- Email: [email protected]
Genome sequence of Brevibacillus agri strain 5-2, isolated from the formation water of petroleum reservoir
Marine Genomics 18 (2014) 123–125
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/Technical resources
Genome sequence of Brevibacillus agri strain 5-2, isolated from the formation water of petroleum reservoir Yuehui She a,1, Wenqiong Wu a, Chunchun Hang a, Xiawei Jiang b, Lujun Chai c, Gaoming Yu d, Fuchang Shu a, Zhengliang Wang a, Sanbao Su a,1, Tingsheng Xiang a, Zhongzhi Zhang e, DuJie Hou c, Fan Zhang c, Beiwen Zheng b,⁎ a
College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, China State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China c The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing, China d College of Petroleum Engineering, Yangtze University, Jingzhou, China e State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China b
a r t i c l e
i n f o
Article history: Received 28 July 2014 Received in revised form 23 August 2014 Accepted 24 August 2014 Available online 4 September 2014 Keywords: Brevibacillus agri Formation water Oilfield Degrading Comparative genomics
a b s t r a c t Brevibacillus agri strain 5-2 was isolated from the formation water of a deep oil reservoir in Changqing Oilfield, China. This bacterium was found to have a capacity for degrading tetradecane, hexadecane and alkanesulfonate. To gain insights into its efficient metabolic pathway for degrading hydrocarbon and organosulfur compounds, here, we report the high quality draft genome of this strain. Two putative alkane 1-monooxygenases, one putative alkanesulfonate monooxygenase, one putative alkanesulfonate transporter, one putative sulfate permease and five putative sulfate transporters were identified in the draft genome. The genomic data of strain 5-2 may provide insights into the mechanism of microorganisms adapt to the petroleum reservoir after chemical flooding. © 2014 Elsevier B.V. All rights reserved.
1. Introduction Chemical flooding is considered as the most important and broadly applied enhanced oil recovery processes which increasing the viscosity of the injected water and reducing the swept zone permeability, and, consequently, increasing the oil recovery (Bao et al., 2010). Until now, sulfonate surfactants have been widely adopted as flooding agents in China (She et al., 2011). Biodegradation of hydrocarbon in petroleum reservoirs has adversely affected the majority of the world's oil, making recovery and refining of that oil more costly (Jones et al., 2008). Microorganisms isolated from formation waters play a key role in the subsurface hydrocarbon degradation, however, the specific pathway occurring in oil reservoirs remains poorly defined (Zhang et al., 2012). Previously, we isolated and characterized three indigenous microorganisms from a petroleum reservoir after polymer flooding (She et al., 2011). To further the characterization of microorganisms in petroleum reservoir after chemical flooding, currently, we isolated a Brevibacillus agri strain 5-2 (= CGMCC 5645) from a mixture of formation water and petroleum in Changqing oilfield, China. Phylogenetic tree clearly ⁎ Corresponding author. Tel./fax: +86 571 87236423. E-mail address: [email protected] (B. Zheng). 1 These authors contributed equally to this work.
http://dx.doi.org/10.1016/j.margen.2014.08.006 1874-7787/© 2014 Elsevier B.V. All rights reserved.
showed that B. agri type strain NRRL NRS-1219 is most closely related to the strain 5-2 (Fig. S1). Interestingly, strain 5-2 growing aerobically with tetradecane and hexadecane as the sole carbon, and was also found to have a capacity for metabolizing sulfonate. Previous studies have documented the capability of hydrocarbon biodegradation in Brevibacillus borstelensis strain 707 (Hadad et al., 2005), Brevibacillus sp. strain PDM-3 (Reddy et al., 2010) and Brevibacillus panacihumi strain W25 (Wang et al., 2014). However, no metabolism pathways involved in petroleum degradation was further characterized in B. agri. Therefore, B. agri strain 5-2 was subjected to the whole genome sequencing for genomic analysis, and this can add more knowledge about the potential industrial applications of B. agri. The draft genome sequence of B. agri 5-2 strain was performed by using Illumina Hieseq 2000 genomic sequencer at BGI (Shenzhen, China). One 500-bp insert-size DNA library was generated then sequenced with Illumina Hiseq 2000 by using 2 × 100 bp pair end sequencing strategy. Filtered clean reads were assembled into scaffolds using the Velvet version 1.2.07 (Zerbino and Birney, 2008), PAGIT flow was used to prolong the initial contigs and correct sequencing errors (Swain et al., 2012). Predict genes were identified using Glimmer version 3.0 (Delcher et al., 2007), tRNAscan-SE version 1.21 (Lowe and Eddy, 1997) was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer version 1.2 (Lagesen et al., 2007).
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Y. She et al. / Marine Genomics 18 (2014) 123–125
Table 1 Genome features. B. agri strain 5-2 Size (bp) Contigs G + C content (bp) Coding region (bp) Protein-coding genes tRNA genes rRNA genes Genes assigned to COGs Genes with signal peptides Genes with transmembrane helices
5,513,716 146 2,985,927 4,796,373 5746 91 6 3624 395 1419
Table 2 Summary of proteins involved in hydrocarbon and sulfur compound metabolisms. Start
Stop
Protein product
Length Description
2189392 2190414 WP_025846643.1 340 2458070 2459125 WP_005835715.1 351 4476480 4477565 WP_025844074.1 361 683518 684324 WP_005827080.1 268 1402981 1404048 WP_007779654.1 355 1404089 1404925 WP_007779650.1 278 1404938 1405804 WP_005833522.1 288 1405801 1406916 WP_025847578.1 371 4822711 4823796 WP_005828402.1 361 5489225 5490979 WP_025843683.1 584
Alkane 1-monooxygenase Alkanesulfonate monooxygenase Alkane 1-monooxygenase Sulfonate ABC transporter permease Sulfate transporter subunit Sulfate/thiosulfate transporter subunit Sulfate ABC transporter permease Sulfate ABC transporter Sulfate permease Sulfate transporter
KAAS server (Moriya et al., 2007) was used to assign translated amino acids into KEGG Pathway with SBH (single-directional best hit) method (Kanehisa et al., 2008). Translated genes were aligned with COG database (Tatusov et al., 2003) using NCBI blastp (hits should have scores no less than 60, e value is no more than 1e-6). To find genes with hypothetical or putative function, we aligned genes against NCBI nucleotide sequence database (nt database was downloaded at Sep 20, 2013) by using NCBI blastn, only if hits have identity no less than 0.95, coverage no less than 0.9, and reference gene had annotation of putative or hypothetical. To define genes with signal peptide, we use SignalP version 4.1 (Petersen et al., 2011) to identify genes with signal peptide with default parameters. TMHMM 2.0 (Krogh et al., 2001) was used to identify genes with transmembrane helices. The draft genome of B. agri 5-2 revealed a genome size of 5,513,716 bp and a G + C content of 54.15% (146 contigs with N50 of 97,214 bp). These contigs contain 5260 coding sequences (CDSs), 91 tRNAs and 6 incomplete rRNA operons (2 small subunit rRNA and 4 large subunit rRNAs).
A total of 5067 protein-coding genes were assigned as putative function or hypothetical proteins. 3624 genes were categorized into COGs functional groups (including putative or hypothetical genes). The properties and the statistics of the genome are summarized in Table 1. Consistent with its metabolic versatility and environmental adaptability, B. agri strain 5-2 possesses extensive transport capabilities. 517 genes encode transport related proteins for amino acid, inorganic ions, carbohydrates, nucleotide and lipid found in the genome. Two putative alkane 1monooxygenase, one putative alkanesulfonate monooxygenase, one putative alkanesulfonate transporter, one putative sulfate permease and five putative sulfate transporters were identified in the draft genome (Table 2). Alkane 1-monooxygenase was found as one of the key enzymes responsible for the aerobic transformation of midchain-length nalkanes (C5 to C16) and in some cases even longer alkanes (van Beilen and Funhoff, 2007). It is hypothesized that sulfate transporters and alkanesulfonate transporter may be responsible for organosulfur compound degradation (Erwin et al., 2005; Van Hamme et al., 2013). Moreover, a genome alignment of the only two sequenced B. agri genomes (B. agri 5-2 and B. agri BAB-2500 (Joshi et al., 2013)) showed that some functional regions are highly homologous between two assemblies. The alignment also reveals some discrepancies between them, some short stretches of the 5-2 genome absent from the contigs in BAB-2500 (Fig. 1). For example, none of the alkane monooxygenases were identified in the genome of BAB-2500 by further genomic analysis. In summary, the genomic data of strain 5-2 may provide insights into the mechanism of microorganisms adapt to the petroleum reservoir after chemical flooding. 2. Nucleotide sequence accession numbers This whole genome sequence project is deposited in DDBJ/EMBL/ GenBank under the accession JATL00000000. Supplementary data to this article can be found online at http://dx. doi.org/10.1016/j.margen.2014.08.006. Acknowledgments This study was sponsored by the National Natural Science Foundation of China (Grant No. 81301461, 50974022, and 51074029), and the 863 Program of the Ministry of Science and Technology (Grant No. 2008AA06Z204 and 2013AA064402). The authors wish to thank the technical personnel in the oil field under study for kindly collecting the samples. References Bao, M., Chen, Q., Li, Y., Jiang, G., 2010. Biodegradation of partially hydrolyzed polyacrylamide by bacteria isolated from production water after polymer flooding in an oil field. J. Hazard. Mater. 184, 105–110. 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.
200000 400000 600000 800000 1000000 1200000 1400000 1600000 1800000 2000000 2200000 2400000 2600000 2800000 3000000 3200000 3400000 3600000 3800000 4000000 4200000 4400000 4600000 4800000 5000000 5200000 5400000
Brevibacillus agri 5-2 200000 400000 600000 800000 1000000 1200000 1400000 1600000 1800000 2000000 2200000 2400000 2600000 2800000 3000000 3200000 3400000 3600000 3800000 4000000 4200000 4400000 4600000 4800000 5000000 5200000
Brevibacillus agri BAB-2500 Fig. 1. Genome alignment between B. agri strain 5-2 (JATL00000000) and B. agri strain BAB-2500 (AOBR00000000). The contigs of both assemblies were prepared for alignment using Mauve (http://asap.ahabs.wisc.edu/mauve/). Alignment is represented as local colinear blocks (colored) filled with a similarity plot. Height of the similarity plot indicates nucleotide identity of both assemblies.
Y. She et al. / Marine Genomics 18 (2014) 123–125 Erwin, K.N., Nakano, S., Zuber, P., 2005. Sulfate-dependent repression of genes that function in organosulfur metabolism in Bacillus subtilis requires Spx. J. Bacteriol. 187, 4042–4049. Hadad, D., Geresh, S., Sivan, A., 2005. Biodegradation of polyethylene by the thermophilic bacterium Brevibacillus borstelensis. J. Appl. Microbiol. 98, 1093–1100. Jones, D.M., Head, I.M., Gray, N.D., Adams, J.J., Rowan, A.K., Aitken, C.M., Bennett, B., Huang, H., Brown, A., Bowler, B.F., Oldenburg, T., Erdmann, M., Larter, S.R., 2008. Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature 451, 176–180. Joshi, M.N., Sharma, A., Pandit, A.S., Pandya, R.V., Saxena, A.K., Bagatharia, S.B., 2013. Draft genome sequence of Brevibacillus sp. strain BAB-2500, a Strain that might play an important role in agriculture. Genome Announc. 1. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., Yamanishi, Y., 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480–D484. Krogh, A., Larsson, B., Von Heijne, G., Sonnhammer, E.L., 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580. 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, 3100–3108. 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, 0955–0964. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M., 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182–W185. Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785–786.
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Reddy, M.S., Naresh, B., Leela, T., Prashanthi, M., Madhusudhan, N., Dhanasri, G., Devi, P., 2010. Biodegradation of phenanthrene with biosurfactant production by a new strain of Brevibacillus sp. Bioresour. Technol. 101, 7980–7983. She, Y.H., Zhang, F., Xia, J.J., Kong, S.Q., Wang, Z.L., Shu, F.C., Hu, J.M., 2011. Investigation of biosurfactant-producing indigenous microorganisms that enhance residue oil recovery in an oil reservoir after polymer flooding. Appl. Biochem. Biotechnol. 163, 223–234. Swain, M.T., Tsai, I.J., Assefa, S.A., Newbold, C., Berriman, M., Otto, T.D., 2012. A postassembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat. Protoc. 7, 1260–1284. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Rao, B.S., Smirnov, S., Sverdlov, A.V., Vasudevan, S., Wolf, Y.I., Yin, J.J., Natale, D.A., 2003. The COG database: an updated version includes eukaryotes. BMC Bioinforma. 4, 41. van Beilen, J.B., Funhoff, E.G., 2007. Alkane hydroxylases involved in microbial alkane degradation. Appl. Microbiol. Biotechnol. 74, 13–21. Van Hamme, J.D., Bottos, E.M., Bilbey, N.J., Brewer, S.E., 2013. Genomic and proteomic characterization of Gordonia sp. NB4-1Y in relation to 6: 2 fluorotelomer sulfonate biodegradation. Microbiology 159, 1618–1628. Wang, X., Jin, D., Zhou, L., Wu, L., An, W., Chen, Y., Zhao, L., 2014. Draft genome sequence of Brevibacillus panacihumi strain W25, a halotolerant hydrocarbon-degrading bacterium. Genome Announc. 2. Zerbino, D.R., Birney, E., 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829. Zhang, F., She, Y.H., Chai, L.J., Banat, I.M., Zhang, X.T., Shu, F.C., Wang, Z.L., Yu, L.J., Hou, D.J., 2012. Microbial diversity in long-term water-flooded oil reservoirs with different in situ temperatures in China. Sci. Rep. 2, 760.
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/Technical resources
Genome sequence of Brevibacillus agri strain 5-2, isolated from the formation water of petroleum reservoir Yuehui She a,1, Wenqiong Wu a, Chunchun Hang a, Xiawei Jiang b, Lujun Chai c, Gaoming Yu d, Fuchang Shu a, Zhengliang Wang a, Sanbao Su a,1, Tingsheng Xiang a, Zhongzhi Zhang e, DuJie Hou c, Fan Zhang c, Beiwen Zheng b,⁎ a
College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, China State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China c The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing, China d College of Petroleum Engineering, Yangtze University, Jingzhou, China e State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China b
a r t i c l e
i n f o
Article history: Received 28 July 2014 Received in revised form 23 August 2014 Accepted 24 August 2014 Available online 4 September 2014 Keywords: Brevibacillus agri Formation water Oilfield Degrading Comparative genomics
a b s t r a c t Brevibacillus agri strain 5-2 was isolated from the formation water of a deep oil reservoir in Changqing Oilfield, China. This bacterium was found to have a capacity for degrading tetradecane, hexadecane and alkanesulfonate. To gain insights into its efficient metabolic pathway for degrading hydrocarbon and organosulfur compounds, here, we report the high quality draft genome of this strain. Two putative alkane 1-monooxygenases, one putative alkanesulfonate monooxygenase, one putative alkanesulfonate transporter, one putative sulfate permease and five putative sulfate transporters were identified in the draft genome. The genomic data of strain 5-2 may provide insights into the mechanism of microorganisms adapt to the petroleum reservoir after chemical flooding. © 2014 Elsevier B.V. All rights reserved.
1. Introduction Chemical flooding is considered as the most important and broadly applied enhanced oil recovery processes which increasing the viscosity of the injected water and reducing the swept zone permeability, and, consequently, increasing the oil recovery (Bao et al., 2010). Until now, sulfonate surfactants have been widely adopted as flooding agents in China (She et al., 2011). Biodegradation of hydrocarbon in petroleum reservoirs has adversely affected the majority of the world's oil, making recovery and refining of that oil more costly (Jones et al., 2008). Microorganisms isolated from formation waters play a key role in the subsurface hydrocarbon degradation, however, the specific pathway occurring in oil reservoirs remains poorly defined (Zhang et al., 2012). Previously, we isolated and characterized three indigenous microorganisms from a petroleum reservoir after polymer flooding (She et al., 2011). To further the characterization of microorganisms in petroleum reservoir after chemical flooding, currently, we isolated a Brevibacillus agri strain 5-2 (= CGMCC 5645) from a mixture of formation water and petroleum in Changqing oilfield, China. Phylogenetic tree clearly ⁎ Corresponding author. Tel./fax: +86 571 87236423. E-mail address: [email protected] (B. Zheng). 1 These authors contributed equally to this work.
http://dx.doi.org/10.1016/j.margen.2014.08.006 1874-7787/© 2014 Elsevier B.V. All rights reserved.
showed that B. agri type strain NRRL NRS-1219 is most closely related to the strain 5-2 (Fig. S1). Interestingly, strain 5-2 growing aerobically with tetradecane and hexadecane as the sole carbon, and was also found to have a capacity for metabolizing sulfonate. Previous studies have documented the capability of hydrocarbon biodegradation in Brevibacillus borstelensis strain 707 (Hadad et al., 2005), Brevibacillus sp. strain PDM-3 (Reddy et al., 2010) and Brevibacillus panacihumi strain W25 (Wang et al., 2014). However, no metabolism pathways involved in petroleum degradation was further characterized in B. agri. Therefore, B. agri strain 5-2 was subjected to the whole genome sequencing for genomic analysis, and this can add more knowledge about the potential industrial applications of B. agri. The draft genome sequence of B. agri 5-2 strain was performed by using Illumina Hieseq 2000 genomic sequencer at BGI (Shenzhen, China). One 500-bp insert-size DNA library was generated then sequenced with Illumina Hiseq 2000 by using 2 × 100 bp pair end sequencing strategy. Filtered clean reads were assembled into scaffolds using the Velvet version 1.2.07 (Zerbino and Birney, 2008), PAGIT flow was used to prolong the initial contigs and correct sequencing errors (Swain et al., 2012). Predict genes were identified using Glimmer version 3.0 (Delcher et al., 2007), tRNAscan-SE version 1.21 (Lowe and Eddy, 1997) was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer version 1.2 (Lagesen et al., 2007).
124
Y. She et al. / Marine Genomics 18 (2014) 123–125
Table 1 Genome features. B. agri strain 5-2 Size (bp) Contigs G + C content (bp) Coding region (bp) Protein-coding genes tRNA genes rRNA genes Genes assigned to COGs Genes with signal peptides Genes with transmembrane helices
5,513,716 146 2,985,927 4,796,373 5746 91 6 3624 395 1419
Table 2 Summary of proteins involved in hydrocarbon and sulfur compound metabolisms. Start
Stop
Protein product
Length Description
2189392 2190414 WP_025846643.1 340 2458070 2459125 WP_005835715.1 351 4476480 4477565 WP_025844074.1 361 683518 684324 WP_005827080.1 268 1402981 1404048 WP_007779654.1 355 1404089 1404925 WP_007779650.1 278 1404938 1405804 WP_005833522.1 288 1405801 1406916 WP_025847578.1 371 4822711 4823796 WP_005828402.1 361 5489225 5490979 WP_025843683.1 584
Alkane 1-monooxygenase Alkanesulfonate monooxygenase Alkane 1-monooxygenase Sulfonate ABC transporter permease Sulfate transporter subunit Sulfate/thiosulfate transporter subunit Sulfate ABC transporter permease Sulfate ABC transporter Sulfate permease Sulfate transporter
KAAS server (Moriya et al., 2007) was used to assign translated amino acids into KEGG Pathway with SBH (single-directional best hit) method (Kanehisa et al., 2008). Translated genes were aligned with COG database (Tatusov et al., 2003) using NCBI blastp (hits should have scores no less than 60, e value is no more than 1e-6). To find genes with hypothetical or putative function, we aligned genes against NCBI nucleotide sequence database (nt database was downloaded at Sep 20, 2013) by using NCBI blastn, only if hits have identity no less than 0.95, coverage no less than 0.9, and reference gene had annotation of putative or hypothetical. To define genes with signal peptide, we use SignalP version 4.1 (Petersen et al., 2011) to identify genes with signal peptide with default parameters. TMHMM 2.0 (Krogh et al., 2001) was used to identify genes with transmembrane helices. The draft genome of B. agri 5-2 revealed a genome size of 5,513,716 bp and a G + C content of 54.15% (146 contigs with N50 of 97,214 bp). These contigs contain 5260 coding sequences (CDSs), 91 tRNAs and 6 incomplete rRNA operons (2 small subunit rRNA and 4 large subunit rRNAs).
A total of 5067 protein-coding genes were assigned as putative function or hypothetical proteins. 3624 genes were categorized into COGs functional groups (including putative or hypothetical genes). The properties and the statistics of the genome are summarized in Table 1. Consistent with its metabolic versatility and environmental adaptability, B. agri strain 5-2 possesses extensive transport capabilities. 517 genes encode transport related proteins for amino acid, inorganic ions, carbohydrates, nucleotide and lipid found in the genome. Two putative alkane 1monooxygenase, one putative alkanesulfonate monooxygenase, one putative alkanesulfonate transporter, one putative sulfate permease and five putative sulfate transporters were identified in the draft genome (Table 2). Alkane 1-monooxygenase was found as one of the key enzymes responsible for the aerobic transformation of midchain-length nalkanes (C5 to C16) and in some cases even longer alkanes (van Beilen and Funhoff, 2007). It is hypothesized that sulfate transporters and alkanesulfonate transporter may be responsible for organosulfur compound degradation (Erwin et al., 2005; Van Hamme et al., 2013). Moreover, a genome alignment of the only two sequenced B. agri genomes (B. agri 5-2 and B. agri BAB-2500 (Joshi et al., 2013)) showed that some functional regions are highly homologous between two assemblies. The alignment also reveals some discrepancies between them, some short stretches of the 5-2 genome absent from the contigs in BAB-2500 (Fig. 1). For example, none of the alkane monooxygenases were identified in the genome of BAB-2500 by further genomic analysis. In summary, the genomic data of strain 5-2 may provide insights into the mechanism of microorganisms adapt to the petroleum reservoir after chemical flooding. 2. Nucleotide sequence accession numbers This whole genome sequence project is deposited in DDBJ/EMBL/ GenBank under the accession JATL00000000. Supplementary data to this article can be found online at http://dx. doi.org/10.1016/j.margen.2014.08.006. Acknowledgments This study was sponsored by the National Natural Science Foundation of China (Grant No. 81301461, 50974022, and 51074029), and the 863 Program of the Ministry of Science and Technology (Grant No. 2008AA06Z204 and 2013AA064402). The authors wish to thank the technical personnel in the oil field under study for kindly collecting the samples. References Bao, M., Chen, Q., Li, Y., Jiang, G., 2010. Biodegradation of partially hydrolyzed polyacrylamide by bacteria isolated from production water after polymer flooding in an oil field. J. Hazard. Mater. 184, 105–110. 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.
200000 400000 600000 800000 1000000 1200000 1400000 1600000 1800000 2000000 2200000 2400000 2600000 2800000 3000000 3200000 3400000 3600000 3800000 4000000 4200000 4400000 4600000 4800000 5000000 5200000 5400000
Brevibacillus agri 5-2 200000 400000 600000 800000 1000000 1200000 1400000 1600000 1800000 2000000 2200000 2400000 2600000 2800000 3000000 3200000 3400000 3600000 3800000 4000000 4200000 4400000 4600000 4800000 5000000 5200000
Brevibacillus agri BAB-2500 Fig. 1. Genome alignment between B. agri strain 5-2 (JATL00000000) and B. agri strain BAB-2500 (AOBR00000000). The contigs of both assemblies were prepared for alignment using Mauve (http://asap.ahabs.wisc.edu/mauve/). Alignment is represented as local colinear blocks (colored) filled with a similarity plot. Height of the similarity plot indicates nucleotide identity of both assemblies.
Y. She et al. / Marine Genomics 18 (2014) 123–125 Erwin, K.N., Nakano, S., Zuber, P., 2005. Sulfate-dependent repression of genes that function in organosulfur metabolism in Bacillus subtilis requires Spx. J. Bacteriol. 187, 4042–4049. Hadad, D., Geresh, S., Sivan, A., 2005. Biodegradation of polyethylene by the thermophilic bacterium Brevibacillus borstelensis. J. Appl. Microbiol. 98, 1093–1100. Jones, D.M., Head, I.M., Gray, N.D., Adams, J.J., Rowan, A.K., Aitken, C.M., Bennett, B., Huang, H., Brown, A., Bowler, B.F., Oldenburg, T., Erdmann, M., Larter, S.R., 2008. Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature 451, 176–180. Joshi, M.N., Sharma, A., Pandit, A.S., Pandya, R.V., Saxena, A.K., Bagatharia, S.B., 2013. Draft genome sequence of Brevibacillus sp. strain BAB-2500, a Strain that might play an important role in agriculture. Genome Announc. 1. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T., Yamanishi, Y., 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480–D484. Krogh, A., Larsson, B., Von Heijne, G., Sonnhammer, E.L., 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580. 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, 3100–3108. 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, 0955–0964. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M., 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182–W185. Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785–786.
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