A nearly complete genome assembly of multi-petal jasmine (Jasminum sambac) shed light into the flower variation and adaptability caused by chromosome variation from domestication

The breeding or domestication process involves selecting species with specific traits to create industrial varieties. This leads to varying degrees of structural variation in the original genome. To advance molecular directive breeding, we sequenced the nearly complete genome of Hutou jasmine (Hutou jasmine, Jasminum sambac var. trifoliatum) a highly valued variety known for its multi-petal flowers. The assembled monoploid genome had a size of 495.89 Mb with 25 gaps and 12 double-ended telomeres, 21431 protein-coding genes, further phased into haplotype 1 and 2. Analysis of structural variations revealed that genes involved in energy metabolism and protein transport played key roles in differentiating hutou jasmine from single-petal and double-petal jasmine varieties. Synteny analysis identified two whole-genome duplication events in Hutou jasmine: one recent event shared among Oleaceae plants and the other ancient event shared among dicotyledonous plants. Six HtMADS genes along with HtAP2_9 may collectively contribute to floral development leading to multipetalization. A tail deletion mutation in HtAP2_9 was also found to increase mRNA transcription levels thereby influencing its functional expression. In summary, this high-quality phased genome sequencing of Hutou jasmine provides valuable insights into the genetic basis underlying structural variations and trait formation of cultivated varieties in the genome leading era. • The near complete phased genomes are generated for MP-type jasmine. • Structural variations lead to main phenotypic differences and gene defect of Hutou jasmine. • HtMADS23 and HtAP2_4 may be the core factors into the high multipetalization of flowers.