Whole-Genome Shotgun Optical Mapping of
            <i>Deinococcus radiodurans</i>

Lin, Jun-Hsiang; Qi, Rong; Aston, Christopher E.; Jing, Junping; Anantharaman, Thomas; Mishra, Bud; White, Owen; Daly, Michael J.; Minton, Kenneth W.; Venter, J. Craig; Schwartz, David C.

doi:10.1126/science.285.5433.1558

Cited by 175 publications

(149 citation statements)

References 28 publications

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“…Through repeated overlapping of molecules, the assembler reconstructs the ordered restriction map of the genome. This technique has been previously applied to map other bacterial genomes (Lai et al, 1999;Lim et al, 2001;Lin et al, 1999). The map alignments between two different strains were generated with a dynamic programming algorithm based upon previous methods (Myers & Huang, 1992;Tang & Waterman, 2001;Waterman et al, 1984).…”

Section: Methodsmentioning

confidence: 99%

“…The unique ETEC-specific chromosomal sequences can be compared with and annotated in relation to the sequenced enteropathogenic E. coli (EPEC), EHEC, UPEC and Shigella strains (Diatchenko et al, 1996;Winstanley, 2002). Another novel technique to compare two related genomes is optical mapping, which generates high-resolution ordered restriction maps from single DNA molecules including whole bacterial chromosomes (Cai et al, 1998;Lin et al, 1999), and provides a powerful approach to comparative genomic analysis. Comparison of an optical map of a strain with in silico restriction maps of closely related sequenced strains reveals major genomic structural variations such as deletions, inversions, translocations, duplications and gross rearrangements (Zhou et al, 2004a).…”

Section: Introductionmentioning

confidence: 99%

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Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12

2006

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Enterotoxigenic Escherichia coli (ETEC) is a primary cause of diarrhoea in infants in developing countries and in travellers to endemic regions. While several virulence genes have been identified on ETEC plasmids, little is known about the ETEC chromosome, although it is expected to share significant homology in backbone sequences with E. coli K-12. In the absence of genomic sequence information, the subtractive hybridization method and the more recently described optical mapping technique were carried out to determine the degree of genomic variation between virulent ETEC strain H10407 and the non-pathogenic E. coli K-12 strain MG1655. In one round of PCRbased suppression subtractive hybridization, 153 fragments representing sequences unique to strain H10407 were identified. BLAST searches indicated that few unique sequences showed homology to known pathogenicity island genes identified in related E. coli pathogens. A total of 65 fragments contained sequences that were either linked to hypothetical proteins or showed no homology to any known sequence in the database. The remaining sequences were either phage or prophage related or displayed homology to classifiable genes that function in various aspects of bacterial metabolism. The 153 unique sequences showed variable distribution across different ETEC strains including ETEC strain B7A, which is attenuated in virulence and lacked several H10407-specific sequences. Restriction-enzyme-based optical maps of strain H10407 were compared to in silico restriction maps of strain MG1655 and related E. coli pathogens. The 5?1 Mb ETEC chromosome was~500 kb greater in length than the chromosome of E. coli K-12, collinear with it and indicated several discrete regions where insertions and/or deletions had occurred relative to the chromosome of strain MG1655. No major inversions, transpositions or gross rearrangements were observed on the ETEC chromosome. Based on comparisons with known genomic sequences and related optical-map-based restriction site similarity, the sequence of the H10407 chromosome is expected to demonstrate~96 % identity with that of E. coli K-12.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12

2006

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“…Ionizing radiation induces DNA double-stranded breaks (DSBs) that are the most lethal form of DNA damage (3). After acute exposures to 10 kGy, early stationary phase (ESP) DEIRA can reassemble its 3.285-Mbp genome, which consists of four haploid genomic copies per cell (4), from hundreds of DNA DSB fragments without lethality or induced mutagenesis (5,6). Also remarkable is DEIRA's ability to grow at 60 Gy͞h without any discernable effect on its growth rate (7).…”

mentioning

confidence: 99%

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Liu

Zhou

Omelchenko

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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356

414

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Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering Ϸ94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA, which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.T he Gram-positive aerobic bacterium Deinococcus radiodurans R1 (DEIRA) has an extraordinary resistance to ␥-radiation and a wide range of other DNA-damaging conditions, including desiccation and oxidizing agents (1, 2). Ionizing radiation induces DNA double-stranded breaks (DSBs) that are the most lethal form of DNA damage (3). After acute exposures to 10 kGy, early stationary phase (ESP) DEIRA can reassemble its 3.285-Mbp genome, which consists of four haploid genomic copies per cell (4), from hundreds of DNA DSB fragments without lethality or induced mutagenesis (5, 6). Also remarkable is DEIRA's ability to grow at 60 Gy͞h without any discernable effect on its growth rate (7). Because most organisms, generally, can tolerate so few DSBs (8), radiationinduced DSBs and their repair have been difficult to study. In DEIRA, however, there are so many DSBs in fully viable irradiated cells after high-dose irradiation that the steps in DSB repair can be monitored directly in mass culture (5, 9-11). This characteristic has been exploited and used to examine the timing of DNA recombination (5, 10, 12) after high-dose irradiation and has revealed the sequential action of RecA-independent and -dependent pathways during repair (11).Comparative genomic and experimental analyses support the view that DEIRA's extreme radiation resistance phenotype is complex, likely determined collectively by an assortment o...

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“…Also, automated focusing and image tiling programs have made image acquisition an essentially user-independent task. The rapid evolution of optical mapping and its application to analysis of both cloned and genomic DNA Lin et al 1999) presents us with the possibility of creating, in the near future, complete restriction maps of large genomes or whole clone libraries in a time-and laborefficient way.…”

Section: Discussionmentioning

confidence: 99%

“…Substrates for optical mapping range from long-range PCR products (Skiadas et al 1999), cloned DNA including cosmids and BAC clones (Cai et al 1998;Jing et al 1998), to genomic DNA from microorganisms Lin et al 1999) as well as from humans. The unique capability of optical mapping to create high-resolution multienzyme ordered restriction maps of DNA molecules affords us the opportunity to accurately characterize cloned DNA templates containing potentially confusing arrangements of repetitive coding and noncoding sequences.…”

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confidence: 99%

Optical Mapping of BAC Clones from the Human Y Chromosome DAZ Locus

Giacalone¹,

Delobette²,

Gibaja³

et al. 2000

Genome Res.

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The accurate mapping of clones derived from genomic regions containing complex arrangements of repeated elements presents special problems for DNA sequencers. Recent advances in the automation of optical mapping have enabled us to map a set of 16 BAC clones derived from the DAZ locus of the human Y chromosome long arm, a locus in which the entire DAZ gene as well as subsections within the gene copies have been duplicated. High-resolution optical mapping employing seven enzymes places these clones into two contigs representing four distinct copies of the DAZ gene and highlights a number of differences between individual copies of DAZ.

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Whole-Genome Shotgun Optical Mapping of Deinococcus radiodurans

Cited by 175 publications

References 28 publications

Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12

Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12

Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation

Optical Mapping of BAC Clones from the Human Y Chromosome DAZ Locus

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