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

Flax is a self-pollinated annual species of the Linaceae family that was domesticated about 7000 years ago for its seed oil and stem fibers. Genetic maps of economically important crops, such as flax, are a valuable resource for plant breeders who use molecular breeding strategies and to study evolution and diversification. Today, it is possible to go beyond mapping and to decipher the DNA sequence of an organism, Here, we used a so-called next generation sequencing method to produce a large amount of DNA sequence from the flax cultivar CDC Bethune. The main caveat to this approach is the short length of the sequences produced by this sequencing method which complicate the ascertainment of their positioning onto chromosomes. To solve this problem, we developed an optical map of the CDC Bethune genome that we combined with genetic maps previously obtained from several crosses. Optical maps are physical maps that provide long-range assembly information. Here, large DNA molecules are digested on open glass surfaces and visualized by fluorescence microscopy to generate ordered restriction maps. This single-molecule system provides signature barcodes, especially useful for the alignment and validation of the short-read sequences. Genetic maps reflect the recombination rates along chromosomes and, as such, provide complementary information to assist in properly assign, assemble and orient the sequence. The three typed of data were analyzed using a suite of bioinformatics analyses to generate the first chromosome-scale sequence of the flax genome. Flax was the first plant genome to be sequenced entirely by a Canadian team. It was the 10th plant genome sequenced and this report is the first of its refinement into 15 ordered and oriented chromosomes.