Haplotype-resolved genome assembly of the colored calla lily (Zantedeschia elliottiana) provides new insights into the evolution of the family Araceae

Abstract The colored calla lily, a member of the genus Zantedeschia in the Araceae family native to South Africa, is a valuable ornamental plant. However, the lack of a high-quality genome has hindered genetic analysis and the identification of key trait-related genes. We successfully assembled a haplotype-resolved genome of the colored calla lily, revealing extensive heterozygosity between homologous chromosomes. Comparative genomics analyses demonstrated that transposon insertions have led to significant differences in genome size among Araceae species. Notably, Araceae species experienced two closely-spaced whole-genome duplication (WGD) events before species divergence. Further analysis revealed that in terrestrial True Araceae species, genes associated with lignin synthase, cellulose synthase, expansin, and sugar transport proteins have undergone expansion, likely contributing to environmental adaptation and tuber starch accumulation. Additionally, we identified a key MIKC C gene that may play a crucial role in spathe development. This study not only elucidates the evolutionary history of Araceae species but also provides valuable data to support functional genomics research and breeding efforts for the colored calla lily.