Whole-genome shotgun sequence of phenazine-producing endophytic Streptomyces kebangsaanensis SUK12

Abstract

Streptomyces sp. produces bioactive compounds with a broad spectrum of activities. Streptomyces kebangsaanesis SUK12 has been identified as a novel endophytic bacteria isolated from ethnomedicinal plant Portulaca olerace, and was found to produce the phenazine class of biologically active antimicrobial metabolites. The potential use of the phenazines has led to our research interest in determining the genome sequence of Streptomyces kebangsaanensis SUK12. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number PRJNA269542. The raw sequence data are available [https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP105770].

Specifications
Organism/cell line/tissue	Streptomyces kebangsaanensis
Strain	SUK12T (= DSM 42048T = NRRL B-24860T)
Sex	N/A
Sequencer or array type	Illumina HiSeq 2000
Data format	Raw and processed
Experimental factors	S. kebangsaanensis SUK12 was cultured on International Streptomyces Project-2 (ISP-2) agar for 7 days. Genomic DNA from agar culture was isolated as previously described[1].
Experimental features	Sequencing was performed according to Illumina specific protocols for library preparation and DNA-seq.
Consent	N/A
Sample source location	Streptomyces kebangsaanensis SUK12 has been isolated from Portulaca oleracea L. plant collected from the Nenasi Reserve Forest, Pahang, Malaysia (2° 53.852′ N 103° 25.507′ E) [2].

1. Direct link to deposited data

Data have been deposited in repository https://www.ncbi.nlm.nih.gov/bioproject/269542 and raw sequence files (s_CGATGT_1.fastq.gz and s_CGATGT_2.fastq.gz) are also available under the accession number SRP105770 (https://www.ncbi.nlm.nih.gov/sra/?term=SRP105770).

2. Introduction

In this 21st century, bacterial resistance towards antibiotics is one of the most challenging problems in the medical field. As pathogenic bacteria are increasingly resistant to antibiotics, newer sources of such compounds need to be investigated [3]. It is well accepted that the Streptomyces have a great capability to produce diverse bioactive compounds that have a wide spectrum of activity. Streptomyces kebangsaanensis SUK12, an endophytic bacteria isolated from plant Portulaca oleracea was found to contain a phenazine antibiotic [2]. The first phenazine isolated from Streptomyces griseoluteus was an antibiotic called griseolutien [4]. In recent years, Streptomyces sp. has been a rich source of several diverse and complex phenazine. These include lomofungin from Streptomyces lomondensis [5] and endophenazines from Streptomyces anulatus [6], [7]. Compared to Pseudomonas, Streptomyces species are considered to be more promising sources for bioactive compounds from phenazine owing to their structural complexity [8]. Thus, the genome sequence of S. kebangsaanensis SUK12 would provide an entry point to elucidate the antibiotic-producing capability of this Streptomyces species to identify new sources of novel phenazine based antibacterial compounds. The data set will be valuable for the scientific community working in the area of bacteriology, molecular biology, drug discovery and other related researches. Plus, it also would provide impetus for research involving the development of important genetic tools which can optimize the yield of useful antibiotic(s) and/or other secondary metabolites whilst facilitating the development of new antibiotic analogues via semi-synthetic approach.

3. Experimental design, materials and methods

3.1. Library preparation and sequencing

The strain was obtained from the stock culture of Novel Antibiotic Research Laboratory, Universiti Kebangsaan Malaysia (UKM). Genomic DNA extraction was performed according to Kieser et al. [1] with slight modifications. For library preparation, genomic DNA was fragmented with the targeted size 400–600 bp using Covaris S220 (Covaris Inc., USA). The selected sized DNA was then ligated to Illumina TruSeq adapters and amplified using TruSeq DNA Sample Preparation Kit (Illumina, USA). Quantification was carried out using KAPA kit (KAPA Biosystem, USA) on Agilent Stratagene Mx-3005p quantitative PCR machine (Agilent, USA). Library size was then verified via Agilent Bioanalyzer High Sensitivity DNA Chip. Whole genome sequencing finally was performed using Illumina Genome Analyzer (Illumina, San Diego, CA).

3.2. Preprocessing and genome assembly

In order to evaluate read quality before and after pre-processing, FastQC assessment plots were generated for sequenced reads using Babraham Bioinformatics programme (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The filtered reads were then assembled using an assembler pipeline called MaSuRCA [9]. Both paired-end and single reads were utilized in the assembly process. 560 assembled contigs were further scaffolded using paired-end library information which forms 170 scaffolds.

4. Data description

The presented data summarizes information computed from DNA library preparation (Table 1), the raw DNA sequence reads (Table 2), preprocessing (Fig. 1) as well as assembly and scaffolding (Table 3). The data shown corresponds to the filenames and obtained sequence content following the de-multiplexing of the data, and following the data conversion to the FASTQ format (Table 1). The sequencing produces 2.6 Gbp raw reads (Table 2). These reads were filtered to remove sequences with ambiguous bases, duplicated reads as well as adapter bases (Fig. 1). FastQC assessment plots were generated for sequenced reads to evaluate read quality before (Fig. 1A) and after pre-processing (Fig. 1B). De novo assembly yielded a total of 560 contigs and 170 scaffolds (Table 3). The longest scaffold has 453,879 bp in length and the shortest length in 1072 bp (Table 3).

Table 1.

Summary of the final QC for S. kebangsaanensis library.

Sample QC info			Final library			Multiplexing
Vol. (μl)	Conc. (ng/μl)	Total conc. (μg)	Library conc. (nM)	Average base pair (bp)	Size range (bp)	Adapter	Index
60	31.8	1.9	15.83	590	448–921	2	CGATGT

Table 2.

Overall raw read information of paired-end reads for S. kebangsaanensis.

Strain	Adaptor	Average sample size (bp)	Total raw reads (bp)	Read length (bp)	Total bases (bp)	Sequence files
S. kebangsaa-nensis	CGATGT	482	13,112,394	101	1,324,351,794	s_CGATGT_1.fastq.gz
			13,112,394		1,324,351,794	s_CGATGT_2.fastq.gz

Fig. 1.

Per base quality score distribution raw reads of S. kebangsaanensis sample before (A) and after (B) preprocessing (generated by FastQC).

Table 3.

Statistics of contigs and scaffolds assembled for S. kebangsaanensis.

	Sequences (n)	Bases (nt)	Length range (nt)	Mean length (nt)	N50 (nt)
Clean reads	15,474,727	1,483,526,984	75–101	–	–
Assembled contigs	560	8,308,573	124–78,384	14,837	24,540
Assembled scaffolds	170	8,328,719	1072–453,879	48,992	110,454