Draft genome sequence of strain MC1A, a UV-resistant bacterium isolated from dry soil in Puerto Rico.

We report here the draft genome sequence of a novel UV-resistant bacterium isolated from dry soil on the south coast of Puerto Rico. Based on polyphasic taxonomy, strain MC1A represents a new species and the name Solirubrum puertoriconensis is proposed. Assembly was performed using NGEN Assembler into eight contigs (N50 = 1,292,788), the largest of which included 1,549,887 bp. The draft genome consists of 4,810,875 bp and has a GC content of 58.7%. Several genes related to DNA repair and UV resistance were found. The Whole Genome Shotgun project is available at DDBJ/EMBL/GenBank under the accession LNAL00000000.

Direct link to deposited data

http://www.ncbi.nlm.nih.gov/bioproject/PRJNA293638

Experimental design, materials and methods

MC1A was isolated from soil collected in La Parguera, PR. One gram of dry soil was suspended in sterile water and placed in a plastic uncovered Petri dish. The sample was irradiated with UV-light (254 nm) at room temperature for 30 min. Escherichia coli DH5α was used as negative control. After irradiation, 100 μL was plated in R2A medium, covered with aluminum foil to avoid photo-reactivation, and incubated for 72 h at room temperature (25 °C). DNA extraction was performed using Promega® DNA extraction kit following the manufacturer's recommendations. Genomic DNA quality and concentration was monitored using the NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific Inc.). The genomic DNA was sequenced at the Molecular Research Lab (MR DNA) facility in Shallowater, TX, USA. The library was constructed with Illumina® Nextera DNA Sample Preparation kit following manufacturer's instructions. The starting concentration of DNA was monitored using Life Technologies Qubit® dsDNA HS Assay Kit. Final DNA concentration was achieved diluting 50 ng samples to 2.5 ng/μL. Samples were fragmented and adapters were added to be used by 5 cycles of PCR. The library final concentration was evaluated with Life Technologies Qubit® dsDNA HS Assay Kit. Its average size was measured using Agilent 2100 Bioanalyzer from Agilent Technologies. Samples were pooled in ratios of 2 nM, where 12 pM were sequenced paired-end for 600 cycles in the previews mentioned platform. NGEN Assembler was used to perform the assembly of 8 contigs. Rapid Annotation Subsystem Technology (RAST) was used to predict protein coding sequences, G + C content and genome size [1]. To predict rRNA and tRNA genes, RNAmmer and ARAGORN were used respectively [2], [3].

Summary

Phylogenetic analysis using strain MC1A 16S rRNA gene sequence showed that it is closely related to Hymenobacter spp., Adhaeribacter spp., Pontibacter spp., and Rufibacter spp. The closest relative is Hymenobacter deserti with 96.8% of sequence similarity based on the EZ-taxon database [4], which supports the creation of a new genus [5]. Strain MC1A is a red-pigmented UV-resistant bacterium that grows aerobically in heterotrophic media. The optimum pH is 7.5 with a growth range of pH 5.5–9.0. It is also capable to tolerate up to 10% NaCl (w/v) but growing optimally at 5% NaCl (w/v). The genome sequence consists of 4,804,721 bp with 58.7% G + C content with approximately 40 × coverage of the entire genome. The N50 contig size is 1,292,788 and the largest contig is 1,549,887 bp. Annotation with RAST has shown a total of 4186 coding sequences, where 46% are hypothetical and the other 64% were annotated, 60 RNAs, and 350 subsystems (Fig. 1). Features about draft genome are summarized in Table 1 based on information of the NCBI Bioproject mentioned above.

Fig. 1

Subsystem information of MC1A draft genome. This summary was obtained from the SEED viewer version 2.0 of www.RAST.nmpdr.org.

Table 1

Draft genome features of strain MC1A.

Feature	Strain MC1A
Genome size	4,804,721 bp
G + C content	58.7%
Total contigs	8
Protein coding genes	4180
CDS	4037
Pseudogenes	83
tRNAs	44
rRNAs	5 (5S), 6 (16S), 4 (23S)
Complete rRNAs	5 (5S), 1 (16S), 1 (23S)
Partial rRNAs	5 (16S), 3 (23S)
ncRNA	1

A total of 57 genes associated with UV resistance and DNA reparation were identified and annotated with RAST: Uracil-DNA glycosylase (2), DNA repair bacterial MutL-MutS system (4), DNA repair–UvrABC (5), DNA repair bacterial photolyase (1), DNA repair bacterial DinG and relatives (1), RecA and RecX (2), DNA repair system including RecA, MutS and hypothetical protein (3), DNA repair bacterial (17), DNA repair, bacterial RecFOR pathway (10), DNA Repair Base Excision (11), DNA repair, bacterial UvrD and related helicases (1). Also, strain MC1A has several genes for tolerance to stress conditions such as osmotic (6), oxidative (39) and periplasmic (7) stress, cold (4) and heat (15) shock, detoxification (13), and 3 genes of stress response with subcategory. The presence of these genes might contribute to the high tolerance of UV irradiation in strain MC1A. This strain also shares similar UV-resistant features compared to closer species of Hymenobacter. However, it seems that strain MC1A has a higher number of UV-resistant genes than other strains. For example, strain IS2118 has only 51 genes related to DNA repair including rec and uvr system [6].

Accession number of nucleotide sequence

The Whole Genome Shotgun project (WGS) can be found in DDBJ/EMBL/GenBank under the accession code LNAL01000000 which consists of the sequences LNAL01000001:LNAL01000008. This project will allow information to understand available mechanisms of different organisms to survive under stress conditions.

Conflict of interest

The authors declare that no conflict of interest exists about the work published in this paper.

Draft genome specifications
Organism	Bacterium
Strain	MC1A
Sequencer or array type	Illumina MiSeq
Data format	Analyzed
Experimental factors	Bacterial strain
Experimental features	Annotated and assembled draft genome sequence of the strain MC1A named Solirubrum puertoriconensis
Consent	N/A
Sample source location	Soil in La Parguera, Lajas, Puerto Rico (17°58′37″ N 67°2′32″ W, 50 m elevation)