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

Rhodobacter sphaeroides 2.4.1 is a facultative photoheterotrophic bacterium with tremendous metabolic diversity, which has significantly contributed to our understanding of the molecular genetics of photosynthesis, photoheterotrophy, nitrogen fixation, hydrogen metabolism, carbon dioxide fixation, taxis, and tetrapyrrole biosynthesis. To further understand this remarkable bacterium, and to accelerate an ongoing sequencing project, two whole-genome restriction maps (EcoRI and HindIII) of R. sphaeroides strain 2.4.1 were constructed using shotgun optical mapping. The approach directly mapped genomic DNA by the random mapping of single molecules. The two maps were used to facilitate sequence assembly by providing an optical scaffold for high-resolution alignment and verification of sequence contigs. Our results show that such maps facilitated the closure of sequence gaps by the early detection of nascent sequence contigs during the course of the whole-genome shotgun sequencing process.

[1]  David C. Schwartz,et al.  Genomics via Optical Mapping III: Contiging Genomic DNA , 1998, ISMB.

[2]  S. Kaplan,et al.  Intracytoplasmic membrane synthesis in synchronous cell populations of Rhodopseudomonas sphaeroides. Fate of "old" and "new" membrane. , 1978, The Journal of biological chemistry.

[3]  S Kaplan,et al.  Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome. , 1997, Microbiology.

[4]  S. Kaplan,et al.  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 , 1992, Journal of bacteriology.

[5]  S Kaplan,et al.  Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes , 1989, Journal of bacteriology.

[6]  E. Dimalanta,et al.  A Whole-Genome Shotgun Optical Map of Yersinia pestis Strain KIM , 2002, Applied and Environmental Microbiology.

[7]  C R Woese,et al.  Mitochondrial origins. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[8]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[9]  T. Anantharaman,et al.  High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[10]  O. White,et al.  Whole-genome shotgun optical mapping of Deinococcus radiodurans. , 1999, Science.

[11]  D. Schwartz,et al.  Optical mapping of lambda bacteriophage clones using restriction endonucleases , 1995, Nature Genetics.

[12]  D. Schwartz,et al.  Optical mapping: an approach for fine mapping. , 1999, Methods in enzymology.

[13]  Carol Soderlund,et al.  FPC: a system for building contigs from restriction fingerprinted clones , 1997, Comput. Appl. Biosci..

[14]  S Kaplan,et al.  Multiple chromosomes in bacteria: structure and function of chromosome II of Rhodobacter sphaeroides 2.4.1T , 1994, Journal of Bacteriology.

[15]  Sequencing Microbial Genomes , 1999 .

[16]  W. R. Sistrom,et al.  The photosynthetic bacteria , 1978 .

[17]  D. Schwartz,et al.  Optical mapping and its potential for large-scale sequencing projects. , 1999, Trends in biotechnology.

[18]  R. Wilson,et al.  High throughput fingerprint analysis of large-insert clones. , 1997, Genome research.

[19]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[20]  Judith P. Armitage,et al.  The home stretch, a first analysis of the nearly completed genome of Rhodobacter sphaeroides 2.4.1 , 2004, Photosynthesis Research.

[21]  D. Schwartz,et al.  Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis , 1984, Cell.

[22]  R. Herrmann,et al.  B4 – PHYSICAL AND GENETIC MAPPING , 1995 .

[23]  J. Venter,et al.  Optical mapping of Plasmodium falciparum chromosome 2. , 1999, Genome research.

[24]  David C. Schwartz,et al.  A shotgun optical map of the entire Plasmodium falciparum genome , 1999, Nature Genetics.

[25]  E. Dimalanta,et al.  Shotgun optical maps of the whole Escherichia coli O157:H7 genome. , 2001, Genome research.

[26]  S Kaplan,et al.  Characterization of genes encoding dimethyl sulfoxide reductase of Rhodobacter sphaeroides 2.4.1T: an essential metabolic gene function encoded on chromosome II , 1997, Journal of bacteriology.

[27]  S. Kaplan,et al.  A Sensory Transducer Homologous to the Mammalian Peripheral-type Benzodiazepine Receptor Regulates Photosynthetic Membrane Complex Formation in Rhodobacter sphaeroides 2.4.1 (*) , 1995, The Journal of Biological Chemistry.

[28]  S Kaplan,et al.  Chromosome transfer in Rhodobacter sphaeroides: Hfr formation and genetic evidence for two unique circular chromosomes , 1992, Journal of bacteriology.

[29]  T. Donohue,et al.  Function of a glutathione-dependent formaldehyde dehydrogenase in Rhodobacter sphaeroides formaldehyde oxidation and assimilation. , 1998, Biochemistry.

[30]  E. Neidle,et al.  Expression of the Rhodobacter sphaeroides hemA and hemT genes, encoding two 5-aminolevulinic acid synthase isozymes , 1993, Journal of bacteriology.