Draft genome of iron-oxidizing bacterium Leptospirillum sp. YQP-1 isolated from a volcanic lake in the Wudalianchi volcano, China.

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.

Direct link to deposited data

http://www.ncbi.nlm.nih.gov/bioproject/?term=LIEB00000000.

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

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.

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