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. 2002 Jan 15;30(2):E6.
doi: 10.1093/nar/30.2.e6.

A new approach to genome mapping and sequencing: slalom libraries

Veronika I Zabarovska  1 , Rinat Z Gizatullin, Ali N Al-Amin, Raf Podowski, Alexei I Protopopov, Sven Löfdahl, Claes Wahlestedt, Gösta Winberg, Vladimir I Kashuba, Ingemar Ernberg, Eugene R Zabarovsky
Affiliations

A new approach to genome mapping and sequencing: slalom libraries

Veronika I Zabarovska et al. Nucleic Acids Res. .

Abstract

We describe here an efficient strategy for simultaneous genome mapping and sequencing. The approach is based on physically oriented, overlapping restriction fragment libraries called slalom libraries. Slalom libraries combine features of general genomic, jumping and linking libraries. Slalom libraries can be adapted to different applications and two main types of slalom libraries are described in detail. This approach was used to map and sequence (with approximately 46% coverage) two human P1-derived artificial chromosome (PAC) clones, each of approximately 100 kb. This model experiment demonstrates the feasibility of the approach and shows that the efficiency (cost-effectiveness and speed) of existing mapping/sequencing methods could be improved at least 5-10-fold. Furthermore, since the efficiency of contig assembly in the slalom approach is virtually independent of length of sequence reads, even short sequences produced by rapid, high throughput sequencing techniques would suffice to complete a physical map and a sequence scan of a small genome.

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Figures

Figure 1
Figure 1
General scheme of computer-assisted large scale mapping, using NotI linking and jumping libraries. Arrowheads show the sequenced part of the DNA fragments. In the genomic DNA, the NotI sites are positioned at junctions between the numbered boxes. BamHI sites are indicated by small vertical arrows (8).
Figure 2
Figure 2
The scheme demonstrating the main principle of slalom libraries. R, EcoRI sites; B, BamHI sites. Horizontal arrows show sequenced ends of the clones and vertical arrows designate the position of the restriction sites in the genomic DNA. The end sequences from the R and BR libraries were compared using a suitable computer program (e.g. DNASIS) and assembled by combining the information on the relative positions of slalom clone ends
Figure 3
Figure 3
General scheme showing construction of libraries used in the slalom approach. Different types of clones present in the libraries are shown. R and B represent EcoRI and BamHI sites, respectively.
Figure 4
Figure 4
Simplified slalom library scheme. Small horizontal arrows indicate the sequenced part of the DNA fragments. Red vertical arrows indicate EcoRI sites and blue vertical arrows indicate BamHI sites. Dashed lines designate genomic DNA sequences missing in the RBR library.
Figure 5
Figure 5
Schematic picture of slalom mapping of PAC clone 36b12. (A) Slalom clones in the B library. (B) Restriction map of the PAC clone. (C) The minimal set of overlapping clones established using the slalom type I libraries approach. (D) The minimal set of overlapping clones established using the slalom type II libraries approach. (E) Slalom clones in the RBR or connecting library. (F) Slalom clones in the R library. The vector region in (B) is shown without details. Small blue horizontal arrows indicate sequences generated from BamHI sites and red arrows indicate sequences from EcoRI sites. Vertical arrows indicate BamHI (Bn), EcoRI (Rn), left (End1) and right (End2) ends of the inserts. Vector EcoRI sites are labeled V. Dashed lines designate genomic DNA sequences missing in the connecting RBR library. Fragments printed in yellow were not actually cloned (R2-3 and R11-12).
Figure 6
Figure 6
Schematic picture of slalom mapping of PAC clone 55a10. All designations are as in Figure 5. Clone B6-7 was not recovered from the libraries.
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