BioNano Optical Map Improves the Flax Reference Genome

The flax genome, first sequenced in 2012 using short reads, was assembled into 3,852 scaffolds larger than 1Kb covering a total of 300Mb. A number of genomic resources were developed to assign, order and orient the scaffolds by chromosomes. These included a physical map generated from 43K BAC clones assembled into 419 FPC contigs, 54Mb of BAC-end sequences, three genetic maps with >100K SNPs and 770 SSRs and the resequencing of 407 flax accessions which yielded 1.7M SNPs. Using these resources, a total of 768 scaffolds were refined and assigned to 15 linkage groups. To further improve the assembly, we recently constructed an optical map using BioNano technology. A total of 82Gb of raw DNA molecules were obtained representing more than 200x genome equivalent with N50 of 249 Kb. These raw molecules were assembled into 251 contigs with an improved N50 of 2.15 Mb and a total size of 317 Mb. The optical map was particularly useful for orienting scaffolds of the reference assembly. To date, a total of 286 Mb of scaffold sequences were anchored to 317 Mb BioNano map, covering 97% of all predicted genes of the WGS assembly. The draft pseudomolecules contained ~330 Mb of sequences (including gaps) with linkage groups varying in sizes from 13.8 to 25.1 Mb.