High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping

Abstract

Large insert clone libraries have been the primary resource used for the physical mapping of the human genome. Research directions in the genome community now are shifting direction from purely mapping to large-scale sequencing, which in turn, require new standards to be met by physical maps and large insert libraries. Bacterial artificial chromosome libraries offer enormous potential as the chosen substrate for both mapping and sequencing studies. Physical mapping, however, has come under some scrutiny as being ''redundant'' in the age of large-scale automated sequencing. We report the development and applications of nonelectrophoretic, optical approaches for high-resolution mapping of bacterial artificial chromosome that offer the potential to complement and thereby advance large-scale sequencing projects.

Optical maps distinguish individual strains of Escherichia coli O157 : H7

“…Optical mapping, which can scan and assess the architecture of complete bacterial genomes, thus should prove useful for comparative genomics as well as for epidemiology and microbial forensics (Cai et al, 1998). Optical mapping was pivotal in closing the genome sequence of E. coli O157 : H7 EDL933 (Lim et al, 2001), and its value was further underscored when optical maps were used to compare particular subtypes of Shigella with a sequenced strain (Zhou et al, 2004).…”

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 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).…”

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

“…New map construction algorithms were developed that specifically deal with problems encountered in working with BAC clones as compared with cosmid clones (Anantharaman et al 1997;Jing et al 1998). Algorithms were constructed that modeled errors unique to large insert clones; these included increased DNA breakage and an increased number of small DNA map fragments (see Advancements in Map Construction Techniques in the Methods section below).…”

“…The most significant improvement in our system is the development of an automated mapmaking function. Previously (Cai et al 1998) mapmaking required the use of spreadsheet programs to calculate average fragment lengths, a time-consuming process that is now done automatically. Further refinements have also made optical mapping more efficient, including development of more consistent mapping surfaces (trimethyl/vinyl silanes with acrylamide overlay), the ability to analyze multiple BACs per optical mapping surface, and the automatic determination of clone contigs.…”

“…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.…”