Halorubrum sp. strain 48-1-W was isolated from a water sample from a saline lake (Novosibirsk Region, Russia, 54°14′N 78°13′E).
ABSTRACT
Halorubrum sp. strain 48-1-W was isolated from a water sample from a saline lake (Novosibirsk Region, Russia, 54°14′N 78°13′E). The sequenced and annotated genome is 3,584,929 bp and contains 3,506 genes.
ANNOUNCEMENT
The genus Halorubrum includes extremely halophilic archaeal species that are widely distributed in high-salinity environments and are a major component of the microbial community of hypersaline environments (1). The genus currently contains 32 validly published species (2, 3).
Halorubrum sp. strain 48-1-W was isolated from a water sample from a saline lake (Novosibirsk Region, Russia, 54°14′N 78°13′E). Isolation and purification of the strain were conducted at 30 to 37°C on agar medium containing 200 g/liter NaCl, 5 g/liter MgCl2, 1 g/liter KCl, 1 g/liter CaCl2, 4 g/liter tryptone, 2 g/liter yeast extract, and 15 g/liter agar. Colonies appeared over the course of a month. We isolated the strain for a collection of biotechnological microorganisms as a source for novel promising objects for biotechnology and bioengineering at the Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (RAS).
A single colony of Halorubrum sp. 48-1-W was inoculated in 20 ml of liquid medium described above (рН 7.5) and cultivated for 2 weeks with shaking at 200 rpm. Eight milliliters of cell culture was pelleted by centrifugation and resuspended in 75 µl of H2O. DNA was isolated using a DNA purification kit (Fermentas). The NEBNext Ultra II DNA library prep kit for Illumina (New England BioLabs, USA) was used to create libraries for genome sequencing. Genome sequencing was performed on a MiSeq platform (Illumina), using MiSeq reagent kit version 3 (single-end reads, 150 cycles; Illumina, USA) at the Institute of Molecular and Cellular Biology at the Siberian Branch of the RAS (IMCB SB RAS). A total of 1,980,123 reads were sequenced. The reads were trimmed with Trimmomatic version 0.36 (using options HEADCROP:10, ILLUMINACLIP, and MINLEN:64) (4).
De novo assembly of short reads into contigs was performed using SPAdes version 3.10.1 using default parameters (with option –only-assembler) (5). Contigs shorter than 1,000 bp were deleted. A total of 69 contigs yielded a genome sequence 3,584,929 bp long, with a GC content of 66.07%. Open reading frame (ORF) prediction and automatic annotation were performed using NCBI PGAAP using the default parameters (6). The complete genome sequence contains 3,506 genes, 3,455 coding sequences (CDS), rRNAs (1 5S, 1 16S, and 1 23S), 46 tRNAs, and 2 noncoding RNAs (ncRNAs).
Data availability.
The raw data have been deposited at DDBJ/EMBL/GenBank under the accession no. SRR8097410. The draft genome sequence for Halorubrum sp. 48-1-W has been deposited at DDBJ/EMBL/GenBank under the accession no. QMIM00000000. The 69 contigs have been deposited under accession no. QMIM01000001 to QMIM01000069.
ACKNOWLEDGMENTS
This research was supported by RFBR and Novosibirsk Region according to the research project 17-44-540815 and by ICG SB RAS Budget project no. 0324-2018-0017, “Genetic basis of biotechnology and bioinformatics.”
This work was done at the Center for Collective Use, “A collection of biotechnological microorganisms as a source of novel promising objects for biotechnology and bioengineering” of the Federal Research Center Institute of Cytology and Genetics of the Siberian Branch of the RAS.
REFERENCES
- 1.McGenity TJ, Grant WD. 1995. Transfer of Halobacterium saccharovorum, Halobacterium sodomense, Halobacterium trapanicum NRC 34021 and Halobacterium lacusprofundi to the genus Halorubrum gen. nov., as Halorubrum saccharovorum comb. nov., Halorubrum sodomense comb. nov., Halorubrum trapanicum comb. nov., and Halorubrum lacusprofundi comb. nov. Syst Appl Microbiol 18:237–243. doi: 10.1016/S0723-2020(11)80394-2. [DOI] [Google Scholar]
- 2.Parte AC. 2014. LSPN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613–D616. doi: 10.1093/nar/gkt1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Corral P, de la Haba RR, Sánchez-Porro C, Amoozegar MA, Thane Papke R, Ventosa A. 2015. Halorubrum persicum sp. nov., an extremely halophilic archaeon isolated from sediment of a hypersaline lake. Int J Syst Evol Microbiol 65:1770–1778. doi: 10.1099/ijs.0.000175. [DOI] [PubMed] [Google Scholar]
- 4.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.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. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.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. doi: 10.1093/nar/gkw569. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
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Data Availability Statement
The raw data have been deposited at DDBJ/EMBL/GenBank under the accession no. SRR8097410. The draft genome sequence for Halorubrum sp. 48-1-W has been deposited at DDBJ/EMBL/GenBank under the accession no. QMIM00000000. The 69 contigs have been deposited under accession no. QMIM01000001 to QMIM01000069.