Abstract
Leptospirillum sp. YQP-1, a member of iron-oxidizing bacteria was isolated from volcanic lake in northeast China. Here, we report the draft genome sequence of the strain YQP-1 with a total genome size of 3,103,789 bp from 85 scaffolds (104 contigs) with 58.64% G + C content. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LIEB00000000.
Keywords: Leptospirillum, Genome, Iron-oxidizing bacteria, Volcanic lake
| Specifications | |
|---|---|
| Organism/cell line/tissue | Leptospirillum sp. |
| Strain (s) | YQP-1 |
| Sequencer or array type | Sequencer; Illumina MiSeq |
| Data format | Processed |
| Experimental factors | Microbial strains |
| Experimental features | Draft genome sequence of Leptospirillum sp. YQP-1 assembly and annotation |
| Consent | N/A |
| Sample source location | Volcanic lake in the Wudalianchi volcano, China |
1. Direct link to deposited data
2. Experimental design, materials and methods
The Leptospirillum genus was validly described by Hippe [1], though the first bacterium of this genus was identified by Markosyan [2]. Phylogenetically, it belongs to the class Nitrospira. Leptospirillum spp. are found in volcano habitat and acid mine drainage environment [3], [4]. Cells of the Leptospirillum genus are Gram-negative, motile vibroid to spirilla-shaped, but cocci or pseudococci also can be formed [3]. This genus comprises four species, viz., Leptospirillum ferrooxidans, Leptospirillum ferriphilum, Leptospirillum feerrodiazotrophum, and Leptospirillum thermoferrooxidans [3], [5]. Until recently, only four genomes are available in the GenBank, including complete genomes of L. ferriphilum ML-04 [6], L. ferriphilum YSK (CP007243), and L. ferrooxidans C2-3 [4], as well as draft genome of L. ferriphilum DSM 14647 [7]. As an important iron-oxidizing genus, more investigations at genomic level are required to improve understanding of its physiology, ecology, genetics and potential in biotechnological applications.
Leptospirillum sp. YQP-1 was isolated from a volcanic lake of the Wudalianchi volcano, northeast China in July 2013. This strain has been deposited in the China Center for Type Culture Collection (accession number: CCTCC M 2014196) (http://www.cctcc.org/index.php). The 16S rRNA gene sequence of YQP-1 available in GenBank database (accession number: KJ573504) showed more than 99% identity with several Leptospirillum strains, such as Leptospirillum sp. 3.2 (accession number: EU372651), L. ferrooxidans P3a (accession number: AF356837). This indicated that this strain belongs to Leptospirillum genus.
Genomic DNA was isolated from Leptospirillum sp. YQP-1 using a Bacterial Genomic DNA Extraction Kit (Biomed, Beijing, China) according to the manufacturer's instructions. Quality check was performed using NanoDrop spectrophotometer (Thermo Scientific, Waltham, USA). The draft genome sequence of the YQP-1strain was obtained by paired-end sequencing on the Illumina MiSeq platform at the Biomarker Technologies Co., Ltd. (Beijing, China). De novo assembly was performed using Velvet Version 1.2.10 [8]. Protein-coding sequences were predicted by Glimmer software version 3.0 [9], while ribosomal RNA (rRNA) and transfer RNA (tRNA) genes were predicted using an RNAmmer 1.2 server [10] and tRNAscan-SE Search Server version 1.21 [11], respectively. Genes annotated using BLAST searches of nonredundant protein sequences from the NCBI, Swiss-Prot, COG [12], and KEGG database [13]. Tandem repeats were predicted using Tandem Repeats Finder Version 4.04.
The genome size of Leptospirillum sp. YQP-1 was estimated to be 3,103,789 bp from 85 scaffolds with a mean G + C content of 58.64%. It contains 104 contigs with N50 contig length of 86,194 bp. A total of 3038 coding sequences (CDS) were identified including 50 RNA genes (8 rRNA and 42 tRNA genes). The number of tandem repeat sequence was 106 with total length of 12,049 bp, which made up 0.3882% of genome (Table 1). Further studies of Leptospirillum sp. YQP-1 which might help many beneficial applications such as for bioremediation and bioleaching, are essential and required to be extended.
Table 1.
Genome features of Leptospirillum sp. YQP-1 draft genome.
| Attributes | Values |
|---|---|
| Genome size (bp) | 3,103,789 |
| Number of scaffolds | 85 |
| Scaffold N50 (bp) | 101,596 |
| G + C content (%) | 58.64 |
| Number of contigs | 104 |
| Contig N50 (bp) | 86,194 |
| CDS | 3038 |
| rRNAs | 8 |
| tRNAs | 42 |
| Pseudo genes | 55 |
| Tandem repeat sequence | 106 |
3. Nucleotide sequence accession number
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession LIEB00000000. The version described in this paper is LIEB00000000.
Conflict of interest
The authors declare that there is no conflict of interests with respect to the work published in this paper.
Acknowledgments
This work was supported by the National Natural Science Foundation of China (41471201, 31100006), Natural Science Foundation of Heilongjiang Province of China (C201442), and Program of Science and Technology Innovation Teams Building in Heilongjiang Province (2012TD006).
References
- 1.Hippe H. Leptospirillum gen. nov. (ex Markosyan 1972), nom. rev., including Leptospirillum ferrooxidans sp. nov. (ex Markosyan 1972), nom. rev. and Leptospirillum thermoferrooxidans sp. nov. (Golovacheva et al. 1992) Int. J. Syst. Evol. Microbiol. 2000;50:501–503. doi: 10.1099/00207713-50-2-501. [DOI] [PubMed] [Google Scholar]
- 2.Markosyan G.E. A new iron-oxidizing bacterium: Leptospirillum ferrooxidans gen. nov sp. Biol. J. Armenia. 1972;25:26–29. [Google Scholar]
- 3.Donati E.R., Sand W. Springer; 2007. Microbial Processing of Metal Sulfides. [Google Scholar]
- 4.Fujimura R., Sato Y., Nishizawa T., Oshima K., Kim S.-W., Hattori M., Kamijo T., Ohta H. Complete genome sequence of Leptospirillum ferrooxidans strain C2-3, isolated from a fresh volcanic ash deposit on the island of Miyake, Japan. J. Bacteriol. 2012;194:4122–4123. doi: 10.1128/JB.00696-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Goltsman D.S.A., Dasari M., Thomas B.C., Shah M.B., VerBerkmoes N.C., Hettich R.L., Banfield J.F. New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics, and transcriptomics of the new species “Leptospirillum group IV UBA BS”. Appl. Environ. Microbiol. 2013;79:5384–5393. doi: 10.1128/AEM.00202-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Mi S., Song J., Lin J., Che Y., Zheng H., Lin J. Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation. J. Microbiol. 2011;49:890–901. doi: 10.1007/s12275-011-1099-9. [DOI] [PubMed] [Google Scholar]
- 7.Cárdenas J.P., Lazcano M., Ossandon F.J., Corbett M., Holmes D.S., Watkin E. Draft genome sequence of the iron-oxidizing acidophile Leptospirillum ferriphilum type strain DSM 14647. Genome Announc. 2014;2 doi: 10.1128/genomeA.01153-14. (e01153-01114) [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–829. doi: 10.1101/gr.074492.107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Delcher A.L., Bratke K.A., Powers E.C., Salzberg S.L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23:673–679. doi: 10.1093/bioinformatics/btm009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Lagesen K., Hallin P., Rødland E.A., Stærfeldt H.-H., Rognes T., Ussery D.W. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Schattner P., Brooks A.N., Lowe T.M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005;33:W686–W689. doi: 10.1093/nar/gki366. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., Krylov D.M., Mazumder R., Mekhedov S.L., Nikolskaya A.N. The COG database: an updated version includes eukaryotes. BMC Bioinforma. 2003;4:41. doi: 10.1186/1471-2105-4-41. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 2004;32:D277–D280. doi: 10.1093/nar/gkh063. [DOI] [PMC free article] [PubMed] [Google Scholar]