Whole-Genome Shotgun Optical Mapping of
            <i>Rhodospirillum rubrum</i>

Reslewic, Susan; Zhou, Shiguo; Place, Mike; Zhang, Yaoping; Briska, Adam; Goldstein, Steve; Churas, Chris; Runnheim, Rod; Forrest, Dan; Lim, Alex; Lapidus, Alla; Han, Cliff; Roberts, Gary P.; Schwartz, David C.

doi:10.1128/aem.71.9.5511-5522.2005

Cited by 64 publications

(60 citation statements)

References 27 publications

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“…For a given alignment, the score is proportional to the log of the length of the alignment, penalized by the differences between the two maps, such that longer, better-matching alignments will have higher scores. The regions of gaps, insertions and deletions were obtained by comparing the ETEC strain H10407 map to the in silico restriction map of E. coli K-12 strain MG1655 using OpGen's MapViewer software, similar to previously reported work (Reslewic et al, 2005).…”

Section: Methodsmentioning

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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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%

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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“…In the present study, repeated attempts to clone inter-operon spacer regions yielded only a single fragment corresponding to a tRNA gene cluster located between rrnI and rrnH in strain 168; spacers corresponding to the rrnJ-rrnW or rrnH-rrnG inter-operon sequences were never found (results not shown). To confirm the number and arrangement of the rRNA operons in strain W23, an ordered NcoI restriction map of its entire genome was created using optical mapping technology (Latreille et al, 2007;Reslewic et al, 2005). The overall sequence assembly for the genome was strongly confirmed, as there were no significant differences in size or order between restriction fragments predicted by in silico analysis and those observed by optical mapping (see Supplementary Fig.…”

Section: Rrna Operons Within the W23 Genomementioning

confidence: 99%

“…An NcoI fragment optical map was prepared for the W23 genome at OpGen Technologies according to methods described previously (Reslewic et al, 2005).…”

Section: Methodsmentioning

confidence: 99%

The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics

Zeigler

2011

Microbiology

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The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics The genome sequence of Bacillus subtilis subsp. spizizenii W23 has been determined. The sequence strongly suggests that W23 is a direct descendant of B. subtilis ATCC 6633. W23 shares a 3.6 Mb core genome with the intensively studied model organism B. subtilis subsp. subtilis 168, and gene order within this core has been strongly conserved. Additionally, the W23 genome has 157 accessory (that is, non-core) genome segments that are not found in 168, while the 168 genome has 141 segments not found in W23. The distribution of sequences similar to these accessory segments among other genomes of the B. subtilis species complex shows that those sequences having entered into the phylogeny of the complex more recently tend to be larger and more AT-rich than those having entered earlier. A simple model can account for these observations, in which parasitic or symbiotic DNAs are transferred into the genome and then are reduced in size and modified in base composition during speciation. INTRODUCTIONStrain W23 holds an important place in the history of Bacillus subtilis genetics. The development of B. subtilis as a bacterial model system began over 60 years ago with the pioneering mutagenesis studies of Burkholder & Giles (1947). Strain 168, a tryptophan auxotrophic mutant isolated in those experiments, was subsequently found to be naturally competent for genetic transformation (Spizizen, 1958). This discovery quickly spawned a research community focused on exploring the genetics and development of this Gram-positive sporeformer and on exploiting its biotechnological potential.In addition to strain 168, a handful of other Burkholder and Giles mutants were also preserved (Spizizen, 1984). One of them, strain 23, was a threonine auxotroph that can readily revert to prototrophy (D. R. Zeigler, unpublished results). Strain W23, believed to be one such revertant, was widely viewed as a 'wild-type' counterpart to strain 168. For several years, W23 served as a 'universal donor' and 168 derivatives as 'universal recipients' for strain construction and genetic mapping (Anagnostopoulos & Spizizen, 1961;Nester & Lederberg, 1961). Evidence gradually accumulated, however, that W23 and 168 were fundamentally different in cell wall composition, resident prophages and genome content (Zeigler et al., 2008). It is now clear that 168 is closely related to -and probably a descendant of -the B. subtilis Marburg strain, which is stocked in the American Type Culture Collection (ATCC) as 6051 T and in the National Collection of Industrial, Marine and Food Bacteria (NCIMB) collection as 3610 T (Srivatsan et al., 2008; Zeigler et al., 2008). It is equally clear that W23 must have arisen from an independent isolate, although its exact origin has remained a mystery (Hemphill & Whiteley, 1975).Strain W23 continues to have relevance for the B. subtilis research community. For example, its c...

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“…Whole-genome mapping (previously referred to as optical mapping by OpGen, Inc.) is a technique that generates high-resolution, ordered restriction maps of whole genomes that can be used to discriminate closely related bacterial strains. The technology has been used to identify macrolevel genomic changes such as inversions, deletions, insertions, and duplications in a bacterial genome (10,12,(20)(21)(22)24). It has also been found useful in closing sequencing gaps and identifying unique sequences in prokaryotes and methylation profiles in eukaryotes (1,4).…”

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confidence: 99%

Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and Clonality

et al. 2012

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cDespite being a clonal pathogen, Staphylococcus aureus continues to acquire virulence and antibiotic-resistant genes located on mobile genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal chromosomal cassette mec (SCCmec) by horizontal gene transfer from other staphylococci. The potential virulence of a S. aureus strain is often determined by comparing its pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing profiles to that of known epidemic or virulent clones and by PCR of the toxin genes. Whole-genome mapping (formerly optical mapping), which is a highresolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that allows comparative analysis across entire bacterial genomes to identify regions of genomic similarities and dissimilarities, including small and large insertions and deletions. We explored whether whole-genome maps (WGMs) of methicillin-resistant S. aureus (MRSA) could be used to predict the presence of methicillin resistance, SCCmec type, and Panton-Valentine leukocidin (PVL)-producing genes on an S. aureus genome. We determined the WGMs of 47 diverse clinical isolates of S. aureus, including well-characterized reference MRSA strains, and annotated the signature restriction pattern in SCCmec types, arginine catabolic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome. WGMs of these isolates accurately characterized them as MRSA or methicillin-sensitive S. aureus based on the presence or absence of the SCCmec motif, ACME and the unique signature pattern for the prophage insertion that harbored the PVL genes. Susceptibility to methicillin resistance and the presence of mecA, SCCmec types, and PVL genes were confirmed by PCR. A WGM clustering approach was further able to discriminate isolates within the same PFGE clonal group. These results showed that WGMs could be used not only to genotype S. aureus but also to identify genetic motifs in MRSA that may predict virulence.

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Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

Cited by 64 publications

References 27 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

The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics

Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and Clonality

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