Pangenome assembly of cultivated flax and pale flax (Linum usitatissimum and L. bienne).

A reference-free graph pangenome for cultivated flax (Linum usitatissimum) and its crop wild relative pale flax (Linum bienne) is presented that reveals structural variation in the clade that will contribute to the study of domestication and agronomic traits. Public genome sequence data from four cultivated flax varieties (CDC Bethune: GCA_000224295.2, Atlant: GCA_030674075.2, Heiya: GCA_010665265.1, Longya: GCA_010665275.2, and one pale flax accession: GCA_010665285.1, was used, as well as newly acquired Hi-C proximity ligation sequencing data for pale flax (PRJEB109795). The pale flax assembly was scaffolded further with the Hi-C data using HapHiC v1.0.6 (https://doi.org/10.1038/s41477-024-01755-3). Each genome assembly was then subjected to homology-based scaffolding against CDC Bethune as a reference using RagTag v2.1 (https://doi.org/10.1186/s13059-022-02823-7) followed by pangenome assembly using PanGenome Graph Builder (PGGB v0.7.2, https://doi.org/10.1038/s41592-024-02430-3).