RT Journal
A1 van Oeveren, Jan
A1 de Ruiter, Marjo
A1 Jesse, Taco
A1 van der Poel, Hein
A1 Tang, Jifeng
A1 Yalcin, Feyruz
A1 Janssen, Antoine
A1 Volpin, Hanne
A1 Stormo, Keith E.
A1 Bogden, Robert
A1 van Eijk, Michiel J.T.
A1 Prins, Marcel
T1 Sequence-based physical mapping of complex genomes by whole genome profiling
JF Genome Research 
JO Genome Research 
YR 2011 
FD April 01 
VO 21 
IS 4 
SP 618 
OP 625 
DO 10.1101/gr.112094.110 
UL http://genome.cshlp.org/content/21/4/618.abstract 
AB We present whole genome profiling (WGP), a novel next-generation sequencing-based physical mapping technology for construction of bacterial artificial chromosome (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.