Near telomere-to-telomere genome assemblies of flax reveal a lineage-specific DNA transposon that reshaped its chromosome architecture

Chromosome number variation and structural reorganization are fundamental drivers of plant evolution, yet the genomic mechanisms underlying these processes remain incompletely understood, largely due to fragmented representation of repetitive chromosome regions in available genome assemblies. The Linum genus exhibits exceptional karyotypic diversity (n = 7–43), providing a remarkable system for investigating chromosome evolution. Here, we generated near telomere-to-telomere (T2T) genome assemblies for four representative Linum species, including cultivated flax (L. usitatissimum cv. CDC Bethune; n = 15), its wild progenitor (L. bienne; n = 15), and two closely related species (L. decumbens and L. grandiflorum; n = 8). Together with the previously published genomes of L. lewisii (n = 9) and L. tenue (n = 10), these assemblies enabled a comprehensive reconstruction of chromosome evolution across six Linum species representing major evolutionary lineages of the genus. Phylogenomic and duplication analyses revealed a shared ancestral whole-genome duplication (WGD) associated with the n = 9 karyotype, followed by multiple lineage-specific WGDs and divergent diploidization trajectories. Remarkably, the transition between n = 8 and the derived n = 15 flax lineages occurred without expansion of total chromosome length, and was accompanied by genome size reduction, indicating extensive internal chromosome restructuring rather than simple genome duplication. Comparative repeat analyses revealed that this restructuring was associated with the lineage-specific expansion of the single DNA transposon family TE_00003234 (hAT superfamily), which accounts for ~14% of the genomes of L. bienne and L. usitatissimum, but is nearly absent from other Linum species. This element is concentrated in expansive pericentromeric regions characterized by low gene and single nucleotide polymorphism (SNP) densities, suppressed recombination, segregation distortion, and extensive synteny disruptions. Taken together, these findings reveal an unconventional mechanism of chromosome evolution in which lineage-specific DNA transposon expansion remodeled pericentromeric architecture and facilitated large-scale chromosome restructuring following polyploidization. The near-T2T genome assemblies generated here provide a complete genomic framework for studying chromosome evolution, and offer an important reference resource for flax genetics, genomics, and breeding. The CDC Bethune v3.0 assembly specifically replaces the previous L. usitatissimum reference genome assembly, offering a nearly complete coordinate system for the community.