Whole-genome shotgun optical mapping of Rhodospirillum rubrum

Applied and Environmental Microbiology

Volumn 71, Issue 9, 2005, Pages 5511-5522

  Reslewic, Susan ^a   Zhou, Shiguo ^a   Place, Mike ^a   Zhang, Yaoping ^a   Briska, Adam ^b   Goldstein, Steve ^a   Churas, Chris ^a   Runnheim, Rod ^a   Forrest, Dan ^a   Lim, Alex ^a   Lapidus, Alla ^c   Han, Cliff S ^d   Roberts, Gary P ^a   Schwartz, David C ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b OpGen Inc   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODEGRADATION; CELLS; DNA; HYDROGEN; SCAFFOLDS;

OPTICAL MAPPING; RHODOSPIRILLUM RUBRUM; SEQUENCE FINISHING PROCESS;

BACTERIA;

CARBON MONOXIDE; ENDONUCLEASE; GENOMIC DNA; HYDROGEN; PLASTIC; PROTEIN HINDIII; PROTEIN NHEI; PROTEIN XBAI; UNCLASSIFIED DRUG;

BACTERIUM;

ARTICLE; CYTOGENETICS; DNA EXTRACTION; GENE MAPPING; GENE SEQUENCE; NITROGEN FIXATION; NONHUMAN; OXIDATION; PHOTOTROPHIC BACTERIUM; RESTRICTION MAPPING; RHODOSPIRILLUM RUBRUM; SEQUENCE ALIGNMENT;

CONTIG MAPPING; GENOME, BACTERIAL; IMAGE PROCESSING, COMPUTER-ASSISTED; RESTRICTION MAPPING; RHODOSPIRILLUM RUBRUM; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); RHODOSPIRILLUM RUBRUM;

EID: 25144504991     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.9.5511-5522.2005     Document Type: Article

References (32)

1. Anantharaman, T. S., B. Mishra, and D. C. Schwartz. 1997. Genomics via optical mapping. II. Ordered restriction maps. J. Comput. Biol. 4:91-118.
2. Anantharaman, T. S., B. Mishra, and D. C. Schwartz. 1999. Genomics via optical mapping. III. Contiging genomic DNA and variations. Seventh International Conference on Intelligent Systems for Molecular Biology, vol. 7, p. 18-27.
3. Anantharaman, T. S., B. Mishra, and D. C. Schwartz. 1998. Genomics via optical mapping. III. Contiging genomic DNA and variations. Courant Technical Report 760. Courant Institute, New York University, New York, N.Y.
4. Armbrust, E. V., J. A. Berges, C. Bowler, B. R. Green, D. Martinez, N. H. Putnam, S. Zhou, A. E. Allen, K. E. Apt, M. Bechner, M. A. Brzezinski, B. K. Chaal, A. Chiovitti, A. K. Davis, M. S. Demarest, J. C. Detter, T. Glavina, D. Goodstein, M. Z. Hadi, U. Hellsten, M. Hildebrand, B. D. Jenkins, J. Jurka, V. V. Kapitonov, N. Kroger, W. W. Y. Lau, T. W. Lane, F. W. Larimer, J. C. Lippmeier, S. Lucas, M. Medina, A. Montsant, M. Obornik, M. S. Parker, B. Palenik, G. J. Pazour, P. M. Richardson, T. A. Rynearson, M. A. Saito, D. C. Schwartz, K. Thamatrakoln, K. Valentin, A. Vardi, F. P. Wilkerson, and D. S. Rokhsar. 2004. The genome of the diatom Thalassiosira pseudonana: Ecology, evolution, and metabolism. Science 306:79-86.
5. Barrett, M., A. Scheffer, A. Ben-Dor, N. Sampas, D. Lipson, R. Kincaid, P. Tsang, B. Curry, K. Baird, P. Meltzer, Z. Yakhini, L. Bruhn, and S. Laderman. 2004. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl. Acad. Sci. USA 101:17765-17770.
6. Bonam, D., L. Lehman, G. P. Roberts, and P. W. Ludden. 1989. Regulation of carbon monoxide dehydrogenase and hydrogenase in Rhodospirillum rubrum: effects of CO and oxygen on synthesis and activity. J. Bacteriol. 171:3102-3107.
7. Brandl, H., E. J. Knee, Jr., R. C. Fuller, R. A. Gross, and R. W. Lenz. 1989. Ability of the phototrophic bacterium Rhodospirillum rubrum to produce various poly (β-hydroxyalkanoates): potential sources for biodegradable polyesters. Int. J. Biol. Macromol. 11:49-55.
8. Dimalanta, E. T., A. Lim, R. Runnheim, C. Lamers, C. Churas, D. K. Forrest, J. J. de Pablo, M. D. Graham, S. N. Coppersmith, S. Goldstein, and D. C. Schwartz. 2004. A microfluidic system for large DNA molecule arrays. Anal. Chem. 76:5293-5301.
9. Fitzmaurice, W. P., L. L. Saari, R. G. Lowery, P. W. Ludden, and G. P. Roberts. 1989. Genes coding for the reversible ADP-ribosylation system of dinitrogenase reductase from Rhodospirillum rubrum. Mol. Gen. Genet. 218:340-347.
10. Fuller, R. C. 1995. Polyesters and photosynthetic bacteria: from lipid cellular inclusions to microbial thermoplastics, p. 991-1003. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
11. Gordon, D., C. Desmarais, and P. Green. 2001. Automated finishing with Autofinish. Genome Res. 11:614-625.
12. Handrick, R., S. Reinhardt, D. Schultheiss, T. Reichart, D. Schuler, V. Jendrossek, and D. Jendrossek. 2004. Unraveling the function of the Rhodospirillum rubrum activator of polyhydroxybutyrate (PHB) degradation: the activator is a PHB granule protein (phasin). J. Bacteriol. 186:2466-2575.
13. Imhoff, J. F. 2000. The anoxygenic phototrophic purple bacteria, p. 631-637. In D. Boone and R. W. Castenholz (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. Springer-Verlag, New York, NY.
14. Imhoff, J. F. 2001, posting date. The prokaryotes: an evolving electronic resource for the microbiological community. Springer-Verlag. [Online.]
15. Kytola, S., J. Rummukainen, A. Nordgren, R. Karhu, F. Farnebo, J. Isola, and C. Larsson. 2000. Chromosomal alterations in 15 breast cancer cell lines by comparative genomic hybridization and spectral karyotyping. Genes Chromosomes Cancer 28:308-317.
16. Lai, Z., J. Jing, C. Aston, V. Clarke, J. Apodaca, E. T. Dimalanta, D. J. Carucci, M. J. Gardner, B. Mishra, T. S. Anantharaman, S. Paxia, S. L. Hoffman, J. C. V. J. Huff, and D. C. Schwartz. 1999. A shotgun optical map of the entire Plasmodium falciparum genome. Nat. Genet. 23:309-313.
17. Lim, A., E. T. Dimalanta, K. D. Potamousis, G. Yen, J. Apodoca, C. Tao, J. Lin, R. Qi, J. Skiadas, A. Ramanathan, N. T. Perna, G. Plunkett, V. Burland, B. Mau, J. Hackett, F. R. Blattner, T. S. Anantharaman, B. Mishra, and D. C. Schwartz. 2001. Shotgun optical maps of the whole Escherichia coli O157:H7 genome. Genome Res. 11:1584-1593.
18. Lin, J., R. Qi, C. Aston, J. Jing, T. S. Anantharaman, B. Mishra, O. White, M. J. Daly, K. W. Minton, J. C. Venter, and D. C. Schwartz. 1999. Whole-genome shotgun optical mapping of Deinococcus radiodurans. Science 285:1558-1562.
19. Lucito, R., J. Healy, J. Alexander, A. Reiner, D. Esposito, M. Chi, L. Rogers, A. Brady, et al. 2003. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13:2291-2305.
20. Marra, M. A., T. A. Kucaba, N. L. Dietrich, E. D. Green, B. Brownstein, R. K. Wilson, K. M. McDonald, L. W. Hillier, J. D. McPherson, and R. H. Waterston. 1997. High throughput fingerprint analysis of large-insert clones. Genome Res. 7:1072-1084.
21. Meng, X., K. Benson, K. Chada, J. E. Huff, and D. C. Schwartz. 1995. Optical mapping of lambda bacteriophage clones using restriction endonucleases. Nat. Genet. 9:432-438.
22. Pfennig, N., H. Lünsdorf, J. Silling, and J. F. Imhoff. 1997. Rhodospira trueperi gen. nov., spec, nov., a new phototrophic Proteobacterium of the alpha group. Arch. Microbiol. 168:39-45.
23. Sasaki, S., and I. Karube. 1999. The development of microfabricated biocatalytic fuel cells. TIBTECH 17:50-52.
24. Schick, H. J. 1971. Interrelationship of nitrogen fixation, hydrogen evolution and photoreduction in Rhodospirillum rubrum. Arch. Microbiol. 75:102-109.
25. Schwartz, D., and C. R. Cantor. 1984. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37:67-75.
26. Schwartz, D. C., and C. R. Cantor. 1984. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37:67-77.
27. 2 fixation in purple bacteria, p. 885-914. In R. E. Blankenship, M. T. Madigan, and C. E. Bauer (ed.), Anoxygenic photosynthetic bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
28. von Felten, P., H. Zürrer, and R. Bachofen. 1985. Production of molecular hydrogen with immobilized cells of Rhodospirillum rubrum. Appl. Microbiol. Biotechnol. 23:15-20.
29. Zhang, Y., R. H. Burris, P. W. Ludden, and G. P. Roberts. 1995. Comparison studies of dinitrogenase reductase ADP-ribosyl transferase/ dinitrogenase reductase activating glycohydrolase regulatory systems in Rhodospirillum rubrum and Azospirillum brasilense. J. Bacteriol. 177:2354-2359.
30. Zhou, S., W. Deng, T. S. Anantharaman, A. Lim, E. T. Dimalanta, J. Wang, T. Wu, T. Chunhong, R. Creighton, A. Kile, E. Kvikstad, M. Bechner, G. Yen, A. Garic-Stankovic, J. Severin, D. Forrest, R. Runnheim, C. Churas, C. Lamers, N. T. Perna, V. Burland, F. R. Blattner, B. Mishra, and D. C. Schwartz. 2002. A whole-genome shotgun optical map of Yersinia pestis strain KIM. Appl. Environ. Microbiol. 68:6321-6331.
31. Zhou, S., A. Kile, M. Bechner, M. Place, E. Kvikstad, W. Deng, J. Wei, J. Severin, R. Runnheim, C. Churas, D. Forrest, E. T. Dimalanta, C. Lamers, V. Burland, F. R. Blattner, and D. C. Schwartz. 2004. A single-molecule approach to bacterial genomic comparisons via optical mapping. J. Bacteriol. 186:7773-7782.
32. Zhou, S., E. Kvikstad, A. Kile, J. Severin, D. Forrest, R. Runnheim, C. Churas, J. W. Hickman, C. Mackenzie, M. Choudhary, T. Donahue, S. Kaplan, and D. C. Schwartz. 2003. Whole-genome shotgun optical mapping of Rhodabacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly. Genome Res. 13:2142-2151.