A chromosome-scale genome of wild sesame Sesamum alatum reveals 3D chromatin and seed-quality divergence from cultivated sesame

Wild Sesamum species provide valuable resources for investigating genome evolution and seed-quality divergence within the genus. Here, an improved 541.11-Mb chromosome-scale reference genome of Sesamum alatum was generated, with a contig N50 of 8.74 Mb and 98.65% of the assembly anchored to 13 pseudochromosomes. Comparative genomic analyses placed S. alatum as an early-diverging lineage among the sampled Sesamum species and showed that its high transposable element content was mainly associated with the accumulation of long terminal repeat retrotransposons. Comparative high-throughput chromosome conformation capture (Hi-C) analysis further revealed distinct transposable element coverage around orthologous genes with conserved or switched compartment states, indicating an association between local transposable element distribution and chromatin compartment divergence. The evolution of sesamin biosynthesis related CYP81Q genes was also examined across representative Lamiales species. Microsynteny analysis showed that the CYP81Q3 locus is conserved in S. alatum , whereas molecular docking suggested that amino acid substitutions near key substrate-recognition sites, rather than loss of the locus, are associated with the absence of sesamin biosynthesis in S. alatum . Seed transcriptome comparisons further showed that genes downregulated during late seed development were enriched in lipid biosynthesis-related pathways, which may be associated with the lower seed oil content of S. alatum . This study provides an improved genomic resource for S. alatum and the first comparative Hi-C analysis within Sesamum , advancing our understanding of three-dimensional genome evolution and seed-quality divergence in sesame.