- Short genome report
- Open Access
Draft genome sequence of Halopiger salifodinae KCY07-B2T, an extremly halophilic archaeon isolated from a salt mine
Standards in Genomic Sciences volume 10, Article number: 124 (2015)
Halopiger salifodinae strain KCY07-B2T, isolated from a salt mine in Kuche county, Xinjiang province, China, belongs to the family Halobacteriaceae. It is a strictly aerobic, pleomorphic, rod-shaped, Gram-negative and extremely halophilic archaeon. In this work, we report the features of the type strain KCY07-B2T, together with the draft genome sequence and annotation. The draft genome sequence is composed of 83 contigs for 4,350,718 bp with 65.41 % G + C content and contains 4204 protein-coding genes and 50 rRNA genes.
The genus Halopiger , which belongs to the family Halobacteriaceae , was originally established in 2007 by Gutiérrez et al. . The type species of the genus Halopiger is Halopiger xanaduensis SH-6T. To date, the genus is comprised of three validly published species and two effectively but not validly published species: H. xanaduensis , Halopiger aswanensis , Halopiger salifodinae , Halopiger djelfamassiliensis  and Halopiger goleamassiliensis . The species of the genus were reported to be isolated from hypersaline environments such as salt lake sediment [1, 4, 5], hypersaline soil  and salt mine . All are Gram-negative, strictly aerobic and extremely halophilic [1–5]. In this genus, three genome sequences, including one finished genome sequence H. xanaduensis SH-6T, and two draft genome sequences H. djelfamassiliensis IIH2T and H. goleamassiliensis IIH3T, are available in Standards in Genomic Sciences [4–6], except H. aswanensis 56T which showed highest 16S rRNA gene similarity to H. xanaduensis SH-6T (99.1 %). Here we present a summary of the classification and a set of features of strain H. salifodinae KCY07-B2T, together with a description of the non-contiguous finished genomic sequencing and annotation.
Classification and features
A representative genomic 16S rRNA gene sequence of H. salifodinae KCY07-B2T was compared with sequences deposited in the GenBank database using BLASTN . The 16S rRNA gene sequence analysis showed that H. salifodinae KCY07-B2T shared the highest sequence identities to H. xanaduensis SH-6T (95.8 %), followed by H. aswanensis 56T (95.5 %), H. djelfamassiliensis IIH2T (94.9 %) and H. goleamassiliensis IIH3T (94.8 %), and shared low sequence similarities (<94.8 %) to species of other genera. The phylogenetic tree was reconstructed by the neighbor-joining method using MEGA 5 and Kimura’s 2-parameter model for distance calculation [8, 9]. The phylogenetic tree was assessed by boot-strapping for 1000 replications, and the consensus tree was shown in Fig. 1.
H. salifodinae KCY07-B2T can tolerant high salinity (5.4 M NaCl ) and high temperature (50 °C) . Cells lyse in distilled water. The optimal growth condition of strain KCY07-B2T occured in medium NOM-3 with 2.9–3.4 M NaCl . The optimum temperature was 37–45 °C. The optimum pH was 7.0, with a growth range of pH 6.0–8.0 . Cells of strain KCY07-B2T are strictly aerobic, non-motile and pleomorphic rod-shaped (Fig. 2). Several sugars, organic acids and amino acids can serve as sole carbon and energy sources, and amino acids are not required in the growth medium . The features of H. salifodinae KCY07-B2T are listed in Table 1.
Genome sequencing information
Genome project history
This genome was selected for sequencing on the basis of its phylogenetic position and 16S rRNA sequence similarity to other members of the genus Halopiger . This whole genome shotgun project of strain H. salifodinae KCY07-B2T was deposited at DDBJ/EMBL/GenBank under the accession number JROF00000000 and the sequence consisted of 83 contigs (further assembling constructed these contigs into 81 scaffolds). Table 2 shows the project information and its association with MIGS version 2.0 compliance .
Growth conditions and genomic DNA preparation
H. salifodinae KCY07-B2T was cultivated aerobically on 37 °C for 4 days in NOM-3 medium, which contains (per liter distilled water) 5.4 g KCl, 0.3 g K2HPO4, 0.25 g CaCl2, 0.25 g NH4Cl, 26.8 g MgSO4 · 7H2O, 23.0 g MgCl2 · 6H2O, 184.0 g NaCl, 1.0 g yeast extract, 0.25 g fish peptone, 0.25 g sodium formate, 0.25 g sodium acetate, 0.25 g sodium lactate and 0.25 g sodium pyruvate (adjusted to pH 7.0 with 1 M NaOH) . Genomic DNA was extracted using the method described by Marmur . The purity, quality and the concentration of genomic DNA preparation were analyzed by 0.7 % agarose gel electrophoresis with λ-Hind III digest DNA Marker (TaKaRa, Dalian, China) and measured using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc., USA).
Genome sequencing and assembly
The genome of H. salifodinae KCY07-B2T was sequenced using Solexa paired-end sequencing technology (HiSeq2000 system, Illumina, Inc., USA) . A shotgun library was constructed with a 500 bp-span paired-end library (~500 Mb available reads, ~130-fold genome coverage) and a 2000 bp-span paired-end library (~250 Mb available reads, ~65-fold genome coverage). The sequence data from an Illumina HiSeq 2000 were assembled with SOAPdenovo v.1.05 [13–15]. The final assembly identified 83 contigs and 81 scaffolds (the minimum length is 523 bp) generating a genome size of 4.35 Mb. The quality of the sequencing reads data was estimated by G + C content and sequencing depth correlation analysis.
The tRNAs and rRNAs were identified using tRNAscan-SE , RNAmmer  and Rfam database ; The open reading frames and the functional annotation of translated ORFs were predicted and achieved by using the RAST server online [19, 20]. Classification of some predicted genes and pathways were analyzed using COGs [21, 22] and KEGG [23–25] databases. Meanwhile, we used CRISPRs web server  to predict CRISPRs and InterPro [27, 28] to obtain the GO annotation with the database of Pfam .
To estimate the mean level of nucleotide sequence similarity at the genome level between e KCY07-B2T and the genus Halopier genomes available to date ( H. xanaduensis SH-6T, H. djelfamassiliensis IIH2T and H. goleamassiliensis IIH3T), we compared the ORFs only using comparison sequence based in the server RAST  at a query coverage of ≥60 % and a minimum nucleotide length of 100 bp.
The draft genome sequence of H. salifodinae KCY07-B2T revealed a genome size of 4,350,718 bp (scaffold length) with a 65.41 % G + C content. Of the 4254 predicted genes, 4204 were protein-coding genes, and 50 were rRNA genes. There were one 16S rRNA gene, two 23S rRNA genes and two 5S rRNA genes. A total of 2887 genes (68.67 %) were assigned a putative function (Table 3). Table 4 showed the distribution of genes into COG functional categories.
Insights from the genome sequence
Strain H. salifodinae KCY07-B2T was isolated from a salt mine sample. The experiments showed this strain could grow at 2.9–3.4 M NaCl for optimal growth, and the cells lysed in distilled water. So the analysis of the genome sequence focused on the adaption mechanism of the halophilic archaea in hypersaline-environments. Strain H. salifodinae KCY07-B2T mainly utilized “the salt-in strategy” to maintain osmotic balance. According to the annotation of genome sequence, Trk system potassium uptake protein were found, which were responsible for K+ uptake and transport, including 9 copies TrkH genes and 5 copies TrkA genes. Five copies of Kef-type K+ transport proteins, one copy glutathione-regulated potassium-efflux protein KefB and 8 pH adaptation potassium efflux system proteins were found that were related to K+ efflux. And there also existed 8 copies of potassium channel proteins. In addition, the genome contains 13 copies of Na+/ H+ antiporter proteins related to Na+ efflux. The genome of strain H. salifodinae KCY07-B2T contains 12 genes related to the synthesis and transport of the compatible-solute glycine betaine for resistance to osmotic stress including: 7 choline-sulfatases, 2 high-affinity choline uptake protein BetTs, 2 glucose-methanol-choline oxidoreductase and 1 glycine betaine transporter OpuD coding genes. These proteins were also related to the metabolic pathway converting choline sulfate to glycine betaine. All these proteins and systems mentioned played an important role in the adaption of osmotic stress in high salt environment.
Currently, three genomes from Halopiger species are available. Here, we compare the genome of strain H. salifodinae KCY07-B2T with strains H. xanaduensis SH-6T, H. djelfamassiliensis IIH2T and H. goleamassiliensis IIH3T (Table 5). The size of genome of H. salifodinae KCY07-B2T (4.35 Mb) is similar to H. xanaduensis SH-6T (4.35 Mb) but larger than that of H. djelfamassiliensis IIH2T (3.77 Mb) and H. goleamassiliensis IIH3T (3.90 Mb). The G + C content of H. salifodinae KCY07-B2T (65.41 %) is similar to H. xanaduensis SH-6T (65.18 %) and higher than that of H. djelfamassiliensis IIH2T (64.30 %) but lower than that of H. goleamassiliensis IIH3T (66.06 %). In addition, H. salifodinae KCY07-B2T shares a mean genomic sequence similarity of 79.74 %, 80.16 % and 79.17 % with strains H. xanaduensis SH-6T, H. djelfamassiliensis IIH2T and H. goleamassiliensis IIH3T, respectively.
Strain KCY07-B2T is the third member of the genus Halopiger to be described and the fourth whose genome sequence report is available. These data will provide a new perspective of how microorganisms adapt to halophilic environments, and may also provide a pool of functional enzymes that work at higher salty.
National Center for Biotechnology Information
European Molecular Biology Laboratory
DNA Data Bank of Japan
Basic Local Alignment Search Tool for Nucleotide
Minimum Information about a Genome Sequence
Rapid Annotations using Subsystems Technology
Cluster of Orthologous Groups of proteins
Kyoto Encyclopedia of Genes and Genomes
Clustered Regularly Interspaced Short Palindromic repeat sequences
- 16S rRNA:
ribosomal Ribonucleic Acid
Japan Collection of Microorganisms
China General Microbiological Culture Collection Center
- H. salifodinae KCY07-B2T :
Halopiger salifodinae KCY07-B2T
- H. xanaduensis SH-6T :
Halopiger xanaduensis SH-6T
- H. aswanensis 56T :
Halopiger aswanensis 56T
- H. djelfamassiliensis IIH2T :
Halopiger djelfamassiliensis IIH2T
- H. goleamassiliensis IIH3T :
Halopiger goleamassiliensis IIH3T
Gutiérrez MC, Castillo AM, Kamekura M, Xue Y, Ma Y, Cowan DA, et al. Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China. Int J Syst Evol Microbiol. 2007;57:1402–7.
Hezayen FF, Gutiérrez MC, Steinbüchel A, Tindall BJ, Rehm BH. Halopiger aswanensis sp. nov., a polymer-producing and extremely halophilic archaeon isolated from hypersaline soil. Int J Syst Evol Microbiol. 2010;60:633–7.
Zhang WY, Meng Y, Zhu XF, Wu M. Halopiger salifodinae sp. nov., an extremely halophilic archaeon isolated from a salt mine. Int J Syst Evol Microbiol. 2013;63:3563–7.
Hassani II, Robert C, Michelle C, Raoult D, Hacène H, Desnues C. Non-contiguous finished genome sequence and description of Halopiger dielfamassiliensis sp. nov. Stand Genomic Sci. 2013;9:160–74.
Hassani II, Robert C, Michelle C, Raoult D, Hacène H, Desnues C. Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov. Stand Genomic Sci. 2014;9:956–69.
Anderson I, Tindall BJ, Rohde M, Lucas S, Han J, Lapidus A, et al. Complete genome sequence of Halopiger xanaduensis type strain (SH-6T). Stand Genomic Sci. 2012;6:31–42.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406–25.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol. 2011;28:2731–9.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26:541–7.
Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol. 1962;5:109–18.
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456:53–9.
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010;20:265–72.
Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24:713.
SOAP. denovo v.1.05. http://soap.genomics.org.cn/soapdenovo.html.
Lowe TM, Eddy S. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64.
Lagesen K, Hallin P, Rdland EA, Strfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100.
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003;31:439.
Aziz RK, Bartels D, Best A, DeJongh M, Disz T, Edwards R, et al. Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75–89.
RAST server online. http://rast.nmpdr.org/.
Tatusov RL, Natale D, Garkavtsev I, Tatusova T, Shankavaram U, Rao B, et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 2001;29:22–8.
Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:33–6.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36(Database issue):D480–4.
Moriya Y, Itoh M, Okuda S, Kanehisa M. KAAS: KEGG automatic annotation server. Genome Informatics. 2005;5:2005.
Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27.
Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:52–7.
Zdobnov EM, Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001;17:847.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, et al. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 2001;29:37.
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths Jones S, et al. The Pfam protein families database. Nucleic Acids Res. 2004;32 suppl 1:138D.
Ferry JG, Smith PH, Wolfe RS. Methanospirillum, a new genus of methanogenic bacteria, and characterization of Methanospirillum hungatii sp. nov. Int J Syst Bacteriol. 1974;24:465–9.
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.
Garrity GM, Holt JG. Phylum AII. Euryarchaeota phy. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Springer. N Y. 2001;1:211–355.
Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol. 2002; 52: 685–90.
Grant WD, Kamekura M, McGenity TJ, Ventosa A. Class III. Halobacteria class. nov. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s Manual of Systematic Bacteriology. 2nd ed. New York: Springer; 2001. p. 294.
Grant WD, Larsen H. Group III. Extremely halophilic archaebacteria, Order Halobacteriales ord. nov. In: Holt JG, editor. Bergey’s Manual of Systematic Bacteriology, vol. 3. Baltimore: Williams & Wilkins; 1989. p. 2216–28.
Validation List no. 31. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol. 1989; 39:495–97.
Judicial Commission of the International Committee on Systematics of Prokaryotes. The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol. 2005;55:517–8.
Gibbons NE, Family V. Halobacteriaceae fam. nov. In: Buchanan RE, Gibbons NE, editors. Bergey’s Manual of Determinative Bacteriology. 8th ed. Baltimore: The Williams and Wilkins Co.; 1974. p. 269–73.
Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980;30:225–420.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.
Gene Ontology project. http://geneontology.org/
We thank Hong Cheng for her help on offering some websites for data analysis. This work was supported by the China Ocean Mineral Resources R & D Association (COMRA) Special Foundation (grant no. DY125-14-E-02) and the Chinese Natural Science Foundation (grant no. 31170001).
The authors declare that they have no competing interests.
WYZ designed the study, isolated strain Halopiger salifodinae KCY07-B2T, performed the laboratory experiments, analyzed the genome and wrote the manuscript. JH worked on genome assembly, annotated the genome and discussed the results. JP and CS participated in the analysis of the genome and checked the manuscript. MU and XWX helped to supervise the study and revised the manuscript. All authors read and approved the final manuscript.
About this article
Cite this article
Zhang, WY., Hu, J., Pan, J. et al. Draft genome sequence of Halopiger salifodinae KCY07-B2T, an extremly halophilic archaeon isolated from a salt mine. Stand in Genomic Sci 10, 124 (2015). https://doi.org/10.1186/s40793-015-0113-y
- Halopiger salifodinae
- Extreme halophile
- Salt mine