Whole-Genome Shotgun Sequence of Bacillus amyloliquefaciens Strain UASWS BA1, a Bacterium Antagonistic to Plant Pathogenic Fungi F. Lefort,a G. Calmin,b P. Pelleteret,a L. Farinelli,c M. Osteras,c J. Crovadorea Plants and Pathogens Group, Research Institute, Earth Nature and Environment, Hepia, University of Applied Sciences of Western Switzerland, Geneva, Switzerlanda; Faculty of Engineering and Architecture, University of Applied Sciences of Western Switzerland, Delémont, Switzerlandb; Fasteris SA, Plan-les-Ouates, Geneva, Switzerlandc F.L. and G.C. contributed equally to this work.
We report here the whole-genome shotgun sequence of Bacillus amyloliquefaciens strain UASWS BA1, isolated from inner wood tissues of a decaying Platanus ⴛ acerifolia tree. This strain proved to be antagonistic to several plant pathogenic fungi and oomycetes and can be developed as a biological control agent in agriculture. Received 8 January 2014 Accepted 21 January 2014 Published 6 February 2014 Citation Lefort F, Calmin G, Pelleteret P, Farinelli L, Osteras M, Crovadore J. 2014. Whole-genome shotgun sequence of Bacillus amyloliquefaciens strain UASWS BA1, a bacterium antagonistic to plant pathogenic fungi. Genome Announc. 2(1):e00016-14. doi:10.1128/genomeA.00016-14. Copyright © 2014 Lefort et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to F. Lefort,
[email protected].
B
acillus amyloliquefaciens Fukomoto 1943, redescribed by Priest et al. (1), has been extensively used for producing ␣-amylase and proteases for industrial uses (2). Some strains were identified as antibiotic producers, plant growth promoters, and plant health enhancers, and then were used as biocontrol agents. Plant growth-promoting rhizobacterial (PGPR) strains of B. amyloliquefaciens were distinguished as B. amyloliquefaciens subsp. nov. plantarum (3) by genome comparison and classical bacterial taxonomy, while other strains were considered to be B. amyloliquefaciens subsp. nov. amyloliquefaciens. The available complete genome sequences showed variation in their genome sizes, from 3.86 Mb up to 4.24 Mb (4–9), with a G⫹C content range of 45.7 to 46.6%. Plant-associated B. amyloliquefaciens strains usually display antifungal and antibacterial activities mediated by secondary metabolites, such as lipopeptides and polyketides (7–9). The strain B. amyloliquefaciens UASWS BA1 was isolated in Geneva from inner symptomatic wood samples of a decaying Platanus ⫻ acerifolia tree. DNA was purified from axenic isolates according to a modified DNA extraction micromethod (10). Whole-genome shotgun sequencing was then performed in an IIlumina HiSeq 2000, producing 26,331,262 paired-end reads 100 bp long. Assembly was carried out with ABySS 1.3.5 (11) and yielded 24 scaffolds for a genome length of 3,944,088 bp, with a G⫹C content of 46.6% and a scaffold N50 value of 346,879 bp. It included a plasmid of 8,106 bp in length. Annotation was realized upon submission through the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) and allowed for the identification of 113 RNA genes (29 rRNA and 84 tRNA genes). Genome comparisons in RAST 4.0 (12) identified the closest neighbors as B. amyloliquefaciens strains LL3 (13), XH7 (14), IT45, and FZB42 (5). RAST 4.0 analysis also identified 3,980 coding sequences (CDSs), 47% of which were allocated a function. Missing genes were estimated to be about 54. It also confirmed the presence of nonribosomal peptide synthetase (NRPS) gene clusters encoding surfactin production (comS, srfA, rapA), genes for bacilysin (bacA, bacB, bacE) and
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a bacillibactin siderophore, and several polyketide synthase (PKS) genes. The bacterium was equipped for resistance to drugs and heavy metals, aromatic compound degradation, motility, and chemotaxis and for the synthesis of auxin precursors probably useful in the symbiotic relationship with plants. It also harbors genes for capsule exopolysaccharides and endospore proteins. Extended studies and comparisons of the genome of B. amyloliquefaciens UASWS BA1 would enable the elucidation of the mechanisms supporting its antifungal properties, which would make this strain a potential biocontrol agent. Nucleotide sequence accession numbers. This whole-genome shotgun (WGS) project was deposited at GenBank under the accession no. AWQY00000000. The version described in this paper is the first version, AWQY00000000.1 (Genbank assembly ID GCA_000469015.1; RefSeq assembly ID GCF_000469015.1). ACKNOWLEDGMENT This work was partly supported by Fasteris SA.
REFERENCES 1. Priest FG, Goodfellow M, Shute LA, Berkeley RCW. 1987. Bacillus amyloliquefaciens sp. nov., nom. rev. Int. J. Syst. Bacteriol. 37:69 –71. http: //dx.doi.org/10.1099/00207713-37-1-69. 2. Gangadharan D, Sivaramakrishnan S, Nampoothiri KM, Pandey A. 2006. ␣-amylase production by B. amyloliquefaciens. Food Technol. Biotechnol. 44:269 –274. 3. Borriss R, Chen XH, Rueckert C, Blom J, Becker A, Baumgarth B, Fan B, Pukall R, Schumann P, Spröer C, Junge H, Vater J, Pühler A, Klenk HP. 2011. Relationship of Bacillus amyloliquefaciens clades associated with strains DSM7 and FZB42: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. Int. J. Syst. Evol. Microbiol. 61:1786 –1801. http://dx.doi.org/10.1099/ijs.0.023267-0. 4. Blom J, Rueckert C, Niu B, Borriss R. 2012. The complete genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 contains a gene cluster for nonribosomal synthesis of iturin A. J. Bacteriol. 194: 1845–1846. http://dx.doi.org/10.1128/JB.06762-11. 5. Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heine-
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genomea.asm.org 1
Lefort et al.
6.
7.
8.
9.
meyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R. 2007. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat. Biotechnol. 25:1007–1014. http://dx.doi.org/1 0.1038/nbt1325. Hao K, He P, Blom J, Rueckert C, Mao Z, Wu Y, He Y, Borriss R. 2012. The genome of plant growth-promoting Bacillus amyloliquefaciens subsp. plantarum strain YAU B9601-Y2 contains a gene cluster for mersacidin synthesis. J. Bacteriol. 194:3264 –3265. http://dx.doi.org/10.1128/JB.0054 5-12. Lee SY, Kim BY, Ahn JH, Song J, Seol YJ, Kim WG, Weon HY. 2012. Draft genome sequence of the biocontrol bacterium Bacillus amyloliquefaciens strain M27. J. Bacteriol. 194:6934 – 6935. http://dx.doi.org/10.112 8/JB.01835-12. Manzoor S, Niazi A, Bejai S, Meijer J, Bongcam-Rudloff E. 2013. Genome sequence of a plant-associated bacterium, Bacillus amyloliquefaciens strain UCMB5036. Genome Announc. 1(2):e00111-13. http://dx.doi .org/10.1128/genomeA.00111-13. Dunlap CA, Bowman MJ, Schisler DA. 2013. Genomic analysis and secondary metabolite production in Bacillus amyloliquefaciens AS 43.3: a biocontrol antagonist of Fusarium head blight. Biol. Control 64:166 –175. http://dx.doi.org/10.1016/j.biocontrol.2012.11.002.
2 genomea.asm.org
10. Lefort F, Douglas GC. 1999. An efficient micro-method of DNA isolation from mature leaves of four hardwood tree species Acer, Fraxinus, Prunus and Quercus. Ann. For. Sci. 56:259 –263. 11. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, 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. 12. 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. 13. Geng W, Cao M, Song C, Xie H, Liu L, Yang C, Feng J, Zhang W, Jin Y, Du Y, Wang S. 2011. Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-␥-glutamic acid. J. Bacteriol. 193:3393–3394. http://dx.doi.org/10.1 128/JB.05058-11. 14. Yang H, Liao Y, Wang B, Lin Y, Pan L. 2011. Complete genome sequence of Bacillus amyloliquefaciens XH7, which exhibits production of purine nucleosides. J. Bacteriol. 193:5593–5594. http://dx.doi.org/10.112 8/JB.05880-11.
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