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http://dx.doi.org/10.7845/kjm.2017.7067

Complete genome sequence of Betaproteobacteria strain GR16-43 isolated form a freshwater pond in South Korea  

Choi, Ahyoung (Culture Techniques Research Division, Nakdonggang National Institute of Biological Resources)
Baek, Kiwoon (Bacterial Resources Research Division, Nakdonggang National Institute of Biological Resources)
Chung, Eu Jin (Culture Techniques Research Division, Nakdonggang National Institute of Biological Resources)
Kim, Jee-Hwan (Bioresources Culture Collection Division, Nakdonggang National Institute of Biological Resources)
Choi, Gang-Guk (Culture Techniques Research Division, Nakdonggang National Institute of Biological Resources)
Publication Information
Korean Journal of Microbiology / v.53, no.4, 2017 , pp. 320-322 More about this Journal
Abstract
A betaproteobacterium strain GR16-43 was isolated from a surface layer of the Geomnyong Pond in Republic of Korea by a dilution-to-extinction culturing method. We report the whole genome sequence of the strain GR16-43, which contains 4,806,848 bp with a G + C content 67.12%, and to include 4,424 protein-coding genes and 47 transfer RNA genes. The genome was determined to contain the genes encoding carbon monoxide dehydrogenase, nitrate reductase, nitrite reductase, nitric oxide reductase, and the sulfur oxidation (sox) gene cluster, highlighting the potential importance of the bacterial group represented by the strain in the cycling of inorganic elements. These results indicate that strain GR16-43 genome showed several traits indicating adaptation of the bacteria to living in freshwater environments.
Keywords
Betaproteobacterium; complete genome; freshwater;
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1 Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75.   DOI
2 Chin, C.S., Alexander, D.H., Marks, P., Klammer, A.A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler E.E., et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563-569.   DOI
3 Griffiths-Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., and Bateman, A. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33, D121-D124.
4 Krogh, A., Larsson, B., Von Heijne, G., and Sonnhammer, E.L. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580.   DOI
5 Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., Rognes, T., and Ussery, D.W. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108.   DOI
6 Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964.   DOI
7 Newton, R.J., Jones, S.E., Eiler, A., McMahon, K.D., and Bertilsson, S. 2011. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. R. 75, 14-49.   DOI
8 Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin E.V., Krylov, D.M., Mazumdr, R., Mekhedov, S.L., Nikolskaya, A.N., et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.   DOI
9 Petersen, T.N., Brunak, S., von Heijne, G., and Nielsen, H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785-786.   DOI
10 Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., et al. 2012. The Pfam protein families database. Nucleic Acids Res. 40, D290-D301.   DOI
11 Van der Gucht, K., Vandekerckhove, T., Vloemans, N., Cousin, S., Muylaert, K., Sabbe, K., Gillis, M., De Meester, L., and Vyverman, W. 2005. Characterization of bacterial communities in four freshwater lakes differing in nutrient load and food web structure. FEMS Microbiol. Ecol. 53, 205-220.   DOI
12 Wu, C.H., Apweiler, R., Bairoch, A., Natale, D.A., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., et al. 2006. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34, D187-D191.   DOI
13 Zwart, G., Crump, B.C., Kamst-van Agterveld, M.P., Hagen, F., and Han, S.K. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microbiol. Ecol. 28, 141-155.   DOI