Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16

(1)

HAL Id: hal-02392253

https://hal.archives-ouvertes.fr/hal-02392253

Submitted on 7 Dec 2020

HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16

Bukola Rhoda Aremu, Claire Prigent-Combaret, Olubukola Oluranti Babalola

To cite this version:

Bukola Rhoda Aremu, Claire Prigent-Combaret, Olubukola Oluranti Babalola. Draft Genome Se-

quence of Bacillus velezensis Strain ZeaDK315Endo16. Microbiology Resource Announcements, Amer-

ican Society for Microbiology, 2019, 8 (46), �10.1128/MRA.00136-19�. �hal-02392253�

(2)

Draft Genome Sequence of Bacillus velezensis Strain ZeaDK315Endo16

Bukola Rhoda Aremu,^aClaire Prigent-Combaret,^b Olubukola Oluranti Babalola^a

aNorth-West University, Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, Mmabatho, South Africa

bUniversity of Lyon, The Rhizosphere Team, UMR CNRS 5557 Microbial Ecology, Villeurbanne, France

ABSTRACT Here, we report the draft genome sequence of the endophyticBacil- lus velezensis strain ZeaDK315Endo16, isolated from DK315 maize from Lyon, France. B. velezensisZeaDK315Endo16 exhibits a suppressive ability towardFusar- ium graminearum, a widely known threat to maize production and quality.

G

lobally, there is a setback in maize productivity and quality because of Fusarium graminearum infestation, leading to great economic losses (1).F. graminearumnot only contaminates maize but also impairs the health of animals and humans upon consumption of maize. To circumvent the challenge by this fungus, chemical control measures have been implemented which are expensive and increase environmental pol- lution (2). Hence, the need arises for a safer and environmentally friendly control measure like the use of a bioinoculum as a means of biocontrol (3). Thus, the endophytic bacteria were isolated from the maize seed, examined in vitroon potato dextrose agar (PDA) contained in petri dishes for their ability to suppressF. graminearum, and gave a notable inhibition zone (Fig. 1).Bacillus velezensisstrain ZeaDK315Endo16 elicited the most signi- ﬁcant inhibitory factor against this pathogen. The endophytic plant-microbe interaction needs to be investigated to gain insight into the genomic composition of endophyticB.

velezensisstrain ZeaDK315Endo16 and recognition of the gene responsible for this suppressive ability. We isolatedB. velezensisZeaDK315Endo16 from the seed of DK315 maize obtained from Lyon, France.B. velezensisZeaDK315Endo16 was cultivated on Luria-Bertani agar (Sigma-Aldrich Corporation, USA) in a petri dish and was incubated at 25°C for 24 h.

The ZR fungal/bacterial DNA kit (Zymo Research Corp., Irvine, CA, USA) was utilized for genomic DNA extraction of the pure culture. A draft genome of B. velezensis strain ZeaDK315Endo16 was obtained by direct sequencing of genomic DNA using the Illumina HiSeq 2500 system (rapid mode) at MR DNA (Shallowater, TX, USA). The KAPA HyperPlus kit (Roche) was used in library preparation to generate 250-bp Illumina paired-end reads.

FastQC v.1.0.4 was utilized for sequence quality (Babraham Bioinformatics, United Kingdom); the low-quality reads of⬍30 and adapters were removed with PRINSEQ v.0.0.4 (4) and Cutadapt v.1.0.7 (5). The high-quality edited sequence reads werede novoassem- bled with SPAdes v.3.12.0 (6), resulting in a total genome assembly size of 4,452,329 bp with 788 scaffolds. The quality of the genome assemblies was checked using QUAST v.5.0.0 (7).

Reassembly with Filter Assembled Contigs by Length v.1.1.2 in the Kbase platform (8) removed the contigs with unusual G⫹C content and sequencing depth that likely result from contamination. Finally, a genome with a size of 3,925,184 bp with 1 contig, a G⫹C content of 46.4%, anN₅₀value of 3,925,184 bp, and anL₅₀of 1 was obtained. The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v.4.7 was utilized for the genome annotation (9). The genome in total contains 3,930 genes, 3,843 coding DNA sequences (CDSs), 3,747 CDSs (with protein), 87 genes (RNA), 9 rRNAs, 73 tRNAs, 5 noncoding RNAs (ncRNAs), and 96 pseudogenes. There is only one questionable CRISPR in the genome detected by CRISPRFinder (10). Additionally, the major secondary metabolites for the suppressiveness of

CitationAremu BR, Prigent-Combaret C, Babalola OO. 2019. Draft genome sequence of Bacillus velezensisstrain ZeaDK315Endo16.

Microbiol Resour Announc 8:e00136-19.

https://doi.org/10.1128/MRA.00136-19.

EditorIrene L. G. Newton, Indiana University, Bloomington

Address correspondence to Olubukola Oluranti Babalola, [email protected].

Received11 February 2019 Accepted19 September 2019 Published14 November 2019

GENOME SEQUENCES

crossm

Volume 8 Issue 46 e00136-19 mra.asm.org 1

on December 7, 2020 by guest http://mra.asm.org/ Downloaded from

(3)

F. graminearum are macrolactin, bacillaene, fengycin, difﬁcidin, bacillibactin, bacilysin, mersacidin, and surfactin, identiﬁed using antiSMASH v.5.0.0 (11). This draft genome sequence may serve as an inoculum for biocontrol. Analysis (average nucleotide identity [ANI]) of the genome of B. velezensis ZeaDK315Endo16 shows a high similarity withB.

velezensis(identity, 98.5%). Default parameters were used for all software.

Data availability. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numberCP043809. The version described in this paper is the ﬁrst version, SDSJ00000000.1. The raw genome sequence data are under the SRA study accession numberSRP181915.

ACKNOWLEDGMENTS

We acknowledge the ﬁnancial support of the National Research Foundation (NRF) for Freestanding Postdoctoral Fellowships of South Africa (UID106474) and NRF/Protea bilateral grant (UID95111).

REFERENCES

1. Dweba C, Figlan S, Shimelis H, Motaung T, Sydenham S, Mwadzingeni L, Tsilo T. 2017. Fusarium head blight of wheat: pathogenesis and control strategies. Crop Prot 91:114 –122.https://doi.org/10.1016/j.cropro.2016 .10.002.

2. Kalagatur NK, Nirmal Ghosh OS, Sundararaj N, Mudili V. 2018. Anti- fungal activity of chitosan nanoparticles encapsulated with Cym- bopogon martinii essential oil on plant pathogenic fungiFusarium graminearum. Front Pharmacol 9:610 – 610.https://doi.org/10.3389/

fphar.2018.00610.

3. Aremu BR, Alori ET, Kutu RF, Babalola OO. 2017. Potentials of microbial inoculants in soil productivity: an outlook on African legumes, p 53–75.

InPanpatte DG, Jhala YK, Vyas RV, Shelat HN (ed), Microorganisms for green revolution. Springer, New York, NY.

4. Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863– 864. https://doi.org/10 .1093/bioinformatics/btr026.

5. Martin M. 2011. Cutadapt removes adapter sequences from high-

throughput sequencing reads. EMBnet J 17:10 –12.https://doi.org/10 .14806/ej.17.1.200.

6. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clin- genpeel SR, Woyke T, McLean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling single-cell genomes and minimetag- enomes from chimeric MDA products. J Comput Biol 20:714 –737.

https://doi.org/10.1089/cmb.2013.0084.

7. Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A. 2018.

Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34:i142–i150.https://doi.org/10.1093/bioinformatics/bty266.

8. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia J-M, Chia J-M, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, FIG 1 Inhibition of Fusarium graminearum by a single loopful of Bacillus velezensis strain

ZeaDK315Endo16 antagonist streaked 3 days after the fungi was inoculated on the opposite sides.

Aremu et al.

on December 7, 2020 by guest http://mra.asm.org/ Downloaded from

(4)

Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. 2018. KBase: the United States Department of Energy Systems biology knowledgebase. J Nat Biotechnol 36:566 –569.https://doi.org/10.1038/nbt.4163.

9. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI

Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:

6614 – 6624.https://doi.org/10.1093/nar/gkw569.

10. Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a Web tool to identify clustered regularly interspaced short palindromic repeats. Nu- cleic Acids Res 35:W52–W57.https://doi.org/10.1093/nar/gkm360.

11. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, Suarez Duran HG, de Los Santos ELC, Kim HU, Nave M, Dickschat JS, Mitchell DA, Shelest E, Breitling R, Takano E, Lee SY, Weber T, Medema MH. 2017.

antiSMASH 4.0 —improvements in chemistry prediction and gene clus- ter boundary identiﬁcation. Nucleic Acids Res 45:W36 –W41.https://doi .org/10.1093/nar/gkx319.

Microbiology Resource Announcement