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Environmental Microbiology
Announcement
4 February 2021

Draft Genome Sequence of Antarctic Psychrotroph Streptomyces fildesensis Strain INACH3013, Isolated from King George Island Soil

ABSTRACT

The draft genome sequence of Streptomyces fildesensis strain INACH3013, a psychrotrophic bacterium isolated from Northwest Antarctic soil, was reported. The genome sequence totaling 9,306,785 bp resulted from 122 contigs characterized by a GC content of 70.55%.

ANNOUNCEMENT

Streptomyces species are aerobic, spore-forming, filamentous Gram-positive bacteria with large and linear chromosomes characterized by a high GC content (1). Members of this genus are ubiquitous in a broad range of habitats, including extreme environments ranging from tropical to polar regions (2), and are known for their ability to synthesize a wide variety of biologically active secondary metabolites (3).
Here, we report the partial genome sequence of Streptomyces fildesensis strain INACH3013, isolated from soil of the Antarctic Fildes Peninsula (62°12′26.4″S, 58°58′28.7″W) (2, 4). The taxonomic status of the isolate was established in reference 2. This strain shows antibacterial compound production at temperatures below the optimal growth value (28°C) and a temperature-dependent trade-off between secondary compound production and growth (4).
S. fildesensis strain INACH3013 was cultured in triplicate using 500 ml of oatmeal liquid medium (20 g liter−1) with agitation (180 rpm) for 5 days at 12°C ± 1°C. Genomic DNA was isolated from a single colony using a DNeasy blood and tissue kit (Qiagen, Inc., USA), according to the manufacturer’s procedure. The taxonomic affiliation of the strain was confirmed by partial sequencing of the 16S rRNA gene (NCBI accession number KJ624755). The total DNA was processed by using a TruSeq DNA PCR-free library preparation kit and HiSeq 2000 paired-end sequencing (Illumina, Inc., San Diego, CA). The corresponding genome sequencing generated 9,445,886 short reads with an average length of 100 nucleotide bases. The sequence reads were filtered using Trimmomatic v0.39 (5) using default parameters. The de novo genome assembly was performed using SPAdes 3.14.1 with default parameters (6). The partial genome sequence was assembled from 73 large contigs (>10,000 bp) and 49 small contigs (<10,000 bp), with an N50 value of 152,215 bp, with the largest contig of 681,566 bp. The S. fildesensis strain INACH3013 genome sequence had an estimated completion of 99.28% (7) and a mean coverage of 32.7025×. The draft genome was annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) using default settings (8). The final assembly had a GC content of 70.55%, with 8,622 protein-coding genes, 4 rRNAs, 77 tRNAs, and an average gene length of 957.88 bp. antiSMASH v5.0 (9) predicted a total of 32 biosynthetic gene clusters.

Data availability.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JAAIKO000000000. The version described in this paper is the first version, JAAIKO010000000. The SRA accession number is SRX7554417.

ACKNOWLEDGMENTS

This research was supported by the VRII-No1308 project Iniciación de la Investigación de Nuevos Investigadores de la Universidad de Antofagasta, Chile; INACH project RT-20_19; and the Ministry of Science, Technology, and Innovation (MOSTI), Malaysia, under the Antarctica Flagship Program (subproject 1, FP1213E036).

REFERENCES

1.
Whitman WB, Goodfellow M, Kämpfer P. 2012. Bergey’s manual of systematic bacteriology: volume 5: the Actinobacteria. Springer, New York, NY.
2.
Lavin PL, Yong ST, Wong CM, De Stefano M. 2016. Isolation and characterization of Antarctic psychrotroph Streptomyces sp. strain INACH3013. Antarct Sci 28:433–442.
3.
Sivalingam P, Hong K, Pote J, Prabakar K. 2019. Extreme environment Streptomyces: potential sources for new antibacterial and anticancer drug leads? Int J Microbiol 2019:5283948.
4.
Lavin PL, Yong ST, Wong CMV, Perez ARG, Dorador C. 2017. The trade-off between antimicrobial production and growth of an Antarctic psychrotroph Streptomyces sp. strain INACH3013. Antarct Sci 29:427–428.
5.
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.
6.
Bankevich A, Nurk S, 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.
7.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055.
8.
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.
9.
Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T. 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 10Number 54 February 2021
eLocator: 10.1128/mra.01453-20
Editor: Frank J. Stewart, Georgia Institute of Technology

History

Received: 18 December 2020
Accepted: 13 January 2021
Published online: 4 February 2021

Contributors

Authors

Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
Carlos Henríquez-Castillo
Laboratorio de Fisiología y Genética Marina (FIGEMA), Centro de Estudios Avanzados de Zonas Áridas (CEAZA), Coquimbo, Chile
Facultad de Ciencias del Mar, Universidad Catolica del Norte, Coquimbo, Chile
Sheau Ting Yong
Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
Daniel Valenzuela-Heredia
Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Viña del Mar, Chile
Romulo Oses
Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copiapó, Chile
Katherine Frez
Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
Marcela P. Borba
Laboratório de Microbiologia Aplicada, Instituto de Ciências Básicas da Saúde, Departamento de Microbiologia, Imunologia e Parasitologia, Porto Alegre, Brazil
Cristina Purcarea
Department of Microbiology, Institute of Biology, Bucharest, Romania
C. M. V. L. Wong
Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia

Editor

Frank J. Stewart
Editor
Georgia Institute of Technology

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