Novel Whole Genome Sequencing Strategy Using Physical Mapping and Local Sequence Assembly

Whole genome reference sequences are very important tools to identify genes controlling traits in a wide variety of species. Yet developing genome-wide physical maps and reference genomes in complex organisms including many commercial crops is technically challenging and costly. We developed Whole Genome Profiling^TM (WGP), a novel next-generation sequencing (NGS)-based physical mapping technology for construction of BAC contigs of complex genomes (van Oeveren et al., Genome Research, 2011). WGP maps are built by sequence-based fingerprinting high coverage (10-12X) BAC libraries, pooled as individual BAC clones in a multi-dimensional format. Sequence tags spaced 2-4 kbp across each BAC clone are generated using short-read Next Generation Sequencing technology and BAC clones are grouped into contigs by overlapping regions with identical sequence tags using a modified version of FPC software.

Following proof of principle in Arabidopsis, we have successfully applied WGP in melon, tomato, potato, lettuce, pepper, Brassicas, cotton, sunflower, tobacco and a number of other genomes.  Results demonstrate that high-quality WGP maps were generated providing excellent scaffolds to integrate WGS data and anchor genetic linkage maps (e.g. melon, tomato).

Most recently, paired-end (pe) WGP was developed to push forward the integration of sequence-based physical BAC maps with de novo genome assembly. Paired-end WGP leverages local contig assembly, and aids in assembly of duplicated and/or repetitive regions, which are abundant in many (polyploid) crops.  

We will provide an overview of WGP and peWGP results obtained in various crops species in the context of de novo genome sequencing of reference genomes.

Keygene N.V. owns patents and patent applications covering its (paired end) WGP and WGP/WGS integration technologies. WGP is a trademark of Keygene N.V.