Data for: Evolution and diversity of the orchid genus Dendrobium

Zhang, Bin1 ; Li, Yan2 ; Yu, Hao2

Published Dec 11, 2024 on Dryad. https://doi.org/10.5061/dryad.rxwdbrvjk

Data files

Dec 11, 2024 version files 4.76 MB

all_vs_all.blast.m8.solar.forHC.hcluster.orthougroup.rename.zip
3.14 MB
karyotype_reconstruction_coordinates.zip
1.92 KB
MCScan_WGD.zip
1.61 MB
README.md
2.57 KB

Abstract

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.

README: 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.