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.

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

“…The physical map was made using the Keygene WGP fingerprinting technique (van Oeveren et al, 2011). We generated 192,000 BAC-based Illumina sequence tags from 19,200 BACs from two libraries (EcoRI and MseI) with an average insert size of ;125 kb (giving a total of 32X genome equivalents) (see Supplemental Table 5 online).…”

“…Together, the two libraries equal ;8.8 genome equivalents (4.6 GE CLEH library and 4.2 GE CLEE library) at an estimated haploid genome size of 300 Mb. WGP was performed according to the methods detailed by van Oeveren et al (2011). The resulting FPC map was used in further analysis.…”

A Preliminary Genetic Map in <b><i>Solea senegalensis</i></b> (Pleuronectiformes, Soleidae) Using BAC-FISH and Next-Generation Sequencing

“…Especially for the large genomic regions of repetitive sequences and highly heterozygous genomes, sequencing and assembly will not be easily addressed by NGS alone. Additional tools are therefore needed to provide anchor points to link sequence contigs and to bridge the large repetitive regions [van Oeveren et al, 2011]. Physical maps, especially the physical contig maps constructed based on restriction fragment fingerprints of BAC clones, can provide these anchor points, such as BAC end sequences and markers for genome sequence assembly.…”

Development of the BAC Physical Maps of Wheat Chromosome 6B for Its Genomic Sequencing

“…However, restriction fragment sizes shared randomly between two non-overlapping BACs often lead to chimerical contigs or misassembled BACs particularly in the large and repetitive genomic regions. Whole Genome Profi ling (WGP TM ) is an alternative method for the establishment of the chromosome physical maps developed based on a next-generation sequencingbased technology (van Oeveren et al 2011 ). The effi ciency of WGP on physical mappings of wheat chromosomes has been demonstrated by comparison with that of SNaPshot (Philippe et al 2012 ).…”