High Quality Plant Genome Assembly Using PacBio Long Read Whole Genome Sequencing and Short Read Whole Genome Profiling (WGP)TM

We present a de novo assembly of the 450 Mbp melon genome. This assembly was realized through integration of a sequence-based physical map built using Whole Genome Profiling (WGP^TM) with a whole genome sequence (WGS) assembly based on ~44X filtered PacBio reads of 20-kb fragment libraries.  Assembly of the PacBio reads using HGAP (Chin et al., 2013) resulted in 6,332 contigs covering ~400 Mbp of the melon genome with a contig N50 size of 387 kbp.  Subsequently, sequence based physical maps of the melon genome constructed using WGP (van Oeveren et al., 2011) were used for superscaffolding PacBio contigs. WGP maps representing 6X, 8X, 10X and 12X were integrated with  PacBio WGS contigs using a proprietary pipeline. This resulted in 271, 229, 209 and 206 superscaffolds for 6X, 8X, 10X and 12X WGP maps and integration of 349 (87%), 346 (86%), 344 (86%) and 342 (86%) Mbp WGS contigs, respectively. N50 superscaffolds were 2.1 Mbp, 2.4 Mbp, 2.6 Mbp and 2.7 Mbp, respectively.  The over 23-fold smaller number of superscaffolds compared to WGS contigs and over 5-fold larger N50 superscaffold sizes demonstrate the excellent complementarity of PacBio WGS and WGP^TM in de novo genome assembly. This approach is entirely NGS-based and WGP provides access to BACs to utilize the genome assembly for (breeding) research purposes.

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