Data for: Evolution and diversity of the orchid genus Dendrobium

Orchids constitute one of the most diverse families of angiosperms, yet their genome evolution and diversity remain unclear. To thoroughly explore the genome diversity of Dendrobium orchids, we selected representative species from 12 major Dendrobium sections that are the representatives of the genus in terms of life forms (lithophyte or epiphyte), floral morphology, flowering time, geographical distribution, and traditional utility. We first constructed a high-confidence phylogenetic tree and calculated the divergence times using single-copy orthologous families from 27 different plant species. Since whole genome duplication (WGD) and chromosome rearrangement events are considered important factors in genome evolution and speciation, we then investigated WGD events and karyotypic evolution within the Dendrobium genus., 1, The orthologous genes were identified by OrthoFinder (v2.5.4) with default parameters.
2, Based on the previously reported telomere-centric model, the Ancestral Dendrobium Karyotype (ADK) was reconstructed. The karyotype evolutionary trajectories from the ADK to the modern chromosomes were examined using WGDI.
3, The intra-species gene synteny and collinearity were determined by MCScanX., , # Data for: Evolution and diversity of the orchid genus *Dendrobium*

## Description of the data and file structure

The data was collected as part of a supplementary dataset for the study of orchid evolution and diversity. This includes orthogroup data, karyotype reconstruction coordinates, and the data underlying the MCScan WGD calculations.

### Files and variables

#### ./all\_vs\_all.blast.m8.solar.forHC.hcluster.orthougroup.rename.zip

Orthologous genes were identified using OrthoFinder (v2.5.4) with default parameters for 27 species. The content of the file includes the following columns: the first column represents the orthologous group number, the second column indicates the gene number, and the third column contains the gene IDs.

**./karyotype_reconstruction_coordinates.zip**

Based on the previously reported telomere-centric model, the Ancestral Dendrobium Karyotype (ADK) was reconstructed. The karyotype evolutionary trajectories from the ADK to the modern chromosomes were e...