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Full genome sequence of Brevibacillus laterosporus strain B9, a biological control strain isolated from Zhejiang, China
Journal of Biotechnology 207 (2015) 77–78
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome announcement
Full genome sequence of Brevibacillus laterosporus strain B9, a biological control strain isolated from Zhejiang, China Gengmi Li a,b,1 , Jie Xu a,c,1 , Liwen Wu a , Deyong Ren a , Weijun Ye a , Guojun Dong a , Li Zhu a , Dali Zeng a , Longbiao Guo a,∗ a
State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China Center of Laboratory Medicine, Chengdu Military General Hospital, Key Laboratory of High Humidity Medicine PLA, Chengdu 610083, China c Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China b
a r t i c l e
i n f o
Article history: Received 7 May 2015 Accepted 12 May 2015 Available online 26 May 2015 Keywords: Complete genome sequence Pacbio
a b s t r a c t Brevibacillus laterosporus was newly classified from Bacillus laterosporus, which has ability to be used as a biological control agent in crop field. B. laterosporus strain B9 is an aerobic, motile, Gram-positive, sporeforming rod that was isolated from a field of Oryza sativa in Zhejiang, China in 2011. This bacterium has been confirmed to be a strong antagonist against bacterial brown strip of rice caused by Acidovorex avenae subsp. avenae. Here we describe the features of B. laterosporus strain B9, together with the complete genome sequence and its annotation. The 5,272,435 bp genome contains 4804 protein-coding genes and 227 RNA-only encoding genes with 2 plasmids. © 2015 Published by Elsevier B.V.
The genus Brevibacillus was new created as a genus by reclassification of the Bacillus brevis group of species in 1996 (Shida et al., 1996). B. laterosporus, which is one of the species in this genus, has been reported as the effective biocontrol agent against insects, nematodes and phytopathogens in several studies (De Oliveira et al., 2004; Saikia et al., 2011; Tian et al., 2007). In 2011, we isolated B. laterosporus strain B9 from the root of the Oryza sativa in the rice field in Zhejiang Province, China. Further analysis suggested its strong growth inhibition activity on Acidovorex avenae subsp. avenae, which is the causal agent of bacterial brown strip of rice (Liu et al., 2014). Until now, only two B. laterosporus strains (LMG 15,441 and GI9) has been partial sequenced (Djukic et al., 2011; Sharma et al., 2012). However, in these two sequenced strains, one is an invertebrate pathogen, while another one was isolated from soil. This makes our B9 strain to be a good comparative genome analysis model for phytopathogens. Here we present a summary classification and a set of features for B. laterosporus B9 together with the description of the complete genomic sequencing and annotation. The genome of this strain was done by Guhe info by using the PacBio RS II platform. Genome assembly was done by SMRT Analysis 2.2.1 and the coding sequences, tRNA and rRNA annotations was
∗ Corresponding author. Tel.: +86 15988169187. E-mail address: [email protected] (L. Guo). 1 Authors contributed equally. http://dx.doi.org/10.1016/j.jbiotec.2015.05.011 0168-1656/© 2015 Published by Elsevier B.V.
done by applying NCBI Prokaryotic Genome Annotation Pipeline (Angiuoli et al., 2008). The total size of the genome is 5272,435 bp and has a GC content of 41.28% (Table 1), similar to that of other sequenced Brevibacillus isolates. A total of 5031 coding DNA sequences (CDSs) were predicted (Table 1). Of these, 2929 could be assigned to a COG number (Table 1). Then, we compared the genome of B. laterosporus B9 with other two sequenced B. laterosporus strains LMG 15,441 and GI9. The genome size of B9 is a little bit bigger than LMG 15,441 and GI9 (5.27 Mb, 5.11 Mb and 5.18 Mb, respectively). The G + C content of these three strains is very similar (41.28%, 41.1% and 40.8%, respectively). B9 has a higher gene content than LMG 15,441 and GI9, respectively (5031, 4978 and 4986). Interestingly, we found there are 472 unique genes in B9. It has long been well understood that some gram-positive Bacillales bacteria (including Brevibacillus) are good candidates for biocontrol (Stirling et al., 1988). These bacteria mainly use two strategies in biocontrol including biofilm formation and antibiotic secondary metabolism (Chen et al., 2013; Niu et al., 2013). In order to investigate which mechanism was used by B9 strain, we made a local BLAST search based on the reference-associated genes. Only two biofilm mechanism associated genes were found in B9 while genes associated with 5 different antibiotic compound biosynthesis genes were found indicating its biocontrol ability was mainly contributed by the antibiotic secondary metabolism. These genes include bacitracin biosynthesis (Johnson et al., 1945), phenazine biosynthesis (Thomashow and Weller, 1988), molybdopterin biosynthesis (Nichol et al., 1985), streptomycin
78
G. Li et al. / Journal of Biotechnology 207 (2015) 77–78
Table 1 Genome feature of B. laterosporus B9.
References
Attribute
Value
Genome size (bp) DNA coding (bp) DNA G + C (bp) Chromosome Plasmid Total genes Protein coding genes rRNA (5S, 16S, 23S) tRNA RNA genes Genes with function prediction Genes assigned to COGs
5272435 4434027 2176637 1 2 5031 4804 13 112 227 3313 2929
biosynthesis (Schatz et al., 1944) and lanthionine biosynthesis (Kellner et al., 1988), indicating its wide range antibiotic activity. Interestingly, we found many B9 unique genes are located in the clusters or operons of these antibiotic secondary metabolism associated genes. As in bacteria, it has largely been accepted that the unique genes are mainly contributed by horizontal gene transfer (HGT) (Syvanen, 1994), indicating HGT plays important role in B9 evolution and biocontrol ability formation. Overall, the whole genome sequence of this strain will provide us more information about fungal antagonist on this species. Nucleotide sequence accession number The complete chromosome sequence and two plasmid sequences have been deposited in GenBank under the accession number from CP011074-CP011076. This strain has been deposited in CGMCC collection under the accession number of CGMCC 1.15160. Acknowledgements This work was supported by grants from the Natural Science Fund of China (grant No. 31221004), and the Chinese 973 Program (2013CBA01405). Also thanks Dr. Weijie Song for sequencing at Biology Technology Company of Guhe.
Angiuoli, S.V., Gussman, A., Klimke, W., Cochrane, G., Field, D., Garrity, G.M., Kodira, C.D., Kyrpides, N., Madupu, R., Markowitz, V., 2008. Toward an online repository of standard operating procedures (SOPs) for (meta) genomic annotation. OMICS 12, 137–141. Chen, Y., Yan, F., Chai, Y., Liu, H., Kolter, R., Losick, R., Guo h, J., 2013. Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation. Environ. Microbiol. 15, 848–864. De Oliveira, E.J., Rabinovitch, L., Monnerat, R.G., Passos, L.K.J., Zahner, V., 2004. Molecular characterization of Brevibacillus laterosporus and its potential use in biological control. Appl. Environ. Microbiol. 70, 6657–6664. Djukic, M., Poehlein, A., Thürmer, A., Daniel, R., 2011. Genome sequence of Brevibacillus laterosporus LMG 15441, a pathogen of invertebrates. J. Bacteriol. 193, 5535–5536. Johnson, B.A., Anker, H., Meleney, F.L., 1945. Bacitracin: a new antibiotic produced by a member of the B. subtilis group. Science 102, 376–377. Kellner, R., Jung, G., Horner, T., Zahner, H., Schnell, N., Entian, K.D., Gotz, F., 1988. Gallidermin: a new lanthionine-containing polypeptide antibiotic. Eur. J. Biochem. 177, 53–59. Liu, H., Yang, C.L., Ge, M.Y., Ibrahim, M., Li, B., Zhao, W.J., Chen, G.Y., Zhu, B., Xie, G.L., 2014. Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress. Front. Microbiol. 5, 547. Nichol, C.A., Smith, G.K., Duch, D.S., 1985. Biosynthesis and metabolism of tetrahydrobiopterin and molybdopterin. Annu. Rev. Biochem. 54, 729–764. Niu, B., Vater, J., Rueckert, C., Blom, J., Lehmann, M., Ru, J.-J., Chen, X.-H., Wang, Q., Borriss, R., 2013. Polymyxin P is the active principle in suppressing phytopathogenic Erwinia spp. by the biocontrol rhizobacterium Paenibacillus polymyxa M-1. BMC Microbiol. 13, 137. Saikia, R., Gogoi, D.K., Mazumder, S., Yadav, A., Sarma, R.K., Bora, T.C., Gogoi, B.K., 2011. Brevibacillus laterosporus strain BPM3, a potential biocontrol agent isolated from a natural hot water spring of Assam, India. Microbiol. Res. 166, 216–225. Schatz, A., Bugle, E., Waksman, S.A., 1944. Streptomycin, a substance exhibiting antibiotic activity against gram-positive and gram-negative bacteria. Exp. Biol. Med. 55, 66–69. Sharma, V., Singh, P.K., Midha, S., Ranjan, M., Korpole, S., Patil, P.B., 2012. Genome sequence of Brevibacillus laterosporus strain GI-9. J. Bacteriol. 194, 1279. Shida, O., Takagi, H., Kadowaki, K., Komagata, K., 1996. Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int. J. Syst. Bacteriol. 46, 939–946. Stirling, G.R., Poinar Jr, G., Jansson, H.-B., (1988) Biological control of plant-parasitic nematodes. CRC Press Inc. Syvanen, M., 1994. Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28, 237–261. Thomashow, L.S., Weller, D.M., 1988. Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici. J. Bacteriol. 170, 3499–3508. Tian, B., Yang, J., Lian, L., Wang, C., Li, N., Zhang, K., 2007. Role of an extracellular neutral protease in infection against nematodes by Brevibacillus laterosporus strain G4. Appl. Microbiol. Biotechnol. 74, 372–380.
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome announcement
Full genome sequence of Brevibacillus laterosporus strain B9, a biological control strain isolated from Zhejiang, China Gengmi Li a,b,1 , Jie Xu a,c,1 , Liwen Wu a , Deyong Ren a , Weijun Ye a , Guojun Dong a , Li Zhu a , Dali Zeng a , Longbiao Guo a,∗ a
State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou 310006, PR China Center of Laboratory Medicine, Chengdu Military General Hospital, Key Laboratory of High Humidity Medicine PLA, Chengdu 610083, China c Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China b
a r t i c l e
i n f o
Article history: Received 7 May 2015 Accepted 12 May 2015 Available online 26 May 2015 Keywords: Complete genome sequence Pacbio
a b s t r a c t Brevibacillus laterosporus was newly classified from Bacillus laterosporus, which has ability to be used as a biological control agent in crop field. B. laterosporus strain B9 is an aerobic, motile, Gram-positive, sporeforming rod that was isolated from a field of Oryza sativa in Zhejiang, China in 2011. This bacterium has been confirmed to be a strong antagonist against bacterial brown strip of rice caused by Acidovorex avenae subsp. avenae. Here we describe the features of B. laterosporus strain B9, together with the complete genome sequence and its annotation. The 5,272,435 bp genome contains 4804 protein-coding genes and 227 RNA-only encoding genes with 2 plasmids. © 2015 Published by Elsevier B.V.
The genus Brevibacillus was new created as a genus by reclassification of the Bacillus brevis group of species in 1996 (Shida et al., 1996). B. laterosporus, which is one of the species in this genus, has been reported as the effective biocontrol agent against insects, nematodes and phytopathogens in several studies (De Oliveira et al., 2004; Saikia et al., 2011; Tian et al., 2007). In 2011, we isolated B. laterosporus strain B9 from the root of the Oryza sativa in the rice field in Zhejiang Province, China. Further analysis suggested its strong growth inhibition activity on Acidovorex avenae subsp. avenae, which is the causal agent of bacterial brown strip of rice (Liu et al., 2014). Until now, only two B. laterosporus strains (LMG 15,441 and GI9) has been partial sequenced (Djukic et al., 2011; Sharma et al., 2012). However, in these two sequenced strains, one is an invertebrate pathogen, while another one was isolated from soil. This makes our B9 strain to be a good comparative genome analysis model for phytopathogens. Here we present a summary classification and a set of features for B. laterosporus B9 together with the description of the complete genomic sequencing and annotation. The genome of this strain was done by Guhe info by using the PacBio RS II platform. Genome assembly was done by SMRT Analysis 2.2.1 and the coding sequences, tRNA and rRNA annotations was
∗ Corresponding author. Tel.: +86 15988169187. E-mail address: [email protected] (L. Guo). 1 Authors contributed equally. http://dx.doi.org/10.1016/j.jbiotec.2015.05.011 0168-1656/© 2015 Published by Elsevier B.V.
done by applying NCBI Prokaryotic Genome Annotation Pipeline (Angiuoli et al., 2008). The total size of the genome is 5272,435 bp and has a GC content of 41.28% (Table 1), similar to that of other sequenced Brevibacillus isolates. A total of 5031 coding DNA sequences (CDSs) were predicted (Table 1). Of these, 2929 could be assigned to a COG number (Table 1). Then, we compared the genome of B. laterosporus B9 with other two sequenced B. laterosporus strains LMG 15,441 and GI9. The genome size of B9 is a little bit bigger than LMG 15,441 and GI9 (5.27 Mb, 5.11 Mb and 5.18 Mb, respectively). The G + C content of these three strains is very similar (41.28%, 41.1% and 40.8%, respectively). B9 has a higher gene content than LMG 15,441 and GI9, respectively (5031, 4978 and 4986). Interestingly, we found there are 472 unique genes in B9. It has long been well understood that some gram-positive Bacillales bacteria (including Brevibacillus) are good candidates for biocontrol (Stirling et al., 1988). These bacteria mainly use two strategies in biocontrol including biofilm formation and antibiotic secondary metabolism (Chen et al., 2013; Niu et al., 2013). In order to investigate which mechanism was used by B9 strain, we made a local BLAST search based on the reference-associated genes. Only two biofilm mechanism associated genes were found in B9 while genes associated with 5 different antibiotic compound biosynthesis genes were found indicating its biocontrol ability was mainly contributed by the antibiotic secondary metabolism. These genes include bacitracin biosynthesis (Johnson et al., 1945), phenazine biosynthesis (Thomashow and Weller, 1988), molybdopterin biosynthesis (Nichol et al., 1985), streptomycin
78
G. Li et al. / Journal of Biotechnology 207 (2015) 77–78
Table 1 Genome feature of B. laterosporus B9.
References
Attribute
Value
Genome size (bp) DNA coding (bp) DNA G + C (bp) Chromosome Plasmid Total genes Protein coding genes rRNA (5S, 16S, 23S) tRNA RNA genes Genes with function prediction Genes assigned to COGs
5272435 4434027 2176637 1 2 5031 4804 13 112 227 3313 2929
biosynthesis (Schatz et al., 1944) and lanthionine biosynthesis (Kellner et al., 1988), indicating its wide range antibiotic activity. Interestingly, we found many B9 unique genes are located in the clusters or operons of these antibiotic secondary metabolism associated genes. As in bacteria, it has largely been accepted that the unique genes are mainly contributed by horizontal gene transfer (HGT) (Syvanen, 1994), indicating HGT plays important role in B9 evolution and biocontrol ability formation. Overall, the whole genome sequence of this strain will provide us more information about fungal antagonist on this species. Nucleotide sequence accession number The complete chromosome sequence and two plasmid sequences have been deposited in GenBank under the accession number from CP011074-CP011076. This strain has been deposited in CGMCC collection under the accession number of CGMCC 1.15160. Acknowledgements This work was supported by grants from the Natural Science Fund of China (grant No. 31221004), and the Chinese 973 Program (2013CBA01405). Also thanks Dr. Weijie Song for sequencing at Biology Technology Company of Guhe.
Angiuoli, S.V., Gussman, A., Klimke, W., Cochrane, G., Field, D., Garrity, G.M., Kodira, C.D., Kyrpides, N., Madupu, R., Markowitz, V., 2008. Toward an online repository of standard operating procedures (SOPs) for (meta) genomic annotation. OMICS 12, 137–141. Chen, Y., Yan, F., Chai, Y., Liu, H., Kolter, R., Losick, R., Guo h, J., 2013. Biocontrol of tomato wilt disease by Bacillus subtilis isolates from natural environments depends on conserved genes mediating biofilm formation. Environ. Microbiol. 15, 848–864. De Oliveira, E.J., Rabinovitch, L., Monnerat, R.G., Passos, L.K.J., Zahner, V., 2004. Molecular characterization of Brevibacillus laterosporus and its potential use in biological control. Appl. Environ. Microbiol. 70, 6657–6664. Djukic, M., Poehlein, A., Thürmer, A., Daniel, R., 2011. Genome sequence of Brevibacillus laterosporus LMG 15441, a pathogen of invertebrates. J. Bacteriol. 193, 5535–5536. Johnson, B.A., Anker, H., Meleney, F.L., 1945. Bacitracin: a new antibiotic produced by a member of the B. subtilis group. Science 102, 376–377. Kellner, R., Jung, G., Horner, T., Zahner, H., Schnell, N., Entian, K.D., Gotz, F., 1988. Gallidermin: a new lanthionine-containing polypeptide antibiotic. Eur. J. Biochem. 177, 53–59. Liu, H., Yang, C.L., Ge, M.Y., Ibrahim, M., Li, B., Zhao, W.J., Chen, G.Y., Zhu, B., Xie, G.L., 2014. Regulatory role of tetR gene in a novel gene cluster of Acidovorax avenae subsp. avenae RS-1 under oxidative stress. Front. Microbiol. 5, 547. Nichol, C.A., Smith, G.K., Duch, D.S., 1985. Biosynthesis and metabolism of tetrahydrobiopterin and molybdopterin. Annu. Rev. Biochem. 54, 729–764. Niu, B., Vater, J., Rueckert, C., Blom, J., Lehmann, M., Ru, J.-J., Chen, X.-H., Wang, Q., Borriss, R., 2013. Polymyxin P is the active principle in suppressing phytopathogenic Erwinia spp. by the biocontrol rhizobacterium Paenibacillus polymyxa M-1. BMC Microbiol. 13, 137. Saikia, R., Gogoi, D.K., Mazumder, S., Yadav, A., Sarma, R.K., Bora, T.C., Gogoi, B.K., 2011. Brevibacillus laterosporus strain BPM3, a potential biocontrol agent isolated from a natural hot water spring of Assam, India. Microbiol. Res. 166, 216–225. Schatz, A., Bugle, E., Waksman, S.A., 1944. Streptomycin, a substance exhibiting antibiotic activity against gram-positive and gram-negative bacteria. Exp. Biol. Med. 55, 66–69. Sharma, V., Singh, P.K., Midha, S., Ranjan, M., Korpole, S., Patil, P.B., 2012. Genome sequence of Brevibacillus laterosporus strain GI-9. J. Bacteriol. 194, 1279. Shida, O., Takagi, H., Kadowaki, K., Komagata, K., 1996. Proposal for two new genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. Int. J. Syst. Bacteriol. 46, 939–946. Stirling, G.R., Poinar Jr, G., Jansson, H.-B., (1988) Biological control of plant-parasitic nematodes. CRC Press Inc. Syvanen, M., 1994. Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28, 237–261. Thomashow, L.S., Weller, D.M., 1988. Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici. J. Bacteriol. 170, 3499–3508. Tian, B., Yang, J., Lian, L., Wang, C., Li, N., Zhang, K., 2007. Role of an extracellular neutral protease in infection against nematodes by Brevibacillus laterosporus strain G4. Appl. Microbiol. Biotechnol. 74, 372–380.