Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly

Genome Research

Volumn 13, Issue 9, 2003, Pages 2142-2151

  Zhou, Shiguo ^a   Kvikstad, Erika ^a   Kile, Andrew ^a   Severin, Jessica ^a   Forrest, Dan ^a   Runnheim, Rod ^a   Churas, Chris ^a   Hickman, Jason W ^b   Mackenzie, Chris ^b   Choudhary, Madhusudan ^b   Donohue, Timothy ^a   Kaplan, Samuel ^b   Schwartz, David C ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; HYDROGEN; PYRROLE DERIVATIVE;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOSYNTHESIS; CARBON DIOXIDE FIXATION; CONTIG MAPPING; CONTROLLED STUDY; GENE CONSTRUCT; GENE MAPPING; GENE SEQUENCE; GENOME ANALYSIS; HETEROTROPHY; MICROBIAL DIVERSITY; MOLECULAR GENETICS; NITROGEN FIXATION; NONHUMAN; PHOTOSYNTHESIS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; RESTRICTION MAPPING; RHODOBACTER SPHAEROIDES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

CHROMOSOMES, BACTERIAL; CONTIG MAPPING; GENETIC MARKERS; GENOME, BACTERIAL; MICROSCOPY, FLUORESCENCE; OPTICS; RESTRICTION MAPPING; RHODOBACTER SPHAEROIDES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); PROKARYOTA; RHODOBACTER; RHODOBACTER SPHAEROIDES; RHODOBACTER SPHAEROIDES 2.4.1; RHODOPSEUDOMONAS;

EID: 0141519284     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1128803     Document Type: Article

References (33)

1. Anantharaman, T.S., Mishra, B., and Schwartz, D.C. 1997. Genomics via optical mapping 2. Ordered restriction maps. J. Comput. Biol. 4: 91-118.
2. Anantharaman, T.S., Mishra, B., and Schwartz, D.C. 1998. Genomics via optical mapping III: Contiging genomic DNA and variations. In Courant technical report, p. 760. Courant Institute, New York University, NY.
3. Anantharaman, T.S., Mishra, B., and Schwartz, D.C. 1999. Genomics via optical mapping III: Contiging genomic DNA and variations. The Seventh International Conference on Intelligent Systems for Molecular Biology 7: 18-27.
4. Aston, C., Hiort, C., and Schwartz, D.C. 1999a. Optical mapping: An approach for fine mapping. Meth. Enzymol. 303: 55-73.
5. Aston, C., Mishra, B., and Schwartz, D.C. 1999b. Optical mapping and its potential for large-scale sequencing projects. Trends Biotech. 17: 297-302.
6. Barber, R.D. and Donohue, T.J. 1998. Function of a glutothione-dependent formaldehyde dehydrogenase in Rhodobacter sphaeroides, formaldehyde oxidation and assimilation. Biochemistry 37: 530-537.
7. Cai, W., Jing, J., Irvin, B., Ohler, L., Rose, E., Shizuya, H., Kim, U., Simon, M., Anantharaman, T., Mishra, B., et al. 1998. High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping. Proc. Natl. Acad. Sci. 95: 3390-3395.
8. Choudhary, M., Mackenzie, C., Nereng, K.S., Sodergren, E., Weinstock, G.M., and Kaplan, S. 1994. Multiple chromosomes in bacteria: Structure and function of chromosome II of Rhodobacter sphaeroides 2.4.1. J. Bacteriol. 176: 7694-7702.
9. T: Chromosome II is a true chromosome. Microbiol. 143: 3085-3099.
10. Clayton, R.K. and Sistrom, W.R. 1978. The photosynthetic bacteria. Plenum Press, New York.
11. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M., et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496-512.
12. Gordon, D., Albanian, C., and Green, P. 1998. Consed: a graphical tool for sequence finishing. Genome Research. 8: 195-202.
13. Jing, J., Lai, Z., Aston, C., Lin, J., Carucci, D.J., Gardner, M.J., Mishra, B., Anantharaman, T., Tettelin, H., Cummings, L.M., et al. 1999. Optical mapping of Plasmodium falciparum chromosome 2. Genome Res. 9: 175-181.
14. Lai, Z., Jing, J., Aston, C., Clarke, V., Apodaca, J., Dimalanta, E.T., Carucci, D.J., Gardner, M.J., Mishra, B., Anatharaman, T.S., et al. 1999. A shotgun optical map of the entire Plasmodium falciparum genome. Nat. Genet. 23: 309-313.
15. Lim, A., Dimalanta, E.T., Potamousis, K.D., Yen, G., Apodoca, J., Tao, C., Lin, J., Qi, R., Skiadas, J., Ramanathan, A., et al. 2001. Shotgun optical maps of the whole Escherichia coli O157:H7 Genome. Genome Res. 11: 1584-1593.
16. Lin, J., Qi, R., Aston, C., Jing, J., Anatharaman, T.S., Mishra, B., White, O., Daly, M.J., Minton, K.W., Venter, J.C., et al. 1999. Whole-genome shotgun optical mapping of Deinococcus radiodurans. Science 285: 1558-1562.
17. Lueking, D.R., Fraley, R.T., and Kaplan, S. 1978. Intracytoplasmic membrane synthesis in synchronous cell populations of Rhodopseudomonas sphaeroides. J. Biol. Chem. 253: 451-457.
18. Mackenzie, C., Choudhary, M., Larimer, F.W., Predki, P.F., Stilwagen, S., Armitage, J.P., Barber, R.D., Donohue, T.J., Hosler, J.P., Newman, J.E., et al. 2001. The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1. Photosynthesis Research 70: 19-41.
19. Marra, M.A., Kucaba, T.A., Dietrich, N.L., Green, E.D., Brownstein, B., Wilson, R.K., McDonald, K.M., Hillier, L.W., McPherson, J.D., and Waterston, R.H. 1997. High throughput fingerprint analysis of large-insert clones. Genome Res. 7: 1072-1084.
20. Meng, X., Benson, K., Chada, K., Huff, J.E., and Schwartz, D.C. 1995. Optical mapping of λ bacteriophage clones using restriction endonucleases. Nat. Genet. 9: 432-438.
21. Moore, M.D. and Kaplan, S. 1992. Identification of intrinsic high-level resistance to rare-earth oxides and oxyanions in members of the class Proteobacteria: Characterization of tellurite, selenite and rhodium sesquioxide reduction in Rhodobacter sphaeroides. J. Bacteriol. 174: 1505-1514.
22. T: An essential metabolic gene function encoded on chromosome II. J. Bacteriol. 179: 7617-7624.
23. Neidle, E. and Kaplan, S. 1993. Expression of the Rhodobacter sphaeroides 2.4.1 hemA and hemT gebes encoding two aminolevulinic acid synthase isozymes. J. Bacteriol. 175: 2292-2303.
24. Perna, N.T., Plunkett III, G., Burland, V., Mau, B., Glasner, J.D., Rose, D.J., Mayhew, G.F., Evans, P.S., Gregor, J., Kirpatrick, H.A., et al. 2000. Genome sequence of entrohemorrhagic Escherichia coli O157: H7. Nature 409: 529-533.
25. Schwartz, D.C. and Cantor, C.R. 1984. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37: 67-75.
26. Sensen, C.W. 1999. Sequencing microbial genomes. In Organization of the prokaryotic genome (ed. R.L. Charlebois), pp. 1-9. ASM Press, Washington, D.C.
27. Soderlund, C., Longden, I., and Mott, R. 1997. FPC: A system for building contigs from restriction fingerprinted clones. Comput. Appl. Biosci. 13: 523-535.
28. Suwanto, A. and Kaplan, S. 1989a. Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: Presence of two unique circular chromosomes. J. Bacteriol. 171: 5850-5859.
29. Suwanto, A. and Kaplan, S. 1989b. Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: Genome size, fragment identification, and gene localization. J. Bacteriol. 171: 5840-5849.
30. Suwanto, A. and Kaplan, S. 1992. Chromosome transfer in Rhodobacter sphaeroides: Hfr formation and genetic evidence for two unique circular chromosomes. J. Bacteriol. 174: 1135-1145.
31. Yang, D., Oyaizu, Y., Oyaizu, H., Olsen, G.J., and Woese, C.R. 1985. Mitochondrial origins. Proc. Nat. Acad. Sci. 82: 4443-4447.
32. Yeliseev, A.A. and Kaplan, S. 1995. A sensory transducer homologous to the mammalian peripheral-type benzodiazepine receptor regulates photosynthetic membrane complex formation in Rhodobacter sphaeroides 2.4.1. J. Biol. Chem. 270: 21167-21175.
33. Zhou, S., Deng, W., Anatharaman, T.S., Lim, A., Dimalanta, E.T., Wang, J., Wu, T., Tao, C., Creighton, R., Kile, A., et al. 2002. A whole-genome shotgun optical map of Yersinia pestis strain KIM. Appl. Environ. Microbiol. 68: 6321-6331.