A new approach to genome mapping and sequencing: slalom libraries.
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.
Zabarovska
Veronika I
VI
Microbiology and Tumor Biology Center, Karolinska Institute, 171 77 Stockholm, Sweden.
Gizatullin
Rinat Z
RZ
Al-Amin
Ali N
AN
Podowski
Raf
R
Protopopov
Alexei I
AI
Löfdahl
Sven
S
Wahlestedt
Claes
C
Winberg
Gösta
G
Kashuba
Vladimir I
VI
Ernberg
Ingemar
I
Zabarovsky
Eugene R
ER
D022222:Chromosomes, Artificial, Human / Q000235:genetics / Q000378:metabolism; D003001:Cloning, Molecular; D015245:Deoxyribonuclease BamHI / Q000378:metabolism; D015246:Deoxyribonuclease EcoRI / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D015723:Gene Library; D016678:Genome; D015894:Genome, Human; D023281:Genomics / Q000191:economics / Q000379:methods*; D006801:Humans; D020161:Physical Chromosome Mapping / Q000191:economics / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D015183:Restriction Mapping; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D013997:Time Factors
D015245:Deoxyribonuclease BamHI; D015246:Deoxyribonuclease EcoRI; D015252:Deoxyribonucleases, Type II Site-Specific; C038565:GCGGCCGC-specific type II deoxyribonucleases