Chromosome-scale assembly of European flax (Linum usitatissimum L.) genotypes and pangenomic analysis provide genomic tools to improve breeding

Decoding the genome of cultivated species is one of the key starting points for supporting marker-assisted selection to accelerate breeding programmes. To date, five to six flax genotypes, including fiber flax, linseed and related wild flax, mainly from Canada, China and Russia, have been sequenced and assembled. But no genome assembly was available for Western European flax cultivar, although France is the world's leading producer of fiber flax (85% of world production). The Canadian oilseed flax cultivars CDC Bethune have been mainly used as reference for studies and breeding activities. The best assembly to date was the Chinese fiber Yiya5 assembly, which had the best metric of all the flax genome assemblies available. Recent analyses have shown that up to 30% of fiber flax reads from different origins do not map to the oilseed genome. Thus, much genetic information could be neglected using the oilseed genome as a reference. In this study, we sequenced, assembled and annotated the genomes of four European flax cultivars (two fiber Bolchoï and Idéo; two oilseed Marquise and Attila) and present the first flax pangenome. ONT Minion long reads sequence data were -assembled using Flye, -polished, validated and organised into hybrid scaffolds using optical map data (Bionano Genomics), and finally anchored into fifteen T2T pseudomolecules for each genotype using the fiber flax Yiya5 assembly. The final genome size reached 437, 441, 442 and 453 Mb for Idéo, Marquise, Attila and Bolchoï, respectively. Approximately 47,000 protein-coding genes were annotated for each genotype. For the first time, a pangenome graph were constructed for ten flax cultivars, including our four assemblies and six publicly available assemblies (CDC Bethune, Longya10 and Line 3896, Heiya-14, Yiya5 and Atlant). The total pangenome graph size was 835.77 Mbp with the core pangenome size of 172.2 Mbp. A total of 74,123 non-redundant orthologous proteins representing panproteome were identified. The pangenome results should be interpreted with caution given the quality of the publicly available genomes. This study with the resources generated, is a step forward for the development of genomic and genetic tools, useful for the improvement of Western European flax characterization and breeding.