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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Microbiol.</journal-id>
<journal-title>Frontiers in Microbiology</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Microbiol.</abbrev-journal-title>
<issn pub-type="epub">1664-302X</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fmicb.2016.01470</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Microbiology</subject>
<subj-group>
<subject>Data Report</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Draft Genome Sequence of Mangrove-Derived <italic>Streptomyces</italic> sp. MUSC 125 with Antioxidant Potential</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name><surname>Ser</surname> <given-names>Hooi-Leng</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/257477/overview"/></contrib>
<contrib contrib-type="author">
<name><surname>Tan</surname> <given-names>Wen-Si</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/369462/overview"/></contrib>
<contrib contrib-type="author">
<name><surname>Ab Mutalib</surname> <given-names>Nurul-Syakima</given-names></name>
<xref ref-type="aff" rid="aff3"><sup>3</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/201189/overview"/></contrib>
<contrib contrib-type="author">
<name><surname>Yin</surname> <given-names>Wai-Fong</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/205582/overview"/></contrib>
<contrib contrib-type="author">
<name><surname>Chan</surname> <given-names>Kok-Gan</given-names></name>
<xref ref-type="aff" rid="aff2"><sup>2</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/68350/overview"/></contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Goh</surname> <given-names>Bey-Hing</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
<xref ref-type="author-notes" rid="fn001"><sup>&#x0002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/256091/overview"/></contrib>
<contrib contrib-type="author" corresp="yes">
<name><surname>Lee</surname> <given-names>Learn-Han</given-names></name>
<xref ref-type="aff" rid="aff1"><sup>1</sup></xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup></xref>
<xref ref-type="author-notes" rid="fn002"><sup>&#x0002A;</sup></xref>
<uri xlink:href="http://loop.frontiersin.org/people/186181/overview"/></contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup><institution>Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia</institution> <country>Bandar Sunway, Malaysia</country></aff>
<aff id="aff2"><sup>2</sup><institution>Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya</institution> <country>Kuala Lumpur, Malaysia</country></aff>
<aff id="aff3"><sup>3</sup><institution>UKM Medical Molecular Biology Institute, UKM Medical Centre, Universiti Kebangsaan Malaysia</institution> <country>Kuala Lumpur, Malaysia</country></aff>
<aff id="aff4"><sup>4</sup><institution>Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao</institution> <country>Phayao, Thailand</country></aff>
<author-notes>
<fn fn-type="edited-by"><p>Edited by: Vijai Kumar Gupta, National University of Ireland Galway, Ireland</p></fn>
<fn fn-type="edited-by"><p>Reviewed by: Hwan You Chang, National Tsing Hua University, Taiwan; Kandasamy Ulaganathan, Osmania University, India</p></fn>
<fn fn-type="corresp" id="fn001"><p>&#x0002A;Correspondence: Bey-Hing Goh <email>goh.bey.hing&#x00040;monash.edu</email></p></fn>
<fn fn-type="corresp" id="fn002"><p>Learn-Han Lee <email>lee.learn.han&#x00040;monash.edu</email>; <email>leelearnhan&#x00040;yahoo.com</email></p></fn>
<fn fn-type="other" id="fn003"><p>This article was submitted to Microbiotechnology, Ecotoxicology and Bioremediation, a section of the journal Frontiers in Microbiology</p></fn>
</author-notes>
<pub-date pub-type="epub">
<day>15</day>
<month>09</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection">
<year>2016</year>
</pub-date>
<volume>7</volume>
<elocation-id>1470</elocation-id>
<history>
<date date-type="received">
<day>23</day>
<month>06</month>
<year>2016</year>
</date>
<date date-type="accepted">
<day>02</day>
<month>09</month>
<year>2016</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x000A9; 2016 Ser, Tan, Ab Mutalib, Yin, Chan, Goh and Lee.</copyright-statement>
<copyright-year>2016</copyright-year>
<copyright-holder>Ser, Tan, Ab Mutalib, Yin, Chan, Goh and Lee</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p></license>
</permissions>
<kwd-group>
<kwd>genome sequence</kwd>
<kwd>mangrove</kwd>
<kwd><italic>Streptomyces</italic></kwd>
<kwd>antioxidant</kwd>
<kwd>bioinformatics</kwd>
</kwd-group>
<contract-num rid="cn001">06-02-10-SF0300</contract-num>
<contract-num rid="cn001">02-02-10-SF0215</contract-num>
<contract-num rid="cn002">H- 50001-A000027</contract-num>
<contract-num rid="cn002">A000001-50001</contract-num>
<contract-sponsor id="cn001">Kementerian Sains, Teknologi dan Inovasi<named-content content-type="fundref-id">10.13039/501100003200</named-content></contract-sponsor>
<contract-sponsor id="cn002">Universiti Malaya<named-content content-type="fundref-id">10.13039/501100004386</named-content></contract-sponsor>
<counts>
<fig-count count="1"/>
<table-count count="1"/>
<equation-count count="0"/>
<ref-count count="21"/>
<page-count count="3"/>
<word-count count="1998"/>
</counts>
</article-meta>
</front>
<body>
<sec sec-type="intro" id="s1">
<title>Introduction</title>
<p>Microorganisms remain as one of the most important source of pharmaceutically important drugs (Berdy, <xref ref-type="bibr" rid="B3">2005</xref>; Debbab et al., <xref ref-type="bibr" rid="B5">2010</xref>; Waditee-Sirisattha et al., <xref ref-type="bibr" rid="B20">2016</xref>). Among the bacteria domain, <italic>Streptomyces</italic> genus has received considerable attention by the Scientific community for its seemingly unmatched capability of producing useful bioactive metabolites. The <italic>Streptomyces</italic> genus was initially proposed by Waksman and Henrici (<xref ref-type="bibr" rid="B21">1943</xref>); as the largest genus of <italic>Actinobacteria</italic>, it is comprised of over 780 species with validly published names (<ext-link ext-link-type="uri" xlink:href="http://www.bacterio.cict.fr/">http://www.bacterio.cict.fr/</ext-link>). These gram-positive bacteria have contributed remarkably in natural product discovery as they synthesize compounds with diverse chemical structures and biological activities such as anticancer, antibacterial, antioxidant, antifungal, and immunosuppresants activities (Berdy, <xref ref-type="bibr" rid="B3">2005</xref>; Gallagher et al., <xref ref-type="bibr" rid="B6">2010</xref>; Manivasagan et al., <xref ref-type="bibr" rid="B13">2013</xref>; Ser et al., <xref ref-type="bibr" rid="B16">2015a</xref>, <xref ref-type="bibr" rid="B18">2016a</xref>).</p>
<p>Over the years, drug screening programs have been focusing on identification of terrestrial microorganisms and investigation of their bioactive potential (Burg et al., <xref ref-type="bibr" rid="B4">1979</xref>; Marcus et al., <xref ref-type="bibr" rid="B14">1999</xref>). However, these efforts have resulted in rediscovery of the known bioactive compounds. Thus, researchers begun to venture into new and/or underexplored areas in the hope of discovering novel, potent bioactive metabolites. The mangrove ecosystem represents one of the world&#x00027;s most dynamic environments that produces commercial forest products, supports coastal fisheries and protects coastlines (Alongi, <xref ref-type="bibr" rid="B1">2008</xref>). Factors such as fluctuations in salinity and tidal gradient are believed to be the driving force for metabolic adaptations, which could in turn lead to production of valuable metabolites. In fact, the growing interest in bioactive potentials of mangrove-derived <italic>Streptomyces</italic> has been demonstrated by the isolation of <italic>Streptomyces pluripotens</italic> (Lee et al., <xref ref-type="bibr" rid="B9">2014a</xref>), <italic>S. fradiae</italic> (Prakash et al., <xref ref-type="bibr" rid="B15">2015</xref>), <italic>S. cheonanensis</italic> (Mangamuri et al., <xref ref-type="bibr" rid="B12">2016</xref>), and <italic>S. malaysiense</italic> (Ser et al., <xref ref-type="bibr" rid="B17">2016b</xref>).</p>
<p>For this study, <italic>Streptomyces</italic> sp. MUSC 125 was initially isolated from mangrove soil in the east coast of Peninsular Malaysia (Lee et al., <xref ref-type="bibr" rid="B10">2014b</xref>). As an attempt to explore the antioxidant capacity of MUSC 125, metal-chelating assay was performed and discovered its potential in quenching ferrous ions with activity ranging from 10.02 to 51.14% (unpublished data). Thus, the strain was selected for whole genome sequencing to obtain further understanding on its genomic potential.</p>
</sec>
<sec sec-type="materials and methods" id="s2">
<title>Materials and methods</title>
<sec>
<title>Isolation and culture of strain MUSC 125</title>
<p><italic>Streptomyces</italic> sp. MUSC 125 was isolated from Tanjung Lumpur mangrove forest located in the city of Kuantan, State of Pahang, in December of the year 2012 (Lee et al., <xref ref-type="bibr" rid="B10">2014b</xref>). Purified cultures were maintained on ISP medium 2 slants at room temperature for short-term storage and as glycerol suspensions (20%, v/v) at &#x02212;80&#x000B0;C for long-term storage.</p>
</sec>
<sec>
<title>Genome sequencing and bioinformatics analysis of MUSC 125</title>
<p>The genomic DNA of MUSC 125 was extracted with Masterpure&#x02122; DNA purification kit (Epicentre, Illumina Inc., Madison, WI, USA) followed by RNase (Qiagen, USA) treatment (Ser et al., <xref ref-type="bibr" rid="B19">2015b</xref>). Quality of the extracted DNA was examined using NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA). Subsequently, DNA library was prepared using Nextera&#x02122; DNA Sample Preparation kit (Nextera, USA), while the library quality was validated by Bioanalyzer 2100 high sensitivity DNA kit (Agilent Technologies, Palo Alto, CA) prior to sequencing. The genome of strain MUSC 125 was sequenced on MiSeq platform with MiSeq Reagent Kit 2 (2 &#x000D7; 250 bp; Illumina Inc., Madison, WI, USA). Following that, the paired-end reads were trimmed and <italic>de novo</italic> assembled with CLC Genomics Workbench version 5.1 (CLC bio, Denmark). Gene prediction was performed using Prodigal version 2.6, whereas rRNA and tRNA were predicted using RNAmmer and tRNAscan SE version 1.21 (Lowe and Eddy, <xref ref-type="bibr" rid="B11">1997</xref>; Lagesen et al., <xref ref-type="bibr" rid="B8">2007</xref>; Hyatt et al., <xref ref-type="bibr" rid="B7">2010</xref>). The assembly was uploaded for annotation to Rapid Annotation using Subsystem Technology (RAST) (Aziz et al., <xref ref-type="bibr" rid="B2">2008</xref>).</p>
</sec>
</sec>
<sec sec-type="results" id="s3">
<title>Results</title>
<p>Sequencing of MUSC 125 genome using Illumina technology generated a total of 4,518,422 reads. After adapter trimming, the reads were <italic>de novo</italic> assembled into 164 contigs using CLC Genomics workbench. The genome size of MUSC 125 is 7,656,461 bp with G &#x0002B; C content of 70.00% (Table <xref ref-type="table" rid="T1">1</xref>). The whole genome project of MUSC 125 was deposited at DDBJ/EMBL/GenBank under accession number <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JUIG00000000">JUIG00000000</ext-link> and the version described in this paper is the first version (JUIG01000000). The analyses of the draft genome identified 5991 open reading frames (ORFs), 68 tRNAs, and 4 rRNA (5S, 16S, 23S rRNA). The RAST annotation has assigned these genes into 419 subsystems, with maximum number of genes associated with amino acids and derivatives metabolism (8.84%), followed by carbohydrates (6.93 %) and protein metabolism subsystems (4.73%) (Figure <xref ref-type="fig" rid="F1">1</xref>).</p>
<table-wrap position="float" id="T1">
<label>Table 1</label>
<caption><p><bold>General features of <italic><bold>Streptomyces</bold></italic> sp. MUSC 125 draft genome</bold>.</p></caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th/>
<th valign="top" align="left"><bold><italic>Streptomyces</italic> sp. MUSC 125</bold></th>
</tr>
</thead>
<tbody>
<tr>
<td valign="top" align="left">Genome size (bp)</td>
<td valign="top" align="left">7,656,461</td>
</tr>
<tr>
<td valign="top" align="left">G&#x0002B;C content (%)</td>
<td valign="top" align="left">70.00</td>
</tr>
<tr>
<td valign="top" align="left">Genome coverage</td>
<td valign="top" align="left">94.0x</td>
</tr>
<tr>
<td valign="top" align="left">Contigs</td>
<td valign="top" align="left">164</td>
</tr>
<tr>
<td valign="top" align="left">Contigs N<sub>50</sub> (bp)</td>
<td valign="top" align="left">139,282</td>
</tr>
<tr>
<td valign="top" align="left">Number of ORFs</td>
<td valign="top" align="left">5991</td>
</tr>
<tr>
<td valign="top" align="left">tRNA genes</td>
<td valign="top" align="left">68</td>
</tr>
<tr>
<td valign="top" align="left">rRNA genes (5S, 16S, 23S)</td>
<td valign="top" align="left">4</td>
</tr>
<tr>
<td valign="top" align="left">Bioproject ID</td>
<td valign="top" align="left">PRJNA261099</td>
</tr>
<tr>
<td valign="top" align="left">Biosample ID</td>
<td valign="top" align="left">SAMN03070123</td>
</tr>
<tr>
<td valign="top" align="left">Genome accession</td>
<td valign="top" align="left"><ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JUIG00000000">JUIG00000000</ext-link></td>
</tr>
</tbody>
</table>
</table-wrap>
<fig id="F1" position="float">
<label>Figure 1</label>
<caption><p><bold>Annotation of MUSC 125 genome using Rapid Annotation using Subsystem Technology (RAST)</bold>.</p></caption>
<graphic xlink:href="fmicb-07-01470-g0001.tif"/>
</fig>
<sec>
<title>Direct link to deposited data and information to users</title>
<p>The genome sequence of <italic>Streptomyces</italic> sp. MUSC 125 (Biosample ID: SAMN03070123) can be accessed at NCBI using the accession number <ext-link ext-link-type="DDBJ/EMBL/GenBank" xlink:href="JUIG00000000">JUIG00000000</ext-link>. The genome project data are also available at GenBank under the genome Bioproject ID PRJNA261099. Users can download and use the data freely for research purpose only with acknowledgement to us and citing this paper as reference to the data.</p>
</sec>
</sec>
<sec id="s4">
<title>Author contributions</title>
<p>The experiments, data analysis and manuscript writing were performed by H-LS and W-ST, while N-SA, W-FY, K-GC, B-HG, and L-HL. provided vital guidance and technical support. L-HL founded the research project.</p>
<sec>
<title>Conflict of interest statement</title>
<p>The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
</sec>
</body>
<back>
<ack><p>This work was supported by PVC Award Grant (Project No. PVC-ECR-2016), External Industry Grant (Biotek Abadi Vote No. GBA-808813), MOSTI eScience funds (Project No. 06-02-10-SF0300) awarded to L-HL and MOSTI eScience funds (Project No. 02-02-10-SF0215) awarded to B-HG, and a University of Malaya for High Impact Research Grant (UM-MOHE HIR Nature Microbiome Grant No. H- 50001-A000027 and No. A000001-50001) and PPP Grant (PG090-2015B) awarded to K-GC.</p>
</ack>
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