 2.5, distilled water 1 L, adjust pH to 7.3 ± 0.2 at 25 °C. Cells were pelleted by centrifugation and genomic DNA extracted using the conventional methods (Gontang et al., 2007). The genome of Pseudomonas sp. 10B238 was sequenced using the Illumina HiSeq2000 technology at the Shanghai Majorbio BiopharmTechnology Co., Ltd. (Shanghai, China). A library with a fragment length of 300 bp was constructed, and a total of 5,869,260 high-quality paired-end reads were generated to reach approximately 200-fold coverage of the genome. These generated reads were assembled into 54 contigs N 1 kb in size with an N50 contig size of 312,794 bp using SOAPdenovo version 1.05 (Li et al., 2010). Gene sequences were predicted by Glimmer software version 3.0 (Delcher et al., 2007), and functions of the gene products were annotated by BLAST searches (Camacho et al., 2009) of non-redundant protein sequences from the NCBI, Swiss-Prot (Bairoch et al., 2004), COG
http://dx.doi.org/10.1016/j.margen.2015.05.003 1874-7787/© 2015 Elsevier B.V. All rights reserved.
Please cite this article as: Pan, H.-Q., Hu, J.-C., Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.05.003
2
H.-Q. Pan, J.-C. Hu / Marine Genomics xxx (2015) xxx–xxx
Pseudomonas oleovorans subsp. lubricantis RS1T(DQ842018) Pseudomonas alcaliphila AL15-21T(AB030583) T 67 Pseudomonas toyotomiensis HT-3 T(AB453701) Pseudomonas chengduensis MBR (EU307111) 93 Pseudomonas mendocina LMG 1223T(Z76664) Pseudomonas indoloxydans IPL-1T(DQ916277) 77 Pseudomonas otitidis MCC10330T(AY953147) 70 67 Pseudomonas alcaligenes NBRC 14159T(BATI01000076) Pseudomonas stutzeri ATCC 17588T(CP002881) 10B238 Pseudomonas kunmingensis HL22-2T(JQ246444) 93 97 Pseudomonas xanthomarina KMM 1447T(AB176954) Pseudomonas seleniipraecipitans CA5T(FJ422810) Pseudomonas flavescens B62T(U01916) 86 Pseudomonas punonensis LMT03T(JQ344321) Pseudomonas argentinensis CH01T(AY691188) 56 84 Pseudomonas straminea IAM1598T(D84023) T 99 Pseudomonas fuscovaginae ICMP 5940 (BATG01000120) T 73 Pseudomonas asplenii LMG 2137 (Z76655) Pseudomonas vranovensis CCM 7279T(AY970951) 68 Pseudomonas japonica IAM 15071T(AB126621) Pseudomonas putida NBRC 14164T(AP013070) Pseudomonas cremoricolorata IAM 1541T(AB060137) 69 Pseudomonas parafulva AJ 2129T(AB060132) T 52 Pseudomonas plecoglossicida FPC951 (AB009457) T (AF064458) Pseudomonas monteilii CIP 104883 66 Pseudomonas taiwanensis BCRC 17751T(EU103629) 83 Pseudomonas guariconensis PCAVU11T(HF674459) Pseudomonas entomophila L48T(AY907566) T 70 Pseudomonas mosselii CIP 105259 (AF072688) T 68 Pseudomonas soli F-279208 (HF930598) Pseudomonas agarici NCPPB 2289T(AKBQ01000002) Pseudomonas lundensis ATCC 49968T(AB021395) Pseudomonas helmanticensis OHA11T(HG940537) 58 Pseudomonas moraviensis CCM 7280T(AY970952) 63 T 62 Pseudomonas baetica a390 (FM201274) Pseudomonas jessenii CIP 105274T(AF068259) Pseudomonas graminis DSM 11363T(Y11150) 99 Pseudomonas lutea OK2T(AY364537) Acinetobacter baumannii ATCC 19606T(ACQB01000091) 57
0.01 Fig. 1. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the position of strain 10B238 in the genus Pseudomonas. Phylogenetic tree was constructed using the MEGA 6.0 program. Acinetobacter baumannii ATCC 19606T was used as an outgroup. Bootstrap values (expressed as percentages of 1000 replications) of above 50% are shown at the branch points. Bar, 0.01 sequence divergence.
(Tatusov et al., 2001), and KEGG (Kanehisa et al., 2004) databases. The rRNA and tRNA genes were identified using RNAmmer (Lagesen et al., 2007) and tRNAscan-SE (Lowe and Eddy, 1997). The antibiotics and secondary metabolites production clusters were examined using the antiSMASH program (Blin et al., 2013) and manually verified. The genome features of Pseudomonas sp. 10B238 are summarized in Table 1. The draft genome is 4,933,052 bp in length, with a G + C content of 60.2%. A total of 4488 coding sequences were predicted with an average length of 950 bp. Single 5S and 16S rRNA genes and 54 tRNA genes for all 20 amino acids were identified. The proteins associated with amino acid transport and metabolism (COG initial, E) were the most abundant group of COG (319 ORFs, 8.4%). Approximately 2.7% proteins (103 ORFs) hit with secondary metabolites biosynthesis, transport and catabolism (COG initial, Q). A total of 11 gene clusters (ClusterFinder probability N 0.9) potentially involved in the biosynthesis of secondary metabolites were identified
in the genome (Table 2). One of these gene clusters, which contained a nonribosomal peptide (NRP), was predicted to direct the synthesis of a new peptide siderophore consisting of Dhb, Lys, Gly and an unpredicted amino acid. Additionally, four secondary metabolite Table 1 General features of Pseudomonas sp. 10B238 draft genome. Attributes/features
Values
Assembly size (bp) No. of all contigs No. of large scaffords (N1000 bp) Scaffold N50 (bp) G + C content% Total number of genes tRNA genes rRNA genes
4,933,052 90 46 312,794 60.23% 4488 54 2
Please cite this article as: Pan, H.-Q., Hu, J.-C., Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.05.003
H.-Q. Pan, J.-C. Hu / Marine Genomics xxx (2015) xxx–xxx Table 2 Secondary metabolite biosynthetic gene clusters (or genes) of Pseudomonas sp. 10B238. Gene cluster
Predicted product
Contig (NCBI accession no.)
Location of gene clusters
Cluster 1 Cluster 2 Cluster 3 Cluster 4 Cluster 5 Cluster 6 Cluster 7 Cluster 8 Cluster 9 Cluster 10 Cluster 11
NRP (siderophore) Unknown Terpene Unknown Arylpolyene Unknown Unknown Ectoine Bacteriocin Unknown Unknown
Contig 1 (JWTL01000001) Contig 2 (JWTL01000002) Contig 2 (JWTL01000002) Contig 2 (JWTL01000002) Contig 9 (JWTL01000009) Contig 14 (JWTL01000014) Contig 16 (JWTL01000016) Contig 16 (JWTL01000016) Contig 17 (JWTL01000017) Contig 17 (JWTL01000017) Contig 18 (JWTL01000018)
455,482–507,895 nt 23,631–33,376 nt 353,639–377,248 nt 401,457–424,299 nt 62,946–106,533 nt 40,885–57,418 nt 2461–16,788 nt 159,965–170,363 nt 90,897–101,733 nt 134,577–167,280 nt 146,556–168,292 nt
biosynthetic gene clusters were predicted for terpene, arylpolyene, ectoine and bacteriocin, respectively. However, this genome did not contain genes related to the biosyntheses of 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin and hydrogen cyanide. Although there were many biosynthetic genes for phenazine precursors (chorismic acid, isochorismic acid and 2,3-dihydro-2,3-dihydroxybenzoate), a complete gene cluster for phenazine and its derivatives was not found in this genome. These results indicated that the 10B238 strain has evolved own species-specific genomic and metabolic features. Further, bioinformatic analysis revealed that strain 10B238 contains genes involved in broad utilization of carbon sources, denitrification, degradation of aromatic compounds, multiple pathways of protection against environmental stress and other functions, which benefit its environmental adaptability and competitiveness in the marine habitats. In particular, there were many anaerobic respiratory terminal enzymes, including nitrate reductase and multiple molybdoenzymes, which are closely associated with life in anaerobic environments. These might support the growth of the bacterium in the deep-sea sediments. The present genomic data will offer insights into the genetic, biological and physiological characteristics of this putatively novel Pseudomonas species, and also will be helpful to thoroughly understand its speciesspecific metabolites. 3. Nucleotide sequence accession number The draft genome sequence of Pseudomonas sp. 10B238 is available in GenBank under the accession no. JWTL01000000.
3
Acknowledgments This research was supported by the National Natural Science Foundation of China (No. 41006088), National High-tech R & D Program of China (863 Program) (2012AA092104). Zhi-Jian Yu deposited the Whole Genome Shotgun project at GenBank. References Bairoch, A., Boeckmann, B., Ferro, S., Gasteiger, E., 2004. Swiss-Prot: juggling between evolution and stability. Brief. Bioinform. 5 (1), 39–55. Blin, K., Medema, M.H., Kazempour, D., Fischbach, M.A., Breitling, R., Takano, E., Weber, T., 2013. antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 41 (W1), W204–W212. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L., 2009. BLAST+: architecture and applications. BMC Bioinformatics 10 (1), 421. 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. Gontang, E.A., Fenical, W., Jensen, P.R., 2007. Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl. Environ. Microbiol. 73 (10), 3272–3282. Goodfellow, M., Fiedler, H., 2010. A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie Van Leeuwenhoek 98, 119–142. Haas, D., Keel, C., Laville, J., Maurhofer, M., OberhÄnsli, T., Schnider, U., Voisard, C., Wüthrich, B., Defago, G., 1991. Secondary metabolites of Pseudomonas fluorescens strain CHA0 Involved in the suppression of root diseases. In: Hennecke, H., Verma, D. (Eds.), Advances in Molecular Genetics of Plant-Microbe Interactions Vol. 10 vol. 10. Springer, Netherlands, pp. 450–456. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M., 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32 (Suppl. 1), D277–D280. Lagesen, K., Hallin, P., Rødland, E.A., Stærfeldt, H.-H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35 (9), 3100–3108. Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20 (2), 265–272. 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), 0955–0964. Pan, H.-Q., Cheng, J., Zhang, D.-F., Yu, S.-Y., Khieu, T.-N., Son, C.K., Jiang, Z., Hu, J.-C., Li, W.-J., 2015. Streptomyces bohaiensis sp. nov., a novel actinomycete isolated from Scomberomorus niphonius in the Bohai Sea. J. Antibiot. 68 (4), 246–252. Shen, X., Hu, H., Peng, H., Wang, W., Zhang, X., 2013. Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. BMC Genomics 14 (1), 271. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., Tatusova, T.A., Shankavaram, U.T., Rao, B.S., Kiryutin, B., Galperin, M.Y., Fedorova, N.D., Koonin, E.V., 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29 (1), 22–28. Walsh, U.F., Morrissey, J.P., O'Gara, F., 2001. Pseudomonas for biocontrol of phytopathogens: from functional genomics to commercial exploitation. Curr. Opin. Biotechnol. 12 (3), 289–295.
Please cite this article as: Pan, H.-Q., Hu, J.-C., Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.05.003
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/Technical resource paper
Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment Hua-Qi Pan ⁎, Jiang-Chun Hu ⁎ Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
a r t i c l e
i n f o
Article history: Received 28 April 2015 Received in revised form 5 May 2015 Accepted 5 May 2015 Available online xxxx Keywords: Pseudomonas Deep-sea bacterium Antimicrobial activity Genome sequence
a b s t r a c t Pseudomonas sp. 10B238 was a putatively novel species of Pseudomonas, isolated from a deep-sea sediment of the South China Sea, which had the genetic potential to produce secondary metabolites related to nonribosomal peptides (NRPs), as well as showed moderate antimicrobial activities. Here we report a high quality draft genome of Pseudomonas sp. 10B238, which comprises 4,933,052 bp with the G + C content of 60.23%. A total of 11 potential secondary metabolite biosynthetic gene clusters were predicted, including a NRP for new peptide siderophore. And many anaerobic respiratory terminal enzymes were found for life in deep-sea environments. Our results may provide insights into biosynthetic pathway for antimicrobial bioactive compounds and be helpful to understand the physiological characteristic of this species. © 2015 Elsevier B.V. All rights reserved.
1. Introduction Marine microorganisms are an important source for the development of new antibiotics due to their vast majority and rich biodiversity as well as abundant and unique metabolites. Notably, it is likely that many of new species as novel taxon will be a promising source of new bioactive compounds (Goodfellow and Fiedler, 2010). Thus, we have focused on the isolation of novel marine bacteria from neglected ecological niches and extreme environments, and on screening for their capacity to produce new metabolites (Pan et al., 2015). Pseudomonas is one of the most diverse and prevalent genera that are present in all natural environments. A number of Pseudomonas strains are known biological control agents (BCAs) and plant growthpromoting rhizobacteria (PGPR) (Walsh et al., 2001). Such strains can produce a variety of secondary metabolites including siderophores and antibiotics which stimulate plant growth and/or suppress many phytopathogens, such as phenazine derivatives, pyoluteorin, pyrrolnitrin, 2,4-diacetylphloroglucinol, hydrogen cyanide, and so on (Haas et al., 1991; Shen et al., 2013). 2. Data description In the present study, a new strain Pseudomonas sp. 10B238 was isolated from a sediment collected at the depth of 1464 m from the South China Sea (6°59.980′ N 113°0.817′ E). And deposited at the China General Microbiological Culture Collection Center with the number CGMCC 115270. This strain had the genetic potential to produce ⁎ Corresponding authors. Tel.: +86 24 83970386; fax: +86 24 83970300. E-mail addresses: [email protected] (H.-Q. Pan), [email protected] (J.-C. Hu).
secondary metabolites related to nonribosomal peptides (NRPs), as well as showed moderate antimicrobial activities. Phylogenetic tree analysis of the 16S rRNA gene sequence (GenBank accession number: KP715167) clearly showed isolate 10B238 formed a distinct lineage clustered with the selected representatives of Pseudomonas (Fig. 1). The low DNA–DNA hybridization relatedness values (b50%) between strain 10B238 and the most closely related type strains of Pseudomonas xanthomarina KMM 1447T and Pseudomonas kunmingensis HL22-2T further demonstrated that the isolate represents a novel species of the genus Pseudomonas. In an effort to better understand the physiological characteristic and metabolic potential as well as to open up new opportunities in the functional genomics of this species, we report the draft genome sequence of Pseudomonas sp. 10B238. Pseudomonas sp. 10B238 was cultivated on tryptic soy broth (TSB), which contains: casein peptone (pancreatic) 17.0, soya peptone (papain digest.) 3.0, sodium chloride 5.0, dipotassium hydrogen phosphate 2.5, glucose 2.5, distilled water 1 L, adjust pH to 7.3 ± 0.2 at 25 °C. Cells were pelleted by centrifugation and genomic DNA extracted using the conventional methods (Gontang et al., 2007). The genome of Pseudomonas sp. 10B238 was sequenced using the Illumina HiSeq2000 technology at the Shanghai Majorbio BiopharmTechnology Co., Ltd. (Shanghai, China). A library with a fragment length of 300 bp was constructed, and a total of 5,869,260 high-quality paired-end reads were generated to reach approximately 200-fold coverage of the genome. These generated reads were assembled into 54 contigs N 1 kb in size with an N50 contig size of 312,794 bp using SOAPdenovo version 1.05 (Li et al., 2010). Gene sequences were predicted by Glimmer software version 3.0 (Delcher et al., 2007), and functions of the gene products were annotated by BLAST searches (Camacho et al., 2009) of non-redundant protein sequences from the NCBI, Swiss-Prot (Bairoch et al., 2004), COG
http://dx.doi.org/10.1016/j.margen.2015.05.003 1874-7787/© 2015 Elsevier B.V. All rights reserved.
Please cite this article as: Pan, H.-Q., Hu, J.-C., Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.05.003
2
H.-Q. Pan, J.-C. Hu / Marine Genomics xxx (2015) xxx–xxx
Pseudomonas oleovorans subsp. lubricantis RS1T(DQ842018) Pseudomonas alcaliphila AL15-21T(AB030583) T 67 Pseudomonas toyotomiensis HT-3 T(AB453701) Pseudomonas chengduensis MBR (EU307111) 93 Pseudomonas mendocina LMG 1223T(Z76664) Pseudomonas indoloxydans IPL-1T(DQ916277) 77 Pseudomonas otitidis MCC10330T(AY953147) 70 67 Pseudomonas alcaligenes NBRC 14159T(BATI01000076) Pseudomonas stutzeri ATCC 17588T(CP002881) 10B238 Pseudomonas kunmingensis HL22-2T(JQ246444) 93 97 Pseudomonas xanthomarina KMM 1447T(AB176954) Pseudomonas seleniipraecipitans CA5T(FJ422810) Pseudomonas flavescens B62T(U01916) 86 Pseudomonas punonensis LMT03T(JQ344321) Pseudomonas argentinensis CH01T(AY691188) 56 84 Pseudomonas straminea IAM1598T(D84023) T 99 Pseudomonas fuscovaginae ICMP 5940 (BATG01000120) T 73 Pseudomonas asplenii LMG 2137 (Z76655) Pseudomonas vranovensis CCM 7279T(AY970951) 68 Pseudomonas japonica IAM 15071T(AB126621) Pseudomonas putida NBRC 14164T(AP013070) Pseudomonas cremoricolorata IAM 1541T(AB060137) 69 Pseudomonas parafulva AJ 2129T(AB060132) T 52 Pseudomonas plecoglossicida FPC951 (AB009457) T (AF064458) Pseudomonas monteilii CIP 104883 66 Pseudomonas taiwanensis BCRC 17751T(EU103629) 83 Pseudomonas guariconensis PCAVU11T(HF674459) Pseudomonas entomophila L48T(AY907566) T 70 Pseudomonas mosselii CIP 105259 (AF072688) T 68 Pseudomonas soli F-279208 (HF930598) Pseudomonas agarici NCPPB 2289T(AKBQ01000002) Pseudomonas lundensis ATCC 49968T(AB021395) Pseudomonas helmanticensis OHA11T(HG940537) 58 Pseudomonas moraviensis CCM 7280T(AY970952) 63 T 62 Pseudomonas baetica a390 (FM201274) Pseudomonas jessenii CIP 105274T(AF068259) Pseudomonas graminis DSM 11363T(Y11150) 99 Pseudomonas lutea OK2T(AY364537) Acinetobacter baumannii ATCC 19606T(ACQB01000091) 57
0.01 Fig. 1. Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showing the position of strain 10B238 in the genus Pseudomonas. Phylogenetic tree was constructed using the MEGA 6.0 program. Acinetobacter baumannii ATCC 19606T was used as an outgroup. Bootstrap values (expressed as percentages of 1000 replications) of above 50% are shown at the branch points. Bar, 0.01 sequence divergence.
(Tatusov et al., 2001), and KEGG (Kanehisa et al., 2004) databases. The rRNA and tRNA genes were identified using RNAmmer (Lagesen et al., 2007) and tRNAscan-SE (Lowe and Eddy, 1997). The antibiotics and secondary metabolites production clusters were examined using the antiSMASH program (Blin et al., 2013) and manually verified. The genome features of Pseudomonas sp. 10B238 are summarized in Table 1. The draft genome is 4,933,052 bp in length, with a G + C content of 60.2%. A total of 4488 coding sequences were predicted with an average length of 950 bp. Single 5S and 16S rRNA genes and 54 tRNA genes for all 20 amino acids were identified. The proteins associated with amino acid transport and metabolism (COG initial, E) were the most abundant group of COG (319 ORFs, 8.4%). Approximately 2.7% proteins (103 ORFs) hit with secondary metabolites biosynthesis, transport and catabolism (COG initial, Q). A total of 11 gene clusters (ClusterFinder probability N 0.9) potentially involved in the biosynthesis of secondary metabolites were identified
in the genome (Table 2). One of these gene clusters, which contained a nonribosomal peptide (NRP), was predicted to direct the synthesis of a new peptide siderophore consisting of Dhb, Lys, Gly and an unpredicted amino acid. Additionally, four secondary metabolite Table 1 General features of Pseudomonas sp. 10B238 draft genome. Attributes/features
Values
Assembly size (bp) No. of all contigs No. of large scaffords (N1000 bp) Scaffold N50 (bp) G + C content% Total number of genes tRNA genes rRNA genes
4,933,052 90 46 312,794 60.23% 4488 54 2
Please cite this article as: Pan, H.-Q., Hu, J.-C., Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.05.003
H.-Q. Pan, J.-C. Hu / Marine Genomics xxx (2015) xxx–xxx Table 2 Secondary metabolite biosynthetic gene clusters (or genes) of Pseudomonas sp. 10B238. Gene cluster
Predicted product
Contig (NCBI accession no.)
Location of gene clusters
Cluster 1 Cluster 2 Cluster 3 Cluster 4 Cluster 5 Cluster 6 Cluster 7 Cluster 8 Cluster 9 Cluster 10 Cluster 11
NRP (siderophore) Unknown Terpene Unknown Arylpolyene Unknown Unknown Ectoine Bacteriocin Unknown Unknown
Contig 1 (JWTL01000001) Contig 2 (JWTL01000002) Contig 2 (JWTL01000002) Contig 2 (JWTL01000002) Contig 9 (JWTL01000009) Contig 14 (JWTL01000014) Contig 16 (JWTL01000016) Contig 16 (JWTL01000016) Contig 17 (JWTL01000017) Contig 17 (JWTL01000017) Contig 18 (JWTL01000018)
455,482–507,895 nt 23,631–33,376 nt 353,639–377,248 nt 401,457–424,299 nt 62,946–106,533 nt 40,885–57,418 nt 2461–16,788 nt 159,965–170,363 nt 90,897–101,733 nt 134,577–167,280 nt 146,556–168,292 nt
biosynthetic gene clusters were predicted for terpene, arylpolyene, ectoine and bacteriocin, respectively. However, this genome did not contain genes related to the biosyntheses of 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin and hydrogen cyanide. Although there were many biosynthetic genes for phenazine precursors (chorismic acid, isochorismic acid and 2,3-dihydro-2,3-dihydroxybenzoate), a complete gene cluster for phenazine and its derivatives was not found in this genome. These results indicated that the 10B238 strain has evolved own species-specific genomic and metabolic features. Further, bioinformatic analysis revealed that strain 10B238 contains genes involved in broad utilization of carbon sources, denitrification, degradation of aromatic compounds, multiple pathways of protection against environmental stress and other functions, which benefit its environmental adaptability and competitiveness in the marine habitats. In particular, there were many anaerobic respiratory terminal enzymes, including nitrate reductase and multiple molybdoenzymes, which are closely associated with life in anaerobic environments. These might support the growth of the bacterium in the deep-sea sediments. The present genomic data will offer insights into the genetic, biological and physiological characteristics of this putatively novel Pseudomonas species, and also will be helpful to thoroughly understand its speciesspecific metabolites. 3. Nucleotide sequence accession number The draft genome sequence of Pseudomonas sp. 10B238 is available in GenBank under the accession no. JWTL01000000.
3
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Please cite this article as: Pan, H.-Q., Hu, J.-C., Draft genome sequence of the novel strain Pseudomonas sp. 10B238 with potential ability to produce antibiotics from deep-sea sediment, Mar. Genomics (2015), http://dx.doi.org/10.1016/j.margen.2015.05.003