10.60507/FK2/ZNVSLAChoudhary, NancyNancyChoudhary0000-0002-2562-7905IZMB, University of BonnHagedorn, MarieMarieHagedorn0009-0009-1312-0531IZMB, University of BonnPucker, BoasBoasPucker0000-0002-3321-7471IZMB, University of Bonnbonndata2025Medicine, Health and Life SciencesChoudhary, NancyNancyChoudharyUniversity of BonnBoas Pucker2025-12-152025-12-152025-12-182024-12-26/2025-07-315165249864605608637277122778172213899219206945677053546517406text/csvtext/csvapplication/gziptext/csvapplication/gziptext/csvapplication/gziptext/csvtext/csvtext/plain1.0CC BY 4.0This dataset contains supplementary data supporting the manuscript "Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae". In this large-scale phylogenomics study, we discovered the systemic absence of anthocyanin and proanthocyanidin biosynthesis genes in the Cucurbitaceae family. The structural genes DFR, ANS, arGST, LAR, and ANR, along with the anthocyanin-related regulatory MYB genes were absent in the family, confirmed via synteny and phylogenetic analysis. The dataset includes details about the sources of datasets used in the study, structural annotation details, detailed taxonomic classification results for all datasets, details about genes used for species and gene phylogenies, coding sequences used for individual anthocyanin biosynthesis gene trees (in FASTA format), sources used for flower and fruit colour mapping, structural annotation files, and gene expression data.GeMoMa, 1.9BUSCO, 5.8.1Kraken, 2.1.3Bracken, 2.9kallisto, 0.44Python, 3.11.8