Open access
Announcement
6 December 2018

Draft Genome Sequence of a Novel Serratia sp. Strain with Antifungal Activity

ABSTRACT

This report describes the draft genome sequence of Serratia sp. strain S40, isolated from potato; it contains 5,383,735 bp and a G+C content of 55.9% and harbors 4,875 predicted coding sequences across 29 contigs. The genomic data provide insight into the genetics underpinning the antifungal activity of this strain.

ANNOUNCEMENT

Serratia species are ubiquitous in the environment and have been isolated from soil, water, and animals, including humans (1). The genus comprises both nonpathogenic species and pathogens of plants, animals, and humans. Several members of the genus have been associated with the rhizosphere of diverse plants and shown to be plant growth promoting and antifungal (24). The application of rhizosphere biocontrol bacteria to control plant-pathogenic fungi is an alternative approach to the use of chemical fungicides.
Serratia sp. strain S40 was isolated from a potato rhizosphere in Zealand, Denmark (5). For whole-genome sequencing, the strain was cultivated in lysogeny broth (LB) for 24 h at 20°C before DNA extraction. Genomic DNA was purified using the Gentra Puregene Yeast/Bact. kit (Qiagen, Germany) according to the manufacturer’s instructions, and purified genomic DNA was verified by 16S RNA gene sequencing as previously described (5). Library preparation for whole-genome sequencing was performed using the Nextera DNA library prep kit (Illumina, Inc., San Diego, CA, USA). Sequencing was carried out with an Illumina MiSeq platform using MiSeq reagent kit V3 (600 cycles) (Illumina, Inc.). A total of 896,235 (539.5 Mbp) paired-end reads with a read size of 301 × 2 bp and average insert size of 478 bp were retrieved. Adapter sequences and low-quality bases (<Q20) were trimmed from raw reads using the TrimGalore! software version 0.4.4 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). A total of 885,343 reads (386.6 Mbp, 71.8× coverage for Serratia sp.) passed quality control and were used for assembly using SPAdes Genome Assembler version 3.7.1 (6). Genome annotation was conducted using P-CAPS (7) and the NCBI Prokaryotic Genome Annotation Pipeline (8).
The draft genome sequence of Serratia sp. S40 is 5,383,735 bp long, and its contigs are set up in 29 scaffolds (L50, 3; N50, 362,774 bp), with a mean G+C content of 55.9%. The annotation of the Serratia sp. S40 genome revealed the presence of 4,875 predicted coding sequences (CDS) and 93 predicted RNA (14 rRNAs, 79 tRNAs) coding sequences.
Using a series of in silico genome mining tools, a total of 8 secondary metabolite gene clusters were predicted by antiSMASH (9), including 4 nonribosomal peptide synthetase/polyketide synthase (NRPS/PKS) clusters; 3 bacteriocin gene clusters were identified by BAGEL3 (10), and NapDos (11) predicted 8 KS-domains and 10 C-domains, while NP Searcher (12) identified 1 NRPS gene cluster.
Further in-depth analysis of this genome will increase our understanding of the antifungal activity of this strain for applications within biocontrol and potentially lead to the discovery of new natural products.

Data availability.

This whole-genome sequence project has been deposited at DDBJ/ENA/GenBank under the accession number QYYG00000000. The version described in this paper is QYYG01000000. Raw sequence files are deposited under the accession number PRJNA491277.

ACKNOWLEDGMENT

This work was supported by the Innovation Fund Denmark grant 5158-00001 A (proPotato: Potato Proteins–Challenges and Industrial Possibilities).

REFERENCES

1.
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Berg G. 2000. Diversity of antifungal and plant-associated Serratia plymuthica strains. J Appl Microbiol 88:952–960.
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Purkavastha GD, Mangar P, Saha A, Saha D. 2018. Evaluation of the biocontrol efficacy of a Serratia marcescens strain indigenous to tea rhizosphere for the management of root rot disease in tea. PLoS One 13:e0191761.
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Zarei M, Aminzadeh S, Zolgharnein H, Safahieh A, Daliri M, Noghabi KA, Ghoroghi A, Motallebi A. 2011. Characterization of a chitinase with antifungal activity from a native Serratia marcescens B4A. Braz J Microbiol 42:1017–1029.
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Hennessy RC, Jørgensen NOG, Scavenius C, Enghild JJ, Greve-Poulsen M, Sørensen OB, Stougaard P. 2018. A screening method for the isolation of bacteria capable of degrading steroidal glycoalkaloids present in potato. Front Microbiol 9:2648.
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Bankevich A, Nurk SS, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.
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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.
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Weber T. 2014. In silico tools for the analysis of antibiotic biosynthetic pathways. Int J Med Microbiol 304:230–235.
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Van Heel AJ, de Jong A, Montalbán-López M, Kok J, Kuipers OP. 2013. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res 41:W448–W453.
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Ziemert N, Podell S, Penn K, Badger JH, Allen E, Jensen PR. 2012. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One 7:e34064.
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Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 7Number 226 December 2018
eLocator: 10.1128/mra.01340-18
Editor: Julie C. Dunning Hotopp, University of Maryland School of Medicine

History

Received: 27 September 2018
Accepted: 5 November 2018
Published online: 6 December 2018

Contributors

Authors

Søs I. Dichmann
Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
Byeonghyeok Park
Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
Duleepa Pathiraja
Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
In-Geol Choi
Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
Peter Stougaard
Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
Rosanna C. Hennessy
Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark

Editor

Julie C. Dunning Hotopp
Editor
University of Maryland School of Medicine

Notes

Address correspondence to Rosanna C. Hennessy, [email protected].

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