Whole Genome Profiling (WGPTM) 2.0: Sequence-Based Physical BAC Maps with Megabasepair Contigs

Since publication of the WGP technology in 2011 (van Oeveren et al., Genome Research), we have successfully constructed more than 40 WGP maps of plant genomes of highly variable genome size and complexity. Among them crops such as melon, tomato, potato, Brassicas, tobacco, wheat chromosomes and others. These projects clearly demonstrated the versatility and consistent performance of the WGP technology using a single standardized workflow, yielding BAC contigs with N50 values of approximately 500 kb under high stringency assembly conditions. The main utilities of these WGP maps have been in the context of whole genome sequence (WGS) assembly, either by serving as sequence-based framework to build superscaffolds or by selecting minimal tiling paths for BAC-by-BAC sequencing approaches. In addition, the availability of a BAC clone resource is considered indispensible for gene cloning efforts, for example in regions harboring trait-genes.

In order to further strengthen WGP for genome assembly, we developed WGP 2.0 which delivers BAC contigs with N50 contig values in the 3 Mbp range, i.e. at least 5-fold larger than per the original protocol. WGP 2.0 is based on three improvements in the sequence data processing: 1) a proprietary filtering step which removes > 90% of putative chimeric BACs; 2) creation of "SuperBACs"  by pre-clustering BACs sharing high proportions of WGP tags and 3) improved FPC assembly (Philippe et al., BMC Genomics, 2012). In tomato, the combined effect of these adaptations is a 5-fold increase in N50 contig size, decreased numbers of BAC contigs and singletons, and comparable genome coverage. Validation of the accuracy of the WGP 2.0 maps against the tomato reference genome sequence demonstrated a minimal amount of non-contiguous contig coverage, probably resulting from chimeric BAC clones that remained after filtering. Taken together, WGP 2.0 provides significantly improved longe-range sequence-based physical maps, boosting genome sequence assembly efforts.

The WGP^TM technology is protected by patents and patent applications owned by Keygene N.V. WGP is a trademark of Keygene N.V.