Integration of WGS Assembly with Physical and Genetic Maps for the Sunflower

Sunflowers are an economically important crop, producing edible oil for cooking or biodiesel, or whole seeds for confectionary purposes. Some varieties exhibit a woody stem suitable for wood pulp production. Currently, no complete, publicly-available reference genome exists for the sunflower or other members of the Compositae family, which include agricultural, medicinal, and noxious plants. We generated chromosome pseudomolecules for the sunflower by anchoring Whole Genome Shotgun (WGS) assembly scaffolds onto all its 17 chromosomes. The chromosomal anchors were obtained through alignment of physical map tags onto a genetic map. Whole Genome Profiling resulted in 20-30bp physical map tags interspersed roughly every 5-6kb within a BAC. SNP segregation patterns found within sequence reads for 96 Recombinant Inbred Lines (RILS) determined genetic map bins in which WGS contigs containing the SNPs were placed. New Perl modules were developed to handle the map integration and chromosomal anchoring in an automated fashion, validating the physical map against the genetic map, ordering and orientating WGS assembly scaffolds, and merging overlapping WGS scaffolds. Custom C++ packages were added to FPC (FingerPrinted Contig) software to split physical map contigs based on conflicting alignments with genetic map markers. Results demonstrate the utility of ultra-high density genetic maps along with sequence-based physical map information, to assemble large eukaryotic genomes based on whole-genome shotgun sequence.