Genome sequence of Novosphingobium malaysiense strain MUSC 273T, novel alpha-pro- teobacterium isolated from intertidal soil Hooi-Leng Ser1,2,3, Wai-Fong Yin4, Kok-Gan Chan4,5, Nurul-Syakima Ab Mutalib6, Learn-Han Lee1,2,3,7* 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 Ban- dar Sunway, Selangor Darul Ehsan, Malaysia 4Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 5Vice Chancellor Office, Jiangsu University, Zhenjiang 212013, PR China 6UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, University Kebangsaan Malaysia, Kuala Lumpur, Ma- laysia 7Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand Progress in Microbes and Molecular Biology Abstract : Novosphingobium malaysiense strain MUSC 273T is a recently identified Gram-negative, aerobic alpha-proteobacterium. The strain was isolated from intertidal soil with strong catalase activity. The genome sequence comprises 5,027,021 bp, with 50 tRNA and 3 rRNA genes. Further analysis identified presence of secondary metabolite gene clusters within genome of MUSC 273T. Knowl- edge of the genomic features of the strain may allow further biotechnological exploitation, particularly for production of secondary metabolites as well as production of industrially important enzymes. Keywords: Proteobacteria; antioxidant, mangrove; secondary metabolite *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 Received: 20th July 2018 Accepted: 5th August 2018 Published Online: 15th August 2018 Citation: Ser HL, Yin WF, Chan KG, et al. Genome sequence of Novosphingobium malaysiense strain MUSC 273T, novel alpha-pro- teobacterium isolated from intertidal soi. Prog Micobes Mol Biol 2018; 1(1): a0000003. Short Introduction Members of the genus Novosphingobium can be found in wide range of habitats including soil, deep sea as well as contami- nated environments[1-3]. Their ability to degrade mono- and polycyclic aromatic hydrocarbons (PAHs) has attracted much biotechnological interest, notably for biomediation purposes. Novosphingobium malaysiense strain MUSC 273T was isolated as novel species from intertidal soil obtained from Pahang, Malaysia[4]. Based on 16S rRNA gene analysis, the strain dis- played highest similarities to Novosphingobium indicum H25T, a type strain which has been shown to be able to degrade PAHs. Furthermore, MUSC 273T exhibited strong catalase activity, thus was selected for genome sequencing. Data description Extraction of genomic DNA was using MasterpureTM DNA purification kit (Epicentre, Illumina Inc., Madison, WI, USA) Genome Report Copyright 2018 by Ser HL et al. and HH Publisher. This work under licensed under the Creative Commons Attribution-NonCommercial 4.0 International Lisence (CC-BY-NC 4.0) treatment[5-7]. Genomic DNA quality was checked using Nano- Drop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA). Following that, DNA library was pre- pared with NexteraTM DNA Sample Preparation kit (Nextera, USA). Prior to sequencing, quality of DNA library was exam- ined with Bioanalyzer 2100 high sensitivity DNA kit (Agilent Technologies, Palo Alto, CA). Whole genome shotgun project of MUSC 273T was carried out using paired sequencing in an Il- lumina MiSeq platform with MiSeq Reagent Kit 2 (2 × 250 bp; Illumina Inc., Madison, WI, USA), producing 4,376,924 paired- end reads. The assembly of trimmed seqeuence was done with CLC Genomic Workbench version 5.1 (CLC Bio, Denmark), resulting in 85 contigs and an N50 contig size of approximately 631,941 bp. The assembled genome size comprised 5,027,021 bp, with an average coverage of 100.0-fold and G + C content of 63.3%. The genome sequence of Novosphingobium malaysiense MUSC 273T has been deposited at DDBJ/EMBL/GenBank un- der accession of JTDI00000000. The strain was deposited at three Figure 1. Subsystem category distribution of Novosphingobium malaysiense MUSC 273T (based on RAST annotation server). 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. url: http://www.journals.hh-publisher.com/index.php/ pmmb/article/view/1/14. Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9: 75. Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nuc Acids Res 1997; 25: 955–964. Lagesen K, Hallin P, Rodland EA, et al. RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nuc Acids Res 2007; 35: 3100–3108. Hyatt D, Chen GL, Locascio PF, et al. Prodigal: Prokaryotic gene recogni- tion and translation initiation site identification. BMC Bioinform 2010; 11: 119. Blin K, Medema MH, Kazempour D, et al. antiSMASH 2.0—A versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res 2013; 41(W1): W204–212. 7. 8. 9. 10. 11. 12. Gupta SK, Lal D, Lal R. Novosphingobium panipatense sp. nov. and No- vosphingobium mathurense sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2009; 59(1): 156–161. Yuan J, Lai Q, Zheng T, et al. Novosphingobium indicum sp. nov., a poly- cyclic aromatic hydrocarbon-degrading bacterium isolated from a deep- sea environment. Int J Syst Evol Microbiol 2009; 59(8): 2084–2088. Kämpfer P, Young CC, Busse HJ, et al. Novosphingobium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61(2):259–263. Lee LH, Azman AS, Zainal N, et al. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment. Int J Syst Evol Microbiol 2014; 64(4): 1194–1201. Ser HL, Tan WS, Cheng HJ, et al. Draft genome of amylolytic actinobac- terium, Sinomonas humi MUSC 117T solated from intertidal soil. Mar Gen 2015; 24: 209–210. Ser HL, Tan WS, Ab Mutalib NS, et al. Genome sequence of Streptomyces pluripotens MUSC 135T exhibiting antibacterial and antioxidant activity. Mar Gen 2015; 24: 281–283. 1. 2. 3. 4. 5. 6. References culture collection centers under accession of DSM 27798T = MCCC 1A00645T = NBRC 109974T. Table 1. General genomic features of Novosphingobium ma- laysiense strain MUSC 273T. Novosphingobium malaysiense MUSC 273T Genome size (bp) 5,027,021 Contigs 85 Contigs N50 (bp) 631,941 G + C content % 63.3 Protein coding genes 4,738 tRNA 50 rRNA 3 Putative secondary metabolite gene clusters 9 Homoserine lactone 2 Type 3 polyketides 1 Bacteriocin 1 The assembled genome was annotated using Rapid Annota- tion using Subsystem Technology (RAST)[8]. Gene predic- tion was performed using Prodigal version 2.6, while ri- bos omal RNA (rRNA) and transfer RNA (tRNA) were pre dicted using RNAmmer and tRNAscan SE version 1.21, respec- tively[9-11]. The analysis from RAST revealed 4,738 protein-coding genes, along with 50 tRNA and 3 rRNA genes. Out of 4,738 pro- tein-coding genes, 35 genes were identified to encode for enzymes involved in aromatic compounds metabolism. Additionally, the genome also contained 3 genes responsible for production of cata- lase (E.C. 1.11.1.6) and/or peroxidase (E.C. 1.11.1.7). Presence of these genes may suggest the genomic potential of strain MUSC 273T, most notably for industrial application and environmental bioremediation purposes. Closer investigation of MUSC 273T genome with antibiotics & Secondary Metabolite Analysis SHell (antiSMASH) unveiled several clusters of secondary metabolite genes[12]. Total of 9 biosynthetic gene clusters were detected: 2 gene clusters associated with production for homoserine lactone; 1 each for type 3 polyketide and bacteriocin. These results indicate that strain MUSC 273T may produce natural bioactive compounds (including antibiotics), thus future studies involving characteriza- tion of these gene clusters and isolation of the secondary metabo- lite may assist in the discovery of these valuable compounds. Acknowledgement This work was supported by the University of Malaya for High Im- pact Research Grant (UM-MOHE HIR Nature Microbiome Grant No. H-50001-A000027) awarded to K.-G. C. and External Indus- try Grant from Biotek Abadi Sdn Bhd (Vote No. GBA-808138 & GBA-808813) awarded to L.-H. L.