Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Genome Information of Maribacter dokdonensis DSW-8 and Comparative Analysis with Other Maribacter Genomes

  • Kwak, Min-Jung (Department of Systems Biology and Division of Life Sciences, Yonsei University) ;
  • Lee, Jidam (Department of Systems Biology and Division of Life Sciences, Yonsei University) ;
  • Kwon, Soon-Kyeong (Department of Systems Biology and Division of Life Sciences, Yonsei University) ;
  • Kim, Jihyun F. (Department of Systems Biology and Division of Life Sciences, Yonsei University)
  • Received : 2016.08.23
  • Accepted : 2016.12.14
  • Published : 2017.03.28
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Abstract

Maribacter dokdonensis DSW-8 was isolated from the seawater off Dokdo in Korea. To investigate the genomic features of this marine bacterium, we sequenced its genome and analyzed the genomic features. After de novo assembly and gene prediction, 16 contigs totaling 4,434,543 bp (35.95% G+C content) in size were generated and 3,835 protein-coding sequences, 36 transfer RNAs, and 6 ribosomal RNAs were detected. In the genome of DSW-8, genes encoding the proteins associated with gliding motility, molybdenum cofactor biosynthesis, and utilization of several kinds of carbohydrates were identified. To analyze the genomic relationships among Maribacter species, we compared publically available Maribacter genomes, including that of M. dokdonensis DSW-8. A phylogenomic tree based on 1,772 genes conserved among the eight Maribacter strains showed that Maribacter speices isolated from seawater are distinguishable from species originating from algal blooms. Comparison of the gene contents using COG and subsystem databases demonstrated that the relative abundance of genes involved in carbohydrate metabolism are higher in seawater-originating strains than those of algal blooms. These results indicate that the genomic information of Maribacter species reflects the characteristics of their habitats and provides useful information for carbon utilization of marine flavobacteria.

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References

  1. Irigoien X, Huisman J, Harris RP. 2004. Global biodiversity patterns of marine phytoplankton and zooplankton. Nature 429: 863-867. https://doi.org/10.1038/nature02593
  2. Ryu SH, Jang KH, Choi EH, Kim SK, Song SJ, Cho HJ, et al. 2012. Biodiversity of marine invertebrates on rocky shores of Dokdo, Korea. Zool. Stud. 51: 710-726.
  3. Kolton M, Sela N, Elad Y, Cytryn E. 2013. Comparative genomic analysis indicates that niche adaptation of terrestrial flavobacteria is strongly linked to plant glycan metabolism. PLoS One 8: e76704. https://doi.org/10.1371/journal.pone.0076704
  4. Hu J, Wang F, Han SB, Wu SL, Wu M, Xu XW. 2015. Genome sequence of facultatively anaerobic marine bacterium Maribacter thermophilus strain HT7-2(T). Mar. Genomics 24: 265-268. https://doi.org/10.1016/j.margen.2015.08.003
  5. Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Rohde M, Rhee MS, et al. 2004. Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov. Int. J. Syst. Evol. Microbiol. 54: 1017-1023. https://doi.org/10.1099/ijs.0.02849-0
  6. Thongphrom C, Kim JH, Kim W. 2016. Maribacter arenosus sp. nov., isolated from marine sediment. Int. J. Syst. Evol. Microbiol. 66: 4826-4831. https://doi.org/10.1099/ijsem.0.001436
  7. Yoon JH, Kang SJ, Lee SY, Lee CH, Oh TK. 2005. Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo. Int. J. Syst. Evol. Microbiol. 55: 2051-2055. https://doi.org/10.1099/ijs.0.63777-0
  8. Green MR, Sambrook J. 2012. Molecular Cloning: A Laboratory Manual, pp. 19-20. 4th Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. USA.
  9. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27: 578-579. https://doi.org/10.1093/bioinformatics/btq683
  10. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75. https://doi.org/10.1186/1471-2164-9-75
  11. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19: 1639-1645. https://doi.org/10.1101/gr.092759.109
  12. Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13: 2178-2189. https://doi.org/10.1101/gr.1224503
  13. Pearson WR. 2013. An introduction to sequence similarity ("homology") searching. Curr. Protoc. Bioinformatics 3: Unit3.1.
  14. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797. https://doi.org/10.1093/nar/gkh340
  15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739. https://doi.org/10.1093/molbev/msr121
  16. Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131. https://doi.org/10.1073/pnas.0906412106
  17. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. 2009. The DOE-JGI standard operating procedure for the annotations of microbial genomes. Stand. Genomic Sci. 1: 63-67. https://doi.org/10.4056/sigs.632
  18. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37: D233-D238. https://doi.org/10.1093/nar/gkn663
  19. Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. 2012. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 40: W445-W451. https://doi.org/10.1093/nar/gks479
  20. Barbeyron T, Carpentier F, L'Haridon S, Schuler M, Michel G, Amann R. 2008. Description of Maribacter forsetii sp. nov., a marine Flavobacteriaceae isolated from North Sea water, and emended description of the genus Maribacter. Int. J. Syst. Evol. Microbiol. 58: 790-797. https://doi.org/10.1099/ijs.0.65469-0
  21. Hu J, Yang QQ, Ren Y, Zhang WW, Zheng G, Sun C, et al. 2015. Maribacter thermophilus sp. nov., isolated from an algal bloom in an intertidal zone, and emended description of the genus Maribacter. Int. J. Syst. Evol. Microbiol. 65: 36-41. https://doi.org/10.1099/ijs.0.064774-0
  22. Zhang GI, Hwang CY, Kang SH, Cho BC. 2009. Maribacter antarcticus sp. nov., a psychrophilic bacterium isolated from a culture of the Antarctic green alga Pyramimonas gelidicola. Int. J. Syst. Evol. Microbiol. 59: 1455-1459. https://doi.org/10.1099/ijs.0.006056-0
  23. Oh HM, Kang I, Yang SJ, Jang Y, Vergin KL, Giovannoni SJ, Cho JC. 2011. Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae. J. Bacteriol. 193: 303-304. https://doi.org/10.1128/JB.01207-10
  24. McBride MJ. 2001. Bacterial gliding motility: multiple mechanisms for cell movement over surfaces. Annu. Rev. Microbiol. 55: 49-75. https://doi.org/10.1146/annurev.micro.55.1.49
  25. Cho KH, Hong SG, Cho HH, Lee YK, Chun J, Lee HK. 2008. Maribacter arcticus sp. nov., isolated from Arctic marine sediment. Int. J. Syst. Evol. Microbiol. 58: 1300-1303. https://doi.org/10.1099/ijs.0.65549-0
  26. Park S, Jung YT, Park JM, Won SM, Yoon JH. 2015. Maribacter confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring. Int. J. Syst. Evol. Microbiol. 65: 3079-3085. https://doi.org/10.1099/ijs.0.000379

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