Genomic basis of scent loss and functional divergence in wild and cultivated carnations (Dianthus spp.)

Domestication reshapes plant genomes and traits, yet the genomic basis of floral scent loss remains unclear. Here, we present an 876 Mb pseudo-chromosome genome assembly of the wild carnation Dianthus broteri (2n = 2x = 30) and compare it with the cultivated D. caryophyllus, which exhibits reduced floral scent. Transposable elements occupy 82.4% of the D. broteri genome, dominated by Gypsy LTRs, whereas D. caryophyllus exhibits more recent insertions near genes, consistent with domestication associated effects. Volatilome profiling of D. broteri revealed 59 floral volatiles, dominated by sesquiterpenoids, with lineage-specific differences in composition. Terpenoid-biosynthesis genes are upregulated in flowers of the scented western lineage, while the weakly scented eastern lineage shows reduced expression of upstream pathway components despite constitutive transcription of some terpene synthases. Variant discovery within terpenoid pathway genes showed that the most highly and constitutively expressed gene, DbrTPS18, accounted for almost 50% of all lineage-specific variants. Several nonsynonymous substitutions in DbrTPS18 were identified within the catalytic domains and the predicted chloroplast transit peptide, and these variants were significantly associated with variation in scent production. These results uncover the basis of terpenoid biosynthesis in the genus Dianthus and, together with the presented reference genome, provides a foundation to explore the genomic consequences of domestication and enhance fragrance in cultivated carnations.