DOI QR코드

DOI QR Code

Genome sequence of Caballeronia sordidicola strain PAMC 26577 isolated from Cladonia sp., an Arctic lichen species

북극 지의류 Cladonia종에서 분리한 Caballeronia sordidicola균주 PAMC 26577의 유전체 서열 분석

  • Yang, Jhung Ahn (Department of Marine-Bio Convergence Science, Specialized Graduate School Science & Technology Convergence, Pukyong National University) ;
  • Hong, Soon Gyu (Division of Polar Life Sciences, Korea Polar Research Institute) ;
  • Oh, Hyun-Myung (Department of Marine-Bio Convergence Science, Specialized Graduate School Science & Technology Convergence, Pukyong National University)
  • 양정안 (부경대학교 과학기술융합전문대학원) ;
  • 홍순규 (극지연구소) ;
  • 오현명 (부경대학교 과학기술융합전문대학원)
  • Received : 2017.06.08
  • Accepted : 2017.06.08
  • Published : 2017.06.30

Abstract

Caballeronia sordidicola strain PAMC 26577 was isolated from Cladonia sp., a lichen collected from Svalbard Archipelago in the Arctic Ocean. Draft genomic sequences of PAMC 26577 were determined using Illumina and 182 contigs were submitted to GenBank and N50 value was 159,226. The genome of PAMC 26577 was comprised of 8,334,211 base pairs and %G+C content was 59.4. The genome included 8 ribosomal RNA genes and 51 tRNA genes as non-coding sequences. Protein-coding genes were 8,065 in number and they included central metabolism genes as well as butanol/butyrate biosynthesis, polyhydroxybutyrate metabolism, serine cycle methylotrophy genes, and glycogen metabolism. Membrane transporters were more than two-hundreds in number, but sugar phosphotransferase system and TRAP transporters were lacking. PAMC 26577 lacked CRISPR-associated sequences and proteins. No transposable elements were observed and there were only limited number of phage remnant regions with 11 phage-related genes.

Keywords

Caballeronia sordidicola;Cladonia;Arctic;genome;lichen

Acknowledgement

Supported by : Pukyong National University

References

  1. Biswas, A., Staals, R.H.J., Morales, S.E., Fineran, P.C., and Brown, C.M. 2016. CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics 17, 356. https://doi.org/10.1186/s12864-016-2627-0
  2. Dobritsa, A.P. and Samadpour, M. 2016. Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia. Int. J. Syst. Evol. Microbiol. 66, 2836-2846. https://doi.org/10.1099/ijsem.0.001065
  3. Garrity, G.M., Bell, J.A., and Lilburn, T. 2005. Class II. Betaproteobacteria class. nov., pp. 575-922. Bergey's manual(R) of systematic bacteriology, Springer.
  4. Kim, J., Kwon, K.K., Kim, B.K., Hong, S.G., and Oh, H.M. 2017. Genome sequence of Caballeronia sordidicola strain PAMC 26592 isolated from an arctic lichen species. Korean J. Microbiol. 53.
  5. Lee, Y.M., Kim, G., Jung, Y.J., Choe, C.D., Yim, J.H., Lee, H.K., and Hong, S.G. 2012. Polar and Alpine Microbial Collection (PAMC): a culture collection dedicated to polar and alpine microorganisms. Polar Biol. 35, 1433-1438. https://doi.org/10.1007/s00300-012-1182-7
  6. Lee, Y.M., Kim, E.H., Lee, H.K., and Hong, S.G. 2014. Biodiversity and physiological characteristics of Antarctic and Arctic lichensassociated bacteria. World J. Microbiol. Biotechnol. 30, 2711-2721. https://doi.org/10.1007/s11274-014-1695-z
  7. Quinlan, A.R. and Hall, I.M. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842. https://doi.org/10.1093/bioinformatics/btq033