Draft genome sequence of the extremely halophilic Halorubrum sp. SAH-A6 isolated from rock salts of the Danakil depression, Ethiopia

Abstract

The draft genome sequence of Halorubrum sp. SAH-A6, isolated from commercial rock salts of the Danakil depression, Ethiopia. The genome comprised 3,325,770 bp, with the G + C content of 68.0%. The strain has many genes which are responsible for secondary metabolites biosynthesis, transport and catabolism as compared to other Halorubrum archaea members. Abundant genes responsible for numerous transport systems, solute accumulation, and aromatic/sulfur decomposition were detected. The first genomic analysis encourages further research on comparative genomics, and biotechnological applications. The NCBI accession number for this genome is SAMN04278861 and ID: 4278861 and strain deposited with accession number KCTC 43215.

1. Resource table

Name of resource	Halorubrum species strain SAH-A6
Institution	This strain is available from Korean Collection for Type Cultures (KCTC) with the accession number KCTC 43215
Person who created resource	Ashagrie Gibtan, Mingyeong Woo, Dokyung Oh, Kyounghee Park, Han-Seung Lee, Jae Hak Sohn, Dong-Woo Lee, Jung-Kue Shin, Sang-Jae Lee,⁎
Contact person and email	Sang-Jae Lee, sans76@silla.ac.kr
Date archived/stock date	June 2, 2016
Type of resource	Whole genome sequence data
Link to directly related literature that employed/validated this resource	http://www.ncbi.nlm.nih.gov/genome/14537?genome_assembly_id=263668
Information in public databases	http://www.ncbi.nlm.nih.gov/genome/14537?genome_assembly_id=263668

2. Resource details

The genus Halorubrum was originally proposed by McGenity and Grant [1] and constitutes a large group of extremely halophilic aerobic archaea belonging to the family Halobacteriaceae. At the time of writing, 31 species have been described in the genus Halorubrum [2] which are widely distributed in diverse natural and artificial hypersaline environments such as marine salterns, salt lakes, soda lakes, saline soils, salt fermented foods, and salt preserved food products [3], [4]. Hence, more investigations at genomic level are required to improve our understanding of its ecology, physiology, genetics, and potentiality in biotechnological applications. Halorubrum sp. SAH-A6 strain was isolated from the commercial rock salt produced from the Danakil depression of Ethiopia. Currently, neither genome of this species nor Halorubrum genome from commercial rock salt of the Danakil depression of Ethiopia reported. To fill this gap, Halorubrum sp. SAH-A6 was chosen for genome sequencing.

3. Specifications

Organism	Halorubrum sp.
Strain	SAH-A6
Sequencer or array type	PacBio RS II
Data format	Analyzed
Experimental factors	Archaea strain
Experimental features	Assembled and annotated whole genome
Consent	N/A
Sample source location	Rock salts of the Danakil depression, Ethiopia

The draft genome sequence of Halorubrum sp. SAH-A6, isolated from commercial rock salts of the Danakil depression, Ethiopia. The assembled genome comprised 3,325,770 bp, with high G + C content of 68.0% (Table 1). The strain has many genes which are responsible for secondary metabolites biosynthesis, transport, and catabolism as compared to other Halorubrum Archaea. In addition, strain SAH-A6 use universal strategies for extreme adaptation as indicated by the genome. Abundant genes responsible for numerous transport systems, solute accumulation, and aromatic/sulfur decomposition were detected. The subsystem category distribution statistics for Halorubrum sp. strain SAH-A6 were shown in Fig. 1.

Table 1.

Comparison of the genomic feature of Halorubrum sp. SAH-A6 strain with various halophilic Halorubrum strains. The information of the reference genomes was obtained from NCBI data base.

Organism	BioProject	Resource	Genome size	Contigs	G + C (%)	r + tRNA
H. sp. SAH-A6a	PRJNA302707	Danakil depression, Ethiopia	3,325,770	3	68.0	6 + 45
H. lipolyticum DSM 21995	PRJNA188614	Xin-Jiang, China	3,425,042	41	68.0	3 + 44
H. aidingense JCM 13560	PRJNA188616	Xin-Jiang, China	3,108,525	37	67.2	4 + 49
H. kocurii JCM 14978	PRJNA188615	Inner Mongolia, China	3,619,738	105	66.9	1 + 46
H. lacusprofundi ATCC 49239	PRJNA58807	Deep Lake, Antarctica	3,692,576	3	64.0	9 + 51
H. saccharovorum DSM 1137	PRJNA188612	California, USA	3,423,703	72	66.9	2 + 445
H. coriense DSM 10284	PRJNA188619	Geelong, Australia	3,645,313	69	67.0	3 + 48
H. distributum JCM 10118	PRJNA188621	Turkmenistan	3,306,135	68	68.1	4 + 43

^aThis study.

Fig. 1.

The subsystem category distribution statistics for Halorubrum sp. strain SAH-A6. The whole genome sequence of SAH-A6 was annotated using the Rapid Annotation System Technology (RAST) server. The pie chart showed the count of each subsystem feature and the subsystem coverage.

The genomic analysis showed that the overall central metabolism of SAH-A6 seems to be similar to other Halorubrum species. All members of Halorubrum share the same genes that are responsible for full glycolysis/gluconeogenesis, citrate cycle, pentose phosphate, and pyruvate pathways and sugars metabolism. This shows a horizontal gene transfer within the genus. However, metabolic differences were predicted in many other pathways. Among them, for example, the number of genes which are responsible for secondary metabolites biosynthesis, transport, and catabolism are very high in SAH-A6 strain as compared to other Halorubrum groups.

Further genomic analysis of strain SAH-A6 showed the genetic capacity for adaptation to harsh environments. Unlike other Halorubrum groups, SAH-A6 has much more genes responsible for inorganic ion transport, energy conversion, amino acid transport, and metabolism which can help it to cope with the hot, saline, and nutrient limited environments. Strain SAH-A6 revealed the presence of numerous ionic regulation genes, including magnesium, and copper transport, arsenic pump-driving, ABC transporters, cobalt-zinc-cadmium resistance, and P-type ATPase. These genes help SAH-A6 and other microbes to overcome the high metallic ion in rock salt as compared to other saline environments. Apart from this, strain SAH-A6 is using genes such as stress response, heat shock proteins, DNA repair systems, maintenance of membrane fluidity, and accumulation of compatible solutes as indicated by the genome. In addition, SAH-A6 also has other unique feature for adaptation in slow growth in nutrient-poor commercial rock salt in that it possesses a single rRNA operon. However, fewer genes encoding transposase, lipid transport, and metabolism were found in the SAH-A6 genome, compared with other Halorubrum members.

Phylogenetic tree was built based on neighbor joining tree with the alignment of the 16S rRNA gene sequences (~ 1470 bp) showing the relationship between Halorubrum genomes available at the EzTaxon data base and SAH-A6 using MEGA6 [5] (Supplementary Fig. 1).

4. Materials and methods

The genome sequencing was performed using a single molecule real-time (SMRT) sequencing platform on the PacBio RS II (Pacific Biosciences, Menlo Park, CA) [6]. Genomic DNA was extracted using a standard genomic DNA isolation kit (Promega, USA). The whole genome sequence of strain SAH-A6 was performed using single SMRT cell with a single 180 min movie (Pacific Biosciences) with P6C4 chemistry. The open reading frames of the assembled genome were predicted and annotated using the hierarchical genome-assembly process (HGAP) [7] protocol RS HGAP Assembly 2 in SMRT analysis version 2.3.0 (Pacific Biosciences; https://github.com/PacificBiosciences/SMRT-Analysis), IMG-ER [8], NCBI COG function [9], Pfam information [10], and EzTaxon [11] database. The rRNA and tRNA genes were identified using RNAmmer 1.2 [12] and tRNA scan-SE 1.23 [13], respectively. The whole genome sequence of SAH-A6 was annotated using the Rapid Annotation System Technology (RAST) server. The pie chart showed the count of each subsystem feature and the subsystem coverage.

5. Direct link to deposited data

http://www.ncbi.nlm.nih.gov/genome/14537?genome_assembly_id=263668

The following are the supplementary data related to this article.

Supplementary Fig. 1

Phylogenetic tree constructed using the neighbor-joining method based on 16SrRNA gene sequences, showing the taxonomic position of strain SAH-A6 in the genus Halorubrum. The information of the reference genomes was obtained from EzTaxon data base.

Supplementary material

Alignment of the 16S rRNA gene of SAH-A6 with other strains.

Conflict of interest

The authors have nothing to disclose.

Verification and authentication

The whole draft genomic sequence of Halorubrum sp. SAH-A6 (Bio project PRJNA302707) has been deposited at NCBI GenBank database under accession numbers SAMN04278861 and ID: 4278861. This strain is available from Korean Collection for Type Cultures (KCTC) with the accession number KCTC 43215.