Genome sequence of Streptomyces antioxidans MUSC 164T isolated from mangrove forest Hooi-Leng Ser1,2,3, Nurul-Syakima Ab Mutalib4, Wai-Fong Yin5, Bey-Hing Goh1,2,3,6, Learn-Han Lee1,2,3,6*, Kok-Gan Chan5,7* 1Novel Bacteria and Drug Discovery (NBDD) Research Group, School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia 2Biofunctional Molecule Exploratory (BMEX) Research Group, School of Pharmacy, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia 3Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia 4UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, University Kebangsaan Malaysia, Kuala Lum- pur, Malaysia 5Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 6Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand 7International Genome Centre, Jiangsu University, Zhenjiang 212013, PR China Progress in Microbes and Molecular Biology Abstract : Members of Streptomyces genus are well known to produce bioactive compounds of various structures[1-3]. Having a complicated development life cycle with the ability to form spores, Streptomyces species are ubiquitous in nature and can be found in interesting places like deep sea, hot springs and also mangrove forest[3-11]. Streptomyces antioxidans MUSC 164T was originally isolated from mangrove forest in the east coast of Peninsular Malaysia and has been deposited at two culture collec- tion centres (=DSM 101523T = MCCC 1K01590T)[12,13]. After rounds of in vitro screening using human neuronal cell line (i.e. SH-SY5Y), the extract of MUSC 164T was found to possess significant neuroprotective effect against hydrogen peroxide[13]. Here, a high quality genome sequence of MUSC 164T is reported, while its genome potential to produce pharmaceutically important compounds is also discussed. Keywords: Streptomyces; antioxidant; genome; mangrove; actinobacteria; next generation sequencing (NGS) *Correspondence to: Learn-Han Lee, School of Pharmacy, Monash Uni- versity Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; lee.learn.han@monash.edu; leelearnhan@yahoo.com; Kok-Gan Chan, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia. kokgan@ um.edu.my Received: 14th January 2018 Accepted: 29th January 2018 Published Online: 16th April 2018 Citation: Ser HL, Ab Mutalib NS, Yin WF, et al. Genome sequence of Streptomyces antioxidans MUSC 164T isolated from mangrove forest. Prog Microbes Mol Biol 2018; 1(1): a0000001. Short Introduction As a Gram-positive bacterium, Streptomyces antioxidans MUSC 164T forms yellowish white aerial mycelium and brilliant greenish yellow substrate mycelium on yeast- malt (ISP 2) agar[13]. Based on polyphasic study, this strain was concluded as a novel species belonging to the genus Streptomyces, displaying with highest partial 16S rRNA gene sequence similarity with type strain Streptomyces javensis NBRC 100777T (99.6 % sequence similarity), Streptomyces yog- yakartensis NBRC 100779T (99.6 %) and Strepto- myces violaceusniger NBRC 13459T (99.6 %). The methanolic extract of MUSC 164T showed signifi- cant antioxidative and neuroprotective activities Genome Report Copyright 2018 by Ser HL et al. and HH Publisher. This work under licensed under the Creative Commons Attribution-NonCommer- cial 4.0 International Lisence (CC-BY-NC 4.0) against hydrogen peroxide. As an attempt to further ex- plore its bioactive potential, the strain was selected for ge- nome sequencing. Data description Genomic DNA of MUSC 164T was extracted using Masterpure TM DNA purification kit (Epicentre, Il- lumina Inc., Madison, WI, USA) before performing RNase (Qiagen, USA) treatment[14,15]. DNA Quality was evaluated using NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA). Whole-genome shotgun sequencing of strain MUSC 164T was carried out on Illumina MiSeq platform with MiSeq Reagent Kit 2 (2 × 250 bp; Illumina Inc., Madison, WI, USA), and it generated 8,806,977 raw reads. Subse- quently, ambiguous nucleotides, reads that are shorter than 50 bps and low quality reads were removed from the data. The draft genome was assembled with CLC Genomics Workbench version 5.1 (CLC bio, Denmark). Contigs with at least 200 bp and 30-fold coverage were selected for gene prediction and annotation. The bacteria identity was also checked by local BLAST against NCBI prokaryotic 16S rRNA database. Bacteria gene coding sequence (CDS) was predicted from the draft genome using Prodigal (version 2.6.1)[16]. Gene annotation was performed by local BLAST of translated predicted CDS against NCBI-nr database and also on Rapid Annotation using Subsystem Technology (RAST) server[17]. Presence of rRNA and tRNA genes were detected using RNAmmer and tRNAscan SE version 1.21[18,19]. A total of 282 contigs were generated with N50 size of 111,730 bp. The assembled genome size of MUSC 164T contains 9,118,065 bp, with an average genome cover- age of 141-fold with a G + C content of 71.5 % (Table 1). The whole genome project was deposited at DDBJ/ EMBL/GenBank under accession LAKD00000000. The version described in this paper is the second version, LAKD02000000. It is composed of 282 contigs and there were 7,214 protein coding genes (out of a total of 7,620 predicted genes) (Figure 1). Table 1. General features of Streptomyces antioxidans MUSC 164T draft genome. Attribute Value Genome size (bp) 9,118,065 DNA G+C (bp) 6,516,852 DNA scaffold 282 Total genes 7,620 Protein coding genes 7,214 RNA genes (5S, 16S, 24S) 4, 4, 2 Pseudo genes 331 CRISPR repeats 7 Using antiSMASH to detect biosynthetic gene clus- ters, the analysis revealed presence of 11 biosynthetic gene clusters which exhibited more than 70 % similarities with known gene clusters[20]. Out of which, five clusters were associated with production of non-ribosomal peptides, including coelichelin, roseoflavin and paenibactin. In- terestingly, the genome of MUSC 164T revealed potential production of valuable siderophores like desferrioxamine B. In short, the availability of genome sequence for Strep- tomyces antioxidans MUSC 164T has suggested its genome potential and prompted further improvement work (e.g. media optimization, strain improvement) to fully invoke the bioactive potential of the strain, particularly for pro- duction of valuable pharmaceutical compounds like des- ferrioxamine B. Figure 1. Subsystem category distribution of Streptomyces antioxidans MUSC 164T (based on RAST annotation server). Acknowledgement This work was supported by MOSTI eScience funds (Project No. 06-02-10-SF0300) and Ex- ternal Industry Grant (Biotek Abadi Vote No. Genome sequence of Streptomyces antixiodans... GBA-808813 & GBA-808138) awarded to L.-H.L., and K.- G.C. was financially support by JBK grants (no. GA001- 2016, GA002-2016) and PPP grant (PG083-2015B). Conflict of Interest The authors declared that there is no conflict of interest. References 1. Berdy J. Bioactive microbial metabolites. J Antibi- otics 2005; 58: 1–26. 2. 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