Abstract
A salt tolerant strain, designated as SUBG004, was isolated from the desert of India, Little Rann of Kutch. The organism is a Gram-negative, facultatively anaerobic and rod shaped bacterium. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Halomonas. Here we report the whole genome sequence of Halomonas sp. SUBG004 deposited in DDBJ/EMBL/GenBank under accession number JPEU0100000 which provides insights for salt stress adaptation through betaine synthesis.
Keywords: Halomonas sp. SUBG004, Desert soil flora, Betaine, Genome sequence
| Specifications | |
|---|---|
| Organism | Halomonas sp. |
| Strain | SUBG004 |
| Sequencer or array type | Ion Torrent PGM |
| Data format | Processed |
| Experimental factors | Microbial strain |
| Experimental features | Whole genome sequence of Halomonas sp. SUBG004, assembly and annotation |
| Consent | N/A |
| Simple source location | Soil of desert Little Rann of Kutch, Gujarat, India |
1. Direct link to deposited data
2. Experimental design, materials and methods
Halomonas sp. strain SUBG004 is a Gram negative, rod-shaped bacterium isolated from the saline desert soil of Little Rann of Kutch in Gujarat, India. The isolate was acquired by culture-plating on 10% w/v NaCl containing nutrient rich medium and then its capacity to survive in M9 minimal medium with 10% w/v NaCl was explored. Here we report the complete genome of Halomonas sp. SUBG004.
Genomic DNA was extracted from 12 hour old culture using protocol [1]. Sequencing of the Halomonas sp. SUBG004 genome was performed by the Ion Torrent Technologies and raw reads were assembled by MIRA v. 2014. A total of 1982 contigs with an accumulated length of 4,897,364 bp (50.0X coverage) were annotated by GeneMarkS + method. The genome contains 93 tRNA genes and 44 rRNA genes as predicted using tRNAscan 1.2 [2] and RNAmmer 1.2 [3], respectively, results enlisted in Table 1.
Table 1.
Genome features of Halomonas sp. SUBG004.
| Features | Chromosome |
|---|---|
| Length [bp] | 4,897,364 bp |
| G + C content [%] | 57.4% |
| Total contigs | 1982 |
| Protein-coding genes | 2029 |
| tRNA genes | 93 |
| rRNA genes | 44 |
Coding sequences were functionally annotated by Rapid Annotation using the Subsystems Technology (RAST) server in 451 subsystems (Fig. 1). Gene sequences of a betaine synthesis operon putatively encoding BetI: HTH type transcriptional regulator, BetA:Choline dehydrogenase (EC 1.1.99.1) and BetB:Betaine aldehyde dehydrogenase (EC 1.2.18) were identified using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database available in RAST [4].
Fig. 1.
Subsystem distribution of Halomonas sp. SUBG004 (based on RAST annotation server).
3. Summary
Genomic analysis of the isolate gives a genetic confirmation to its salt stress adaptation potential. Thus the information obtained from the whole genome sequence about the metabolic pathways of the strain helps reveal the gene coding for enzymes involved in microbe's role in maintaining osmotic balance and its halotolerance potential. The sequence of genome has been deposited in as whole genome shotgun (wgs) project as project accession JPEU00000000 in DDBJ/EMBL/GenBank. After the primary analysis of the assembly described above, the sequence will be taken up for further analysis including comparison with the genome of other Halomonas species to yield better insight into the isolate's adaptation to the oscillating osmotic condition prevailing in environment.
Conflict of interest
The authors declare that there is no conflict of interests on work published in this paper.
Acknowledgments
Funding for this study was provided by Higher Education Department, Gujarat State Government KVT / V1/ 07-08/ 9494 and UGC-CAS-F.5-4/2012(SAP-II) Department of Biosciences, Saurashtra University, Rajkot, India.
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