Chromosome‐scale pseudomolecules refined by optical, physical and genetic maps in flax

Abstract

Genomes of varying sizes have been sequenced with next-generation sequencing platforms. However, mostreference sequences include draft unordered scaffolds containing chimeras caused by mis-scaffolding. A Bio-Nano genome (BNG) optical map was constructed to improve the previously sequenced flax genome (LinumusitatissimumL., 2n=30, about 373 Mb), which consisted of 3852 scaffolds larger than 1 kb and totalling300.6 Mb. The high-resolution BNG map of cv. CDC Bethune totalled 317 Mb and consisted of 251 BNG con-tigs with an N50 of 2.15 Mb. A total of 622 scaffolds (286.6 Mb, 94.9%) aligned to 211 BNG contigs(298.6 Mb, 94.2%). Of those, 99 scaffolds, diagnosed to contain assembly errors, were refined into 225 newscaffolds. Using the newly refined scaffold sequences and the validated bacterial artificial chromosome-based physical map of CDC Bethune, the 211 BNG contigs were scaffolded into 94 super-BNG contigs (N50of 6.64 Mb) that were further assigned to the 15 flax chromosomes using the genetic map. The pseudo-molecules total about 316 Mb, with individual chromosomes of 15.6 to 29.4 Mb, and cover 97% of the anno-tated genes. Evidence from the chromosome-scale pseudomolecules suggests that flax has undergonepalaeopolyploidization and mesopolyploidization events, followed by rearrangements and deletions orfusion of chromosome arms from an ancient progenitor with a haploid chromosome number of eight.