Insights into the Origin and Local Adaptation Evolution of the Cultivated Sesame with Telomere-to-Telomere High-Quality Genome

Sesame (Sesamum indicum L., 2n = 26) is one of the oldest oilseed crops and is often called the 'queen of oilseeds' due to its high content of unsaturated fatty acids and natural antioxidants. Despite its long history, the origin and global spread of cultivated sesame remain unresolved. We assembled a telomere-to-telomere (T2T), high-quality reference genome of sesame (cv. Yuzhi11) to investigate sequence differences between genomes and its origin and the local adaptation evolution of flowering time (DF). We generated a 305 Mb T2T sesame reference genome (cv. Yuzhi11) with > 99.99% base-level accuracy, identifying 31 063 protein-coding genes. Repetitive elements accounted for 52.03% of the genome. Population genomic analysis of 927 accessions from 14 regions identified four major groups. Integrative analyses of linkage disequilibrium decay (LD), nucleotide diversity (π), and fixation index (FST) support East Africa as the center of origin, with subsequent migration through the Middle East, to South Asia, South-East Asia, East Asia and ultimately to other parts of the world. Genome-wide association studies (GWAS) and selection scans identified 30 genes associated with flowering time. SiUBP16 is a candidate associated with 7.6% of DF variation. Early-flowering accessions carried up to 225 favourable alleles. A flowering time prediction model for high-latitude regions achieved 96% accuracy. We present a high-quality T2T reference genome for cultivated sesame, shedding light on its origin, evolutionary history, and regional flowering time adaptation. This genome insights valuable tools for breeding programs aimed at improving yield and environmental adaptation in sesame and related crops.