DOI: 10.5061/dryad.rxwdbrvjk
title: Data for: Evolution and diversity of the orchid genus Dendrobium

description: 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.
description: 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
 <em>Dendrobium</em> 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.
description: # 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 examined using WGDI.
 **./MCScan_WGD.zip** The intra-species gene synteny and collinearity were
 detected by MCScanX. The content of the file includes the following
 columns: the first column represents the first gene (ID-1) of a syntenic
 gene pair, the second column indicates the position of gene ID-1
 corresponding to the gff file, the third column represents the second gene
 (ID-2) of the syntenic gene pair, the fourth column indicates the position
 of gene ID-2 corresponding to the gff file, and the fifth column
 represents coordinate. ## Code/software OrthoFinder (v2.5.4) -f Database
 OrthoFinder is a fast, accurate, and comprehensive platform for
 comparative genomics. It finds orthogroups and orthologs, infers rooted
 gene trees for all orthogroups, and identifies all of the gene duplication
 events in those gene trees. WGDI -d config WGDI -icl config WGDI -bi
 config WGDI -c config WGDI -bk config WGDI -km config WGDI -k config
 WGDI(v0.6.5) (Whole-Genome Duplication Integrated analysis), a
 Python-based command-line tool that facilitates comprehensive analysis of
 recursive polyploidizations and cross-species genome alignments. ./MCScanx
 dir/species The MCScanX package has two major components: a modified
 version of the MCscan algorithm allowing users to handle MCScan more
 conveniently and to view multiple alignments of syntenic blocks more
 clearly, and a variety of downstream analysis tools to conduct different
 biological analyses based on the synteny data generated by the modified
 MCScan algorithm. ## Access information Not Applicable.