Genome evolution and diversity in the orchid genus Dendrobium

Dendrobium orchids, one of the largest orchid genera, exhibit highly diverse morphological forms with ornamental and medicinal values. So far, the genome evolution and diversity have been scarcely explored in the orchid family. Here we analyze chromosome-scale de novo assembled genomes of 17 Dendrobium accessions spanning 12 sections, representing a broad spectrum of phenotypes, lineages, and geographical distributions. We first perform haplotype-resolved genome analysis of a Dendrobium hybrid and uncover heterosis in the heterozygous genome, demonstrating the significance of diverse ancestry. At Dendrobium genus-wide scale, we further elucidate phylogenetic relationships, evolutionary dynamics, entire gene repertoire, and the mechanisms of preserving ancient genetic variants and rapid recent genome evolution for habitat adaption. We also showcase distinctive evolutionary trajectories in MADS-box and PEBP families over 28 MYA. These results considerably contribute to unearthing the mystery of orchid origin, evolution, and diversification, laying the foundation for efficient use of genetic diversity in orchid breeding.