Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1995 May;177(9):2368–2372. doi: 10.1128/jb.177.9.2368-2372.1995

High-resolution alignment of a 1-megabase-long genome region of three strains of Rhodobacter capsulatus.

M Fonstein 1, T Nikolskaya 1, R Haselkorn 1
PMCID: PMC176893  PMID: 7730266

Abstract

A detailed restriction map of the genome of Rhodobacter capsulatus SB1003 was constructed recently by using an ordered set of overlapping cosmids. Pulsed-field gel electrophoresis-generated restriction patterns of the chromosomes of 14 other R. capsulatus strains were compared. Two of them, St. Louis and 2.3.1, were chosen for high-resolution alignment of their genomes with that of SB1003. A 1-Mb segment of the R. capsulatus SB1003 cosmid set was used as a source of ordered probes to group cosmids from the other strains. Selected cosmids were linked into one 800-kb contig and two smaller contigs of 100 kb each. EcoRV and BamHI restriction maps of the newly ordered cosmids were constructed by using lambda terminase. Long-range gene order in the new strains was mainly conserved for the regions studied. However, one large genome rearrangement inverted a 470-kb DNA fragment of the St. Louis strain between the rrnA and rrnB operons. A 50-kb deletion covering three SB1003 probes was found in strain 2.3.1 near rrnB. Conservation of about 50% of the positions of restriction sites in all these strains and nearly 80% for the pair 2.3.1- St. Louis made it possible to produce high-resolution alignment of the contiguous 800-kb genome segment. Ten deletions of 2 to 27 kb, one 30-kb inversion, and three translocations were found in this region. Strong clustering of the positions of polymorphic restriction sites was observed. For a 50-kb size interval, two patterns of the distribution of restriction sites were found, one with about 90% and the other with 5 to 30% conservation of sites. This structure may be explained by independent acquisition of these divergent regions from other Rhodobacter strains.

Full Text

The Full Text of this article is available as a PDF (534.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Birkenbihl R. P., Vielmetter W. Cosmid-derived map of E. coli strain BHB2600 in comparison to the map of strain W3110. Nucleic Acids Res. 1989 Jul 11;17(13):5057–5069. doi: 10.1093/nar/17.13.5057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Canard B., Saint-Joanis B., Cole S. T. Genomic diversity and organization of virulence genes in the pathogenic anaerobe Clostridium perfringens. Mol Microbiol. 1992 Jun;6(11):1421–1429. doi: 10.1111/j.1365-2958.1992.tb00862.x. [DOI] [PubMed] [Google Scholar]
  3. Carlson C. R., Grønstad A., Kolstø A. B. Physical maps of the genomes of three Bacillus cereus strains. J Bacteriol. 1992 Jun;174(11):3750–3756. doi: 10.1128/jb.174.11.3750-3756.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Carlson C. R., Kolstø A. B. A complete physical map of a Bacillus thuringiensis chromosome. J Bacteriol. 1993 Feb;175(4):1053–1060. doi: 10.1128/jb.175.4.1053-1060.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Fonstein M., Haselkorn R. Chromosomal structure of Rhodobacter capsulatus strain SB1003: cosmid encyclopedia and high-resolution physical and genetic map. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2522–2526. doi: 10.1073/pnas.90.6.2522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fonstein M., Nikolskaya T., Zaporojets D., Nikolsky Y., Kulakauskas S., Mironov A. Tn10-mediated inversions fuse uridine phosphorylase (udp) and rRNA genes of Escherichia coli. J Bacteriol. 1994 Apr;176(8):2265–2271. doi: 10.1128/jb.176.8.2265-2271.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fonstein M., Zheng S., Haselkorn R. Physical map of the genome of Rhodobacter capsulatus SB 1003. J Bacteriol. 1992 Jun;174(12):4070–4077. doi: 10.1128/jb.174.12.4070-4077.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gibson T. J., Rosenthal A., Waterston R. H. Lorist6, a cosmid vector with BamHI, NotI, ScaI and HindIII cloning sites and altered neomycin phosphotransferase gene expression. Gene. 1987;53(2-3):283–286. doi: 10.1016/0378-1119(87)90017-5. [DOI] [PubMed] [Google Scholar]
  9. Guttman D. S., Dykhuizen D. E. Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science. 1994 Nov 25;266(5189):1380–1383. doi: 10.1126/science.7973728. [DOI] [PubMed] [Google Scholar]
  10. Knott V., Blake D. J., Brownlee G. G. Completion of the detailed restriction map of the E. coli genome by the isolation of overlapping cosmid clones. Nucleic Acids Res. 1989 Aug 11;17(15):5901–5912. doi: 10.1093/nar/17.15.5901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  12. Liu S. L., Hessel A., Sanderson K. E. Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6874–6878. doi: 10.1073/pnas.90.14.6874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Mazodier P., Davies J. Gene transfer between distantly related bacteria. Annu Rev Genet. 1991;25:147–171. doi: 10.1146/annurev.ge.25.120191.001051. [DOI] [PubMed] [Google Scholar]
  14. Milkman R., Bridges M. M. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics. 1990 Nov;126(3):505–517. doi: 10.1093/genetics/126.3.505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Milkman R., Bridges M. M. Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons. Genetics. 1993 Mar;133(3):455–468. doi: 10.1093/genetics/133.3.455. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nelson K., Selander R. K. Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli. J Bacteriol. 1992 Nov;174(21):6886–6895. doi: 10.1128/jb.174.21.6886-6895.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rackwitz H. R., Zehetner G., Murialdo H., Delius H., Chai J. H., Poustka A., Frischauf A., Lehrach H. Analysis of cosmids using linearization by phage lambda terminase. Gene. 1985;40(2-3):259–266. doi: 10.1016/0378-1119(85)90048-4. [DOI] [PubMed] [Google Scholar]
  18. Schmid M. B., Roth J. R. Selection and endpoint distribution of bacterial inversion mutations. Genetics. 1983 Nov;105(3):539–557. doi: 10.1093/genetics/105.3.539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Selander R. K., Caugant D. A., Ochman H., Musser J. M., Gilmour M. N., Whittam T. S. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol. 1986 May;51(5):873–884. doi: 10.1128/aem.51.5.873-884.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Smith J. M., Smith N. H., O'Rourke M., Spratt B. G. How clonal are bacteria? Proc Natl Acad Sci U S A. 1993 May 15;90(10):4384–4388. doi: 10.1073/pnas.90.10.4384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Suwanto A., Kaplan S. Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. J Bacteriol. 1989 Nov;171(11):5850–5859. doi: 10.1128/jb.171.11.5850-5859.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES