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Draft Genome Sequence of Bacillus amyloliquefaciens XK-4-1, a Plant Growth-Promoting Endophyte with Antifungal Activity Zhengxiang Sun,a,b Tom Hsiang,c Yi Zhou,a Jinglong Zhoua College of Agriculture, Yangtze University, Jingzhou, Hubei, Chinaa; Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou, Hubei, Chinab; Environmental Sciences, University of Guelph, Guelph, Ontario, Canadac
Here, we report the draft genome sequence of a bacterial plant-growth-promoting endophyte, Bacillus amyloliquefaciens XK4-1, which consists of one circular chromosome of 3,941,805 bp with 3,702 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with its plant-beneficial characteristics.
Citation Sun Z, Hsiang T, Zhou Y, Zhou J. 2015. Draft genome sequence of Bacillus amyloliquefaciens XK-4-1, a plant growth-promoting endophyte with antifungal activity. Genome Announc 3(6):e01306-15. doi:10.1128/genomeA.01306-15. Copyright © 2015 Sun et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Zhengxiang Sun, [email protected].
B
acillus amyloliquefaciens is considered to be a member of plant-beneficial bacteria, is known to promote plant growth and suppress plant pathogens, and has been applied widely in agriculture (1). This organism has been shown to produce a number of compounds with antifungal activity (2). B. amyloliquefaciens XK-4-1 was isolated from cotton (Gossypium spp.) during the flower bud formation stage and was found to have high levels of epiphytic populations during this stage. Our previous work showed that B. amyloliquefaciens XK-4-1 provides efficacious control of Verticillium wilt of cotton, in both pot experiment and field tests. Here, we report the draft genome sequence of XK-4-1. The genome sequence will facilitate further studies on the secondary metabolite biosynthetic pathways and broaden the current understanding of the biological control mechanism of B. amyloliquefaciens XK-4-1. Genomic DNA of B. amyloliquefaciens XK-4-1 was extracted (3) and sequenced at Génome Québec, Montreal, Quebec, Canada, using Illumina HiSeq technology. The data were assembled using the freely available software ABySS (4), SOAPdenovo (5), and Velvet (6). Gaps between contigs were closed by using GapCloser version 1.12. Annotation was performed using SEED and the Rapid Annotations using Subsystems Technology (RAST) (7, 8). Analysis of the B. amyloliquefaciens XK-4-1 genome revealed that it consists of a circular chromosome of 3,941,805 bp (about 887⫻ coverage depth; N50, 313,045 bp) in size, with 3,702 coding sequences (CDSs), 82 tRNA genes, 1 noncoding RNA (ncRNA), and 9 rRNAs, and an average G⫹C content of 46.0%. Some of these predicted genes and functions are known to be associated with growth promotion and biocontrol and are considered to play important roles in the biocontrol of some fungal pathogens. These include genes encoding chemotaxis-related proteins, sporulation transcription factors related to biofilm formation, antimicrobial biosynthesis, bacteriocins, siderophore-synthesis, and production of endoglucanases, cellulases, and glucanases. Nucleotide sequence accession numbers. All raw and assembled data of B. amyloliquefaciens XK-4-1 for the project have been
November/December 2015 Volume 3 Issue 6 e01306-15
deposited at DDBJ/EMBL/GenBank under the accession no. LJDI00000000. The version described in this paper is version LJDI01000000. ACKNOWLEDGMENTS Funding for sequencing was provided by an NSERC grant to T.H. This study was supported by the Department of Crop Science, College of Agriculture, Yangtze University.
REFERENCES 1. Köberl M, White RA III, Erschena S, Spanberger N, El-Arabi TF, Jansson JK, Ber G. 2015. Complete genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium of Calendula officinalis. Genome Announc 3(4):e00862-15. http://dx.doi.org/10.1128/ genomeA.00862-15. 2. Nelson BA, Ramaiya P, Lopez de Leon A, Kumar R, Crinklaw A, Jolkovsky E, Crane JM, Bergstrom GC, Rey MW. 2014. Complete genome sequence for the Fusarium head blight antagonist Bacillus amyloliquefaciens strain TrigoCor 1448. Genome Announc 2(2):e00219-14. http:// dx.doi.org/10.1128/genomeA.00219-14. 3. Lema MW, Brown A, Calkins JH. 1994. A general method for the extraction of DNA from bacteria. J Microbiol Methods 19:167–172. http:// dx.doi.org/10.1016/0167-7012(94)90066-3. 4. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117–1123. http://dx.doi.org/10.1101/gr.089532.108. 5. Li R, Li Y, Kristiansen K, Wang J. 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714. http://dx.doi.org/ 10.1093/bioinformatics/btn025. 6. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107. 7. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, 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. http://dx.doi.org/10.1186/1471-2164-9-75. 8. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206 –D214. http://dx.doi.org/10.1093/nar/gkt1226.
Genome Announcements
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Downloaded from http://genomea.asm.org/ on January 11, 2016 by guest
Received 19 September 2015 Accepted 25 September 2015 Published 12 November 2015
Draft Genome Sequence of Bacillus amyloliquefaciens XK-4-1, a Plant Growth-Promoting Endophyte with Antifungal Activity Zhengxiang Sun,a,b Tom Hsiang,c Yi Zhou,a Jinglong Zhoua College of Agriculture, Yangtze University, Jingzhou, Hubei, Chinaa; Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Jingzhou, Hubei, Chinab; Environmental Sciences, University of Guelph, Guelph, Ontario, Canadac
Here, we report the draft genome sequence of a bacterial plant-growth-promoting endophyte, Bacillus amyloliquefaciens XK4-1, which consists of one circular chromosome of 3,941,805 bp with 3,702 coding sequences (CDSs). The data presented highlight multiple sets of functional genes associated with its plant-beneficial characteristics.
Citation Sun Z, Hsiang T, Zhou Y, Zhou J. 2015. Draft genome sequence of Bacillus amyloliquefaciens XK-4-1, a plant growth-promoting endophyte with antifungal activity. Genome Announc 3(6):e01306-15. doi:10.1128/genomeA.01306-15. Copyright © 2015 Sun et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Zhengxiang Sun, [email protected].
B
acillus amyloliquefaciens is considered to be a member of plant-beneficial bacteria, is known to promote plant growth and suppress plant pathogens, and has been applied widely in agriculture (1). This organism has been shown to produce a number of compounds with antifungal activity (2). B. amyloliquefaciens XK-4-1 was isolated from cotton (Gossypium spp.) during the flower bud formation stage and was found to have high levels of epiphytic populations during this stage. Our previous work showed that B. amyloliquefaciens XK-4-1 provides efficacious control of Verticillium wilt of cotton, in both pot experiment and field tests. Here, we report the draft genome sequence of XK-4-1. The genome sequence will facilitate further studies on the secondary metabolite biosynthetic pathways and broaden the current understanding of the biological control mechanism of B. amyloliquefaciens XK-4-1. Genomic DNA of B. amyloliquefaciens XK-4-1 was extracted (3) and sequenced at Génome Québec, Montreal, Quebec, Canada, using Illumina HiSeq technology. The data were assembled using the freely available software ABySS (4), SOAPdenovo (5), and Velvet (6). Gaps between contigs were closed by using GapCloser version 1.12. Annotation was performed using SEED and the Rapid Annotations using Subsystems Technology (RAST) (7, 8). Analysis of the B. amyloliquefaciens XK-4-1 genome revealed that it consists of a circular chromosome of 3,941,805 bp (about 887⫻ coverage depth; N50, 313,045 bp) in size, with 3,702 coding sequences (CDSs), 82 tRNA genes, 1 noncoding RNA (ncRNA), and 9 rRNAs, and an average G⫹C content of 46.0%. Some of these predicted genes and functions are known to be associated with growth promotion and biocontrol and are considered to play important roles in the biocontrol of some fungal pathogens. These include genes encoding chemotaxis-related proteins, sporulation transcription factors related to biofilm formation, antimicrobial biosynthesis, bacteriocins, siderophore-synthesis, and production of endoglucanases, cellulases, and glucanases. Nucleotide sequence accession numbers. All raw and assembled data of B. amyloliquefaciens XK-4-1 for the project have been
November/December 2015 Volume 3 Issue 6 e01306-15
deposited at DDBJ/EMBL/GenBank under the accession no. LJDI00000000. The version described in this paper is version LJDI01000000. ACKNOWLEDGMENTS Funding for sequencing was provided by an NSERC grant to T.H. This study was supported by the Department of Crop Science, College of Agriculture, Yangtze University.
REFERENCES 1. Köberl M, White RA III, Erschena S, Spanberger N, El-Arabi TF, Jansson JK, Ber G. 2015. Complete genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium of Calendula officinalis. Genome Announc 3(4):e00862-15. http://dx.doi.org/10.1128/ genomeA.00862-15. 2. Nelson BA, Ramaiya P, Lopez de Leon A, Kumar R, Crinklaw A, Jolkovsky E, Crane JM, Bergstrom GC, Rey MW. 2014. Complete genome sequence for the Fusarium head blight antagonist Bacillus amyloliquefaciens strain TrigoCor 1448. Genome Announc 2(2):e00219-14. http:// dx.doi.org/10.1128/genomeA.00219-14. 3. Lema MW, Brown A, Calkins JH. 1994. A general method for the extraction of DNA from bacteria. J Microbiol Methods 19:167–172. http:// dx.doi.org/10.1016/0167-7012(94)90066-3. 4. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res 19: 1117–1123. http://dx.doi.org/10.1101/gr.089532.108. 5. Li R, Li Y, Kristiansen K, Wang J. 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714. http://dx.doi.org/ 10.1093/bioinformatics/btn025. 6. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107. 7. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, 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. http://dx.doi.org/10.1186/1471-2164-9-75. 8. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206 –D214. http://dx.doi.org/10.1093/nar/gkt1226.
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on January 11, 2016 by guest
Received 19 September 2015 Accepted 25 September 2015 Published 12 November 2015
