Towards a Sugar Beet Reference Genome Using Optical Mapping

At SESVanderHave a double haploid O-type line was chosen for building a sugar beet reference sequence using mate pair and paired-end sequencing. Total genome assembly covers 531 million bases (Mb), corresponding to 70% of the estimated sugar beet genome size. Fifty percent of the scaffolds have a length longer than 913 kilobases (kb), and up to 90% of the genome assembly is contained in 644 scaffolds. The majority of these scaffolds have been anchored to the nine sugar beet chromosomes through the development and mapping of SNP markers. However using this strategy short scaffolds could either not be anchored to the genetic linkage map, or if they could be anchored they could not be oriented. Moreover scaffolds in our genome sequence often ended at the same point as in other available genome assemblies, suggesting the presence of repetitive or other sequences that would be hard to bridge using next-generation sequencing and the currently available de novo assembly tools . The Irys technology developed by Bionano Genomics aims to build whole genome maps starting from megabase-long labelled DNA molecules. Comparison of these genome maps with our existing genome assembly gives the opportunity to order scaffolds along chromosomes, to determine how they are oriented, as well as to estimate the sizes of any remaining gaps between scaffolds more precisely. We have used this technology with the aim of improving SESVanderHave’s sugar beet genome reference sequence, resolving gap sizes, as well as anchoring orphan scaffolds to the sugar beet chromosomes.