2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2015
Abstrakt

John Huddleston, Swati Ranade, Maika Malig, Francesca Antonacci, Mark Chaisson, Lawrence Hon, Peter H. Sudmant, Tina A. Graves, Can Alkan, Megan Y. Dennis, Richard K. Wilson, Stephen W. Turner, Jonas Korlach, Evan E. Eichler. Reconstructing complex regions of genomes using long-read sequencing technology. Genome research, 24(4):688-696. 2014.

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Abstract:

Obtaining high-quality sequence continuity of complex regions of recent segmental
duplication remains one of the major challenges of finishing genome assemblies.
In the human and mouse genomes, this was achieved by targeting large-insert
clones using costly and laborious capillary-based sequencing approaches. Sanger
shotgun sequencing of clone inserts, however, has now been largely abandoned,
leaving most of these regions unresolved in newer genome assemblies generated
primarily by next-generation sequencing hybrid approaches. Here we show that it
is possible to resolve regions that are complex in a genome-wide context but
simple in isolation for a fraction of the time and cost of traditional methods
using long-read single molecule, real-time (SMRT) sequencing and assembly
technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC
clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31,
demonstrating 99.994% identity to Sanger assemblies of the same clones. We
targeted 44 differences using Illumina sequencing and find that PacBio and Sanger
assemblies share a comparable number of validated variants, albeit with different
sequence context biases. Finally, we targeted a poorly assembled 766-kbp
duplicated region of the chimpanzee genome and resolved the structure and
organization for a fraction of the cost and time of traditional finishing
approaches. Our data suggest a straightforward path for upgrading genomes to a
higher quality finished state.