ABSTRACT
Sinomonas mesophila MPKL 26T can produce silver nanoparticles. Here, we present the 4.0-Mb genome of this type strain, which contains 47 scaffolds with an N50 scaffold length of 261,266 bp. The availability of the genome sequence will provide a better understanding of strain MPKL 26T and the genus Sinomonas.
GENOME ANNOUNCEMENT
The genus Sinomonas was proposed by Zhou et al. (1) and comprises 10 species of Gram-positive actinobacteria (http://www.bacterio.net/sinomonas.html [2]). Members of the genus Sinomonas have the ability to produce silver nanoparticles (3), can hydrolyze starch (4), and are used for biodesulfurization coal (5). Here, we report the draft genome sequence of strain MPKL 26, the type strain of the novel species Sinomonas mesophila, which has the ability to produce silver nanoparticles (3).
Whole-genome sequencing of S. mesophila strain MPKL 26T was performed using a paired-end sequencing method with the HiSeq 2000 platform (Illumina, San Diego, CA, USA). Using 1.49 Gb of clean data, the draft genome was assembled with the SOAPdenovo2 package (6). The draft genome of S. mesophila MPKL 26T contains 47 scaffolds with a total size of 4,008,197 bp and with an N50 scaffold length of 261,266 bp. The G+C content is 71.1%. Gene prediction was carried out using Glimmer version 3.02 (7). The identification of tRNAs and rRNAs was carried out using tRNAscan-SE version 1.23 (8) and RNAmmer version 1.2 (9). A total of 3,742 genes were predicted with four rRNA and 52 tRNA genes. The predicted coding sequences were translated and used to search against the KEGG and COG databases. The functional annotation of the genome was also performed with RAST (10), which revealed 448 genes for carbohydrate metabolism, 235 genes involved in protein metabolism, and 90 genes involved in DNA metabolism. These data sources were combined to assert a product description for each predicted protein.
Accession number(s).
This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number MTIC00000000. The version described in this paper is the first version, MTIC01000000.
ACKNOWLEDGMENTS
This research was supported by the Natural Science Foundation of China (no. 31600015), the Project of China Tobacco Yunnan Industrial Co. Ltd. (no. 2015CP01), Shenzhen New Strategic Industry Special Fund (no. CXZZ20120618172226337), and the China Postdoctoral Science Foundation (2016M592567). W.-J. Li was also supported by the Guangdong Province Higher Vocational Colleges and Schools Pearl River Scholar Funded Scheme (2014).
Footnotes
Citation Narsing Rao MP, Jiao J-Y, Liu L, Fang B-Z, Zhang X-T, Chen W, Zhao J, Xiao M, Li W-J. 2017. Draft genome sequence of MPKL 26, the type strain of the novel species Sinomonas mesophila. Genome Announc 5:e00247-17. https://doi.org/10.1128/genomeA.00247-17.
REFERENCES
- 1.Zhou Y, Wei W, Wang X, Lai R. 2009. Proposal of Sinomonas flava gen. nov., sp. nov., and description of Sinomonas atrocyanea comb. nov. to accommodate Arthrobacter atrocyaneus. Int J Syst Evol Microbiol 59:259–263. doi: 10.1099/ijs.0.000695-0. [DOI] [PubMed] [Google Scholar]
- 2.Parte AC. 2014. LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613–D616. doi: 10.1093/nar/gkt1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Manikprabhu D, Cheng J, Chen W, Sunkara AK, Mane SB, Kumar R, das M, N Hozzein W, Duan YQ, Li WJ. 2016. Sunlight mediated synthesis of silver nanoparticles by a novel actinobacterium (Sinomonas mesophila MPKL 26) and its antimicrobial activity against multi drug resistant Staphylococcus aureus. J Photochem Photobiol B 158:202–205. doi: 10.1016/j.jphotobiol.2016.01.018. [DOI] [PubMed] [Google Scholar]
- 4.Ser HL, Tan WS, Cheng HJ, Yin WF, Chan KG, Lee LH. 2015. Draft genome of amylolytic actinobacterium, Sinomonas humi MUSC 117T isolated from intertidal soil. Mar Genomics 24:209–210. doi: 10.1016/j.margen.2015.05.012. [DOI] [PubMed] [Google Scholar]
- 5.Mishra S, Panda PP, Pradhan N, Satapathy D, Subudhi U, Biswal SK, Mishra BK. 2014. Effect of native bacteria Sinomonas flava 1C and Acidithiobacillus ferrooxidans on desulphurization of Meghalaya coal and its combustion properties. Fuel 117:415–421. doi: 10.1016/j.fuel.2013.09.049. [DOI] [Google Scholar]
- 6.Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18. doi: 10.1186/2047-217X-1-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679. doi: 10.1093/bioinformatics/btm009. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]