Geographic divergence of "sulfolobus islandicus" strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 105, Issue 2, 2014, Pages 431-435

  Zuo, Guanghong ^a   Hao, Bailin ^a   Staley, James T ^b  

^a FUDAN UNIVERSITY   (China)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Archaea biogeography; Average nucleotide identity; In silico DNA hybridization; Prokaryote species concept; Sulfolobus islandicus geovars; Whole genome CVTree phylogeny

Indexed keywords

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENETIC VARIATION; ICELAND; NORTH AMERICA; NUCLEIC ACID HYBRIDIZATION; PHYLOGEOGRAPHY; RUSSIA; SULFOLOBUS;

EID: 84895904422     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-013-0081-4     Document Type: Article

References (23)

1. Auch AF, Von Jan M, Klenk H-P, Gröker M (2010a) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117-134
2. Auch AF, Klenk H-P, Gröker M (2010b) Standard operating procedure for calculating genome-to-genome distance based on high-scoring sequence segments. Stand Genomic Sci 2:142-148
3. Brenner DJ, Staley JT, Krieg NR (2005) Classification of procaryotic organisms and the concept of bacterial speciation. In: Garrity G, Krieg N, Brenner D, Staley JT (eds) Bergey's manual of systematic bacteriology, vol 2A, 2nd edn. Springer, New York, pp 27-32
4. De Vos P, Trüper HG (2000) Judicial Commission of the International Committee on Systematic bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int J Syst Evol Microbiol 50:2239-2244
5. DSMZ (2013) Deutsche sammlung von mikroorganismen und zellkulturen GGDC. http://ggdc.dsmz.de. Accessed 29 Aug 2013
6. Goris J, Knostantinidis KT, Klappenbach JA et al (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81-91
7. Guo L, Bruegger K, Liu C, Shah SA, Zheng H, Zhu Y, Wang S, Lillestol RK, Chen L, Frank J, Prangishvili D, Pulin L, She Q, Huang L, Garett RA (2011) Genome analysis of Icelandic strains of Sulfolobus islandicus: model organisms for genetic and virus-host interaction studies. J Bacteriol 193:1672-1680
8. Hao B (2011) CVTrees support the Bergey's systematics and provide high resolution at species levels and below. Bull BISMiS 2:181-188
9. Jaubert C, Danioux C, Oberto J, Cortez D, Bize A, Krupovic M, She Q, Forterre P, Prangishvili D, Sezonov G (2013) Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon. Open Biol 3:130010
10. Krichevsky MI (2011) What is a bacterial species? I will know it when I see it. Bull BISMiS 2:17-23
11. Lapage SP, Sneath PHA, Lessal EF et al (1992) International code of nomenclature of bacteria: bacteriological code 1990. ASM Press, Washington, DC
12. Li Q, Xu Z, Hao B (2010) Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations. J Biotechnol 149:115-119
13. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence based species delineation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60
14. Qi J, Wang B, Hao B (2004) Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 58:1-11
15. Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ (2009) Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci USA 106:8605-8610 (correction, ibid, 18873)
16. Richter M, Roselló-Móra R (2009) Shifting the gold standard for the prokaryote species definition. Proc Natl Acad Sci USA 106:19126-19131
17. Staley JT (2004) Speciation and bacterial phylospecies. In: Bull AT (ed) Microbial diversity and bioprospecting. ASM Press, Washington, DC, pp 40-48
18. Staley JT (2006) The bacterial species dilemma and the genomic-phylogenetic species concept. Phil Trans R Soc B 361:1899-1909
19. Staley JT, Gosink JJ (1999) Poles apart: biodiversity and biogeography of polar sea ice bacteria. Annu Rev Microbiol 53:189-215
20. Ward DM (1998) A natural species concept for prokaryotes. Curr Opin Microbiol 1:271-277
21. Wayne LG (1987) Report of the ad hoc committee on reconcilliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463-464
22. Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barrier isolate endemic populations of hyperthermophilic archaea. Science 301:976-978
23. Xu Z, Hao B (2009) CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes. Nucl Acids Res 37 (Web Server Issue): W174-W178. The new version to be published in 2014 was used: http://tlife.fudan.edu.cn/cvtree3/. Accessed 5 July 2013