Data for manuscript "Phylogenomics provides insights into the phylogeny of Liliales and the evolution of colchicine biosynthesis genes"

In this study, we focus on the phylogeny of Liliales and the evolution of genes involved in colchicine biosynthesis. The datasets are as follows:01_allsample_cdspep.7z – Includes the CDS and PEP files from transcriptome assemblies and annotations of 210 samples. Detailed sample information is provided in Supporting tables.txt.02Treeshrink_DISCO_seq_tre.7z – Includes 801 orthologous gene sequence FASTA files and corresponding tree files after removing abnormal branch lengths using TreeShrink v.1.3.9. Each tree has an associated name file listing the full taxon names.03_raxml_astral_tre.7z – Includes two phylogenetic trees: the RAxML tree inferred from the concatenated sequences of the 801 orthologs, and the ASTRAL tree inferred from the 801 individual ortholog trees. Both trees have corresponding name files with the full taxon names.04_19genes_colchicine_biosynthesis.7z – Includes 19 genes involved in colchicine biosynthesis.05_divergence_time.7z – Includes the treePL configuration files for divergence time estimation of Liliales and the resulting dated phylogenetic tree.06_Supplementary_figures S23-41.pdf – Includes phylogenetic trees for genes in the colchicine biosynthesis pathway.We will make every effort to upload our raw data to public databases, allowing other researchers to benefit from it.If you have any questions, please contact Ling-Yun Chen: [e-mail]