title: Sequence-based physical mapping of complex genomes by whole genome profiling.
abstract: 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.
authors.affiliation: Keygene N.V., Wageningen, The Netherlands.
authors.forename: Jan
authors.initials: J
authors.lastname: van Oeveren
authors.forename: Marjo
authors.initials: M
authors.lastname: de Ruiter
authors.forename: Taco
authors.initials: T
authors.lastname: Jesse
authors.forename: Hein
authors.initials: H
authors.lastname: van der Poel
authors.forename: Jifeng
authors.initials: J
authors.lastname: Tang
authors.forename: Feyruz
authors.initials: F
authors.lastname: Yalcin
authors.forename: Antoine
authors.initials: A
authors.lastname: Janssen
authors.forename: Hanne
authors.initials: H
authors.lastname: Volpin
authors.forename: Keith E
authors.initials: KE
authors.lastname: Stormo
authors.forename: Robert
authors.initials: R
authors.lastname: Bogden
authors.forename: Michiel J T
authors.initials: MJ
authors.lastname: van Eijk
authors.forename: Marcel
authors.initials: M
authors.lastname: Prins
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D019295:Computational Biology; D020451:Contig Mapping; D018745:Genome, Plant / Q000235:genetics*; D015698:Genomic Library; D059014:High-Throughput Nucleotide Sequencing