Sequence-based physical mapping of complex genomes by whole genome profiling
- Jan van Oeveren1,
- Marjo de Ruiter1,
- Taco Jesse1,
- Hein van der Poel1,
- Jifeng Tang1,
- Feyruz Yalcin1,
- Antoine Janssen1,
- Hanne Volpin1,
- Keith E. Stormo2,
- Robert Bogden2,
- Michiel J.T. van Eijk1 and
- Marcel Prins1,3
- * Corresponding author; email: marcel.prins{at}keygene.com
Abstract
We present Whole Genome Profiling (WGP), a novel next-generation sequencing based physical mapping technology for construction of BAC contigs of complex genomes, using Arabidopsis thaliana as an example. WGP leverages short read sequences derived from restriction fragments of two-dimensionally pooled BAC clones to generate sequence tags. These sequence tags are assigned to individual BAC clones, followed by assembly of BAC contigs based on shared regions containing identical sequence tags. Following in silico analysis of WGP sequence tags and simulation of a map of Arabidopsis chromosome 4 and maize, a WGP map of Arabidopsis thaliana ecotype Columbia was constructed de novo using a six genome equivalent BAC library. Validation of the WGP map using the Columbia reference sequence confirmed that 350 BAC contigs (98%) were assembled correctly, spanning 97% of the 102 Mb calculated genome coverage. We demonstrate that WGP maps can also be generated for more complex plant genomes and will serve as excellent scaffolds to anchor genetic linkage maps and integrate whole genome sequence data.
- Received June 23, 2010.
- Accepted January 26, 2011.
- Copyright © 2011, Cold Spring Harbor Laboratory Press
