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Complete genome sequence of deoxynivalenol-degrading bacterium Devosia sp. strain A16
Journal of Biotechnology 218 (2016) 21–22
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome announcement
Complete genome sequence of deoxynivalenol-degrading bacterium Devosia sp. strain A16 Xianchao Yin a,b,c , Ziwei Zhu a , Yidong Zhou a , Fang Ji c,e , Zhenyu Yao a , Jianrong Shi c,d,e,∗∗ , Jianhong Xu a,b,∗ a
Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding, Nanjing 210014, China c Key Laboratory of Control Technology and Standard for Agro-Product Quality and Safety, Ministry of Agriculture, Nanjing 210014, China d Key Laboratory of Agro-Product Safety Risk Evaluation, Ministry of Agriculture, Nanjing 210014, China e Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210014, China b
a r t i c l e
i n f o
Article history: Received 17 November 2015 Accepted 20 November 2015 Available online 26 November 2015 Keywords: Devosia sp. strain A16 Deoxynivalenol degradation Biotransformation Mycotoxin
a b s t r a c t The strain A16, capable of degrading deoxynivalenol was isolated from a wheat field and identified preliminarily as Devosia sp. Here, we present the genome sequence of the Devosia sp. A16, which has a size of 5,032,994 bp, with 4913 coding sequences (CDSs). The annotated full genome sequence of the Devosia sp. A16 strain might shed light on the function of its degradation. © 2015 Elsevier B.V. All rights reserved.
The trichothecens mycotoxin deoxynivalenol (DON) is a hazardous and globally prevalent mycotoxin in cereals (Pestka, 2010; Mirocha et al., 1976). It commonly accumulates in the grain of wheat and barley affected by Fusarium head blight (Larsen et al., 2004; Ramakrishna et al., 1989). We reported the isolation of a new Devosia species, Devosia sp. strain A16, which is capable of biotransforming DON (Xu et al., 2010). The strain A16, a gram negative bacterium was isolated from wheat field soil using deoxynivalenol riched medium (Xu et al., 2010). The strain A16 can not only degrade DON in liquid medium, but also degrade DON in feedstuff. Devosia sp. A16 can survive and degrade DON in several surroundings, supplying a feasible solution for biodetoxification of DON. In order to investigate its genetic background of physiological, genetic, and the pathway of degrading DON, this strain was subjected to the whole genome sequencing analysis. The genome of A16 strain was sequenced using single molecule sequencing technology with the PacBio® RS II system (Pacific Biosciences, Menlo Park, CA) (Chin et al., 2013). Around 826 Mb data was obtained with 164.0× average coverage. After quality control,
∗ Corresponding author at: Zhongling Street, Nanjing, Jiangsu 210014, China. Fax: +86 25 8439 2001. ∗∗ Corresponding author. E-mail addresses: [email protected] (J. Shi), [email protected] (J. Xu). http://dx.doi.org/10.1016/j.jbiotec.2015.11.016 0168-1656/© 2015 Elsevier B.V. All rights reserved.
the acquired sequence reads were assembled with SMRT analysis 2.2.0, and annotations of the protein coding genes, tRNA and rRNA were predicted by NCBI Prokaryotic Genome Annotation Pipeline (Pruitt et al., 2012). The resulting genome sequence has a size of 5,032,994 bp with a GC content of 65.78% (Table 1). A total of 4913 coding DNA sequences (CDSs) were predicted (Table 1) and 3481 CDS could be assigned to a COG number. In addition, 78 RNAs including rRNA and tRNA were identified. Genome comparison between A16 and reference genome DS-56 (Hassan et al., 2015) was further carried out. More than 50% (2522 CDS) of the genes in A16 cannot find the homologs in DS-56, suggesting the obviousness of genome diversity. 21 candidate genes involved in resistance to antibiotics and toxic compounds were investigated using RAST Server (Aziz et al., 2008), including 6 efflux pumps, 4 -lactamases, 7 cobalt–zinc–cadmium resistance genes and 3 copper-translocating P-type ATPases. Besides, an acetyl-CoA acetyltransferase gene, maybe functioning as converting deoxynivalenol to vulnerable 3-acetyl-deoxynivalenol, was identified (Xu et al., 2013). These candidate genes will be validated by RNAseq analyses and biology experiment. Availability of the A16 genome sequence facilitates to uncover the DON-degrading mechanism and offers a new opportunity for the application of DON-degrading bacteria to reduce DON contamination (Karlovsky, 2001).
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X. Yin et al. / Journal of Biotechnology 218 (2016) 21–22
Table 1 General genome features of the Devosia sp. A16. Features Genome size (bp) Contig numbers G + C% Protein-coding genes tRNA number rRNA number ncRNA number Genes with signal peptides Genes with transmembrane helices
References Value 5,032,994 1 65.78% 4913 58 6 14 469 1226
Strain and nucleotide sequence accession numbers This strain has been deposited in CCTCC with deposit number as CCTCC M 208087. The complete genome sequence of Devosia sp. A16 has been deposited at GenBank under the Accession Number CP012945.1. The BioProject designation for this project is PRJNA298125. Acknowledgements We thank Hangzhou Guhe Information and Technology Co., Ltd., for help in sequencing and bioinformatics analysis. This work was supported by the National Basic Research Program of China (2013CB127805), National Natural Science Foundation of China (31471662), Jiangsu Provincial Natural Science Foundation (BK20130714), Jiangsu Agriculture Science and TechnologyCX(13)3092 and Special Fund for Risk Assessment of China (GJFP201500702).
Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., Meyer, F., Olsen, G.J., Olson, R., Osterman, A.L., Overbeek, R.A., McNeil, L.K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G.D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., Zagnitko, O., 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9, 75. Chin, C.S., Alexander, D.H., Marks, P., Klammer, A.A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E.E., Turner, S.W., Korlach, J., 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569. Hassan, Y.I., Lepp, D., Zhou, T., 2015. Genome assemblies of three soil-associated Devosia species: D. insulae, D. limi, and D. soli. Genome Announc. 3. Karlovsky, P., 2001. Biological detoxification of the mycotoxin deoxynivalenol and its use in genetically engineered crops and feed additives. Appl. Microbiol. Biotechnol. 91, 491–504. Larsen, J.C., Hunt, J., Perrin, I., Ruckenbauer, P., 2004. Workshop on trichothecenes with a focus on DON: summary report. Toxicol. Lett. 153, 1–22. Mirocha, C.J., Pathre, S.V., Schauerhamer, B., Christensen, C.M., 1976. Natural occurrence of Fusarium toxins in feedstuff. Appl. Environ. Microbiol. 32, 553–556. Pestka, J.J., 2010. Deoxynivalenol: mechanisms of action, human exposure, and toxicological relevance. Arch. Toxicol. 84, 663–679. Pruitt, K.D., Tatusova, T., Brown, G.R., Maglott, D.R., 2012. NCBI reference sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 40, D130–D135. Ramakrishna, Y., Bhat, R.V., Ravindranath, V., 1989. Production of deoxynivalenol by Fusarium isolates from samples of wheat associated with a human mycotoxicosis outbreak and from sorghum cultivars. Appl. Environ. Microbiol. 55, 2619–2620. Xu, J., Ji, F., Wang, H., Wang, J., Lin, F., Shi, J., 2010. Isolation and identification of deoxynivalenol degradation strains. Sci. Agric. Sin. 43, 4635–4641. Xu, J., Pan, Y., Hu, X., Ji, F., Yin, X., Shi, J., 2013. Enzymatic characteristics of 3-acetyl deoxynivalenol oxidase by Devosia sp. DDS-1. Sci. Agric. Sin. 46, 2240–2248.
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome announcement
Complete genome sequence of deoxynivalenol-degrading bacterium Devosia sp. strain A16 Xianchao Yin a,b,c , Ziwei Zhu a , Yidong Zhou a , Fang Ji c,e , Zhenyu Yao a , Jianrong Shi c,d,e,∗∗ , Jianhong Xu a,b,∗ a
Institute of Food Quality and Safety, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding, Nanjing 210014, China c Key Laboratory of Control Technology and Standard for Agro-Product Quality and Safety, Ministry of Agriculture, Nanjing 210014, China d Key Laboratory of Agro-Product Safety Risk Evaluation, Ministry of Agriculture, Nanjing 210014, China e Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing 210014, China b
a r t i c l e
i n f o
Article history: Received 17 November 2015 Accepted 20 November 2015 Available online 26 November 2015 Keywords: Devosia sp. strain A16 Deoxynivalenol degradation Biotransformation Mycotoxin
a b s t r a c t The strain A16, capable of degrading deoxynivalenol was isolated from a wheat field and identified preliminarily as Devosia sp. Here, we present the genome sequence of the Devosia sp. A16, which has a size of 5,032,994 bp, with 4913 coding sequences (CDSs). The annotated full genome sequence of the Devosia sp. A16 strain might shed light on the function of its degradation. © 2015 Elsevier B.V. All rights reserved.
The trichothecens mycotoxin deoxynivalenol (DON) is a hazardous and globally prevalent mycotoxin in cereals (Pestka, 2010; Mirocha et al., 1976). It commonly accumulates in the grain of wheat and barley affected by Fusarium head blight (Larsen et al., 2004; Ramakrishna et al., 1989). We reported the isolation of a new Devosia species, Devosia sp. strain A16, which is capable of biotransforming DON (Xu et al., 2010). The strain A16, a gram negative bacterium was isolated from wheat field soil using deoxynivalenol riched medium (Xu et al., 2010). The strain A16 can not only degrade DON in liquid medium, but also degrade DON in feedstuff. Devosia sp. A16 can survive and degrade DON in several surroundings, supplying a feasible solution for biodetoxification of DON. In order to investigate its genetic background of physiological, genetic, and the pathway of degrading DON, this strain was subjected to the whole genome sequencing analysis. The genome of A16 strain was sequenced using single molecule sequencing technology with the PacBio® RS II system (Pacific Biosciences, Menlo Park, CA) (Chin et al., 2013). Around 826 Mb data was obtained with 164.0× average coverage. After quality control,
∗ Corresponding author at: Zhongling Street, Nanjing, Jiangsu 210014, China. Fax: +86 25 8439 2001. ∗∗ Corresponding author. E-mail addresses: [email protected] (J. Shi), [email protected] (J. Xu). http://dx.doi.org/10.1016/j.jbiotec.2015.11.016 0168-1656/© 2015 Elsevier B.V. All rights reserved.
the acquired sequence reads were assembled with SMRT analysis 2.2.0, and annotations of the protein coding genes, tRNA and rRNA were predicted by NCBI Prokaryotic Genome Annotation Pipeline (Pruitt et al., 2012). The resulting genome sequence has a size of 5,032,994 bp with a GC content of 65.78% (Table 1). A total of 4913 coding DNA sequences (CDSs) were predicted (Table 1) and 3481 CDS could be assigned to a COG number. In addition, 78 RNAs including rRNA and tRNA were identified. Genome comparison between A16 and reference genome DS-56 (Hassan et al., 2015) was further carried out. More than 50% (2522 CDS) of the genes in A16 cannot find the homologs in DS-56, suggesting the obviousness of genome diversity. 21 candidate genes involved in resistance to antibiotics and toxic compounds were investigated using RAST Server (Aziz et al., 2008), including 6 efflux pumps, 4 -lactamases, 7 cobalt–zinc–cadmium resistance genes and 3 copper-translocating P-type ATPases. Besides, an acetyl-CoA acetyltransferase gene, maybe functioning as converting deoxynivalenol to vulnerable 3-acetyl-deoxynivalenol, was identified (Xu et al., 2013). These candidate genes will be validated by RNAseq analyses and biology experiment. Availability of the A16 genome sequence facilitates to uncover the DON-degrading mechanism and offers a new opportunity for the application of DON-degrading bacteria to reduce DON contamination (Karlovsky, 2001).
22
X. Yin et al. / Journal of Biotechnology 218 (2016) 21–22
Table 1 General genome features of the Devosia sp. A16. Features Genome size (bp) Contig numbers G + C% Protein-coding genes tRNA number rRNA number ncRNA number Genes with signal peptides Genes with transmembrane helices
References Value 5,032,994 1 65.78% 4913 58 6 14 469 1226
Strain and nucleotide sequence accession numbers This strain has been deposited in CCTCC with deposit number as CCTCC M 208087. The complete genome sequence of Devosia sp. A16 has been deposited at GenBank under the Accession Number CP012945.1. The BioProject designation for this project is PRJNA298125. Acknowledgements We thank Hangzhou Guhe Information and Technology Co., Ltd., for help in sequencing and bioinformatics analysis. This work was supported by the National Basic Research Program of China (2013CB127805), National Natural Science Foundation of China (31471662), Jiangsu Provincial Natural Science Foundation (BK20130714), Jiangsu Agriculture Science and TechnologyCX(13)3092 and Special Fund for Risk Assessment of China (GJFP201500702).
Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., Meyer, F., Olsen, G.J., Olson, R., Osterman, A.L., Overbeek, R.A., McNeil, L.K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G.D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A., Zagnitko, O., 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9, 75. Chin, C.S., Alexander, D.H., Marks, P., Klammer, A.A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E.E., Turner, S.W., Korlach, J., 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569. Hassan, Y.I., Lepp, D., Zhou, T., 2015. Genome assemblies of three soil-associated Devosia species: D. insulae, D. limi, and D. soli. Genome Announc. 3. Karlovsky, P., 2001. Biological detoxification of the mycotoxin deoxynivalenol and its use in genetically engineered crops and feed additives. Appl. Microbiol. Biotechnol. 91, 491–504. Larsen, J.C., Hunt, J., Perrin, I., Ruckenbauer, P., 2004. Workshop on trichothecenes with a focus on DON: summary report. Toxicol. Lett. 153, 1–22. Mirocha, C.J., Pathre, S.V., Schauerhamer, B., Christensen, C.M., 1976. Natural occurrence of Fusarium toxins in feedstuff. Appl. Environ. Microbiol. 32, 553–556. Pestka, J.J., 2010. Deoxynivalenol: mechanisms of action, human exposure, and toxicological relevance. Arch. Toxicol. 84, 663–679. Pruitt, K.D., Tatusova, T., Brown, G.R., Maglott, D.R., 2012. NCBI reference sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res. 40, D130–D135. Ramakrishna, Y., Bhat, R.V., Ravindranath, V., 1989. Production of deoxynivalenol by Fusarium isolates from samples of wheat associated with a human mycotoxicosis outbreak and from sorghum cultivars. Appl. Environ. Microbiol. 55, 2619–2620. Xu, J., Ji, F., Wang, H., Wang, J., Lin, F., Shi, J., 2010. Isolation and identification of deoxynivalenol degradation strains. Sci. Agric. Sin. 43, 4635–4641. Xu, J., Pan, Y., Hu, X., Ji, F., Yin, X., Shi, J., 2013. Enzymatic characteristics of 3-acetyl deoxynivalenol oxidase by Devosia sp. DDS-1. Sci. Agric. Sin. 46, 2240–2248.