This file was generated on 2025-12-15 by Nancy Choudhary A GENERAL INFORMATION 1. Title of the dataset: Supplementary data to "Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae" 2. Brief description of the research project and its aims: This 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 include 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. 3. Author Information A. Investigator Contact Information Name: Nancy Choudhary Institution: Plant Biotechnology and Bioinformatics, Institute for Cellular and Molecular Botany - IZMB, University of Bonn Address: Kirschallee 1, 53115 Bonn, Germany Email: n.choudhary@uni-bonn.de B. Investigator Contact Information Name: Marie Hagedorn Institution: Plant Biotechnology and Bioinformatics, Institute for Cellular and Molecular Botany - IZMB, University of Bonn Address: Kirschallee 1, 53115 Bonn, Germany Email: mhagedo1@uni-bonn.de C. Project Supervisor (Principal Investigator) Contact Information Name: Prof. Dr. Boas Pucker Institution: Plant Biotechnology and Bioinformatics, Institute for Cellular and Molecular Botany - IZMB, University of Bonn Address: Kirschallee 1, 53115 Bonn, Germany Email: pucker@uni-bonn.de D. In case of questions related to this dataset, please contact: Name: Nancy Choudhary Institution: Plant Biotechnology and Bioinformatics, Institute for Cellular and Molecular Botany - IZMB, University of Bonn Address: Kirschallee 1, 53115 Bonn, Germany Email: n.choudhary@uni-bonn.de 4. Date of data collection: 2024-12-26 - 2025-07-31 5. Acknowledgement: This work was supported by the de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) and ELIXIR-DE (Forschungszentrum Jülich and W-de.NBI-001, W-de.NBI-004, W-de.NBI-008, W-de.NBI-010, W-de.NBI-013, W-de.NBI-014, W-de.NBI-016, W-de.NBI-022). 6. Language of the dataset: English B DATA & FILE OVERVIEW The supplementary materials are provided as three additional files and two additional datasets. 1. Files and Folders List: Dataset_sources.csv Description: Sources of genomic and transcriptomic datasets used in the study Gene_annotation_stats.csv Description: Statistics of gene annotation of 82 species and re-annotation of 7 species Kraken_classification.csv Description: Detailed results of Kraken and Bracken classification of all datasets BUSCO_genes_for_species_phylogeny.csv Description: List of BUSCO genes from eudictoyledons_odb12 lineage used for coalescence and concatenation-based species phylogeny Fruit_flower_colour_sources.csv Description: Links to websites used as reference for mapping fruit and flower colours used in Figure 2. Bait_sequences_gene_trees.csv Description: List of reference sequences used for phylogenetic trees Gene_Annotation_dataset/ Ampelosycios_bosseri/ Ampelosycios_bosseri.cds.fa Ampelosycios_bosseri.gff3 Ampelosycios_bosseri.pep.fa Ampelosycios_humblotii/ Ampelosycios_humblotii.cds.fa Ampelosycios_humblotii.gff3 Ampelosycios_humblotii.pep.fa Ampelosycios_leandrii/ Ampelosycios_leandrii.cds.fa Ampelosycios_leandrii.gff3 Ampelosycios_leandrii.pep.fa Ampelosycios_scandens/ Ampelosycios_scandens.cds.fa Ampelosycios_scandens.gff3 Ampelosycios_scandens.pep.fa Austrobryonia_micrantha/ Austrobryonia_micrantha.cds.fa Austrobryonia_micrantha.gff3 Austrobryonia_micrantha.pep.fa Bayabusua_clarkei/ Bayabusua_clarkei.cds.fa Bayabusua_clarkei.gff3 Bayabusua_clarkei.pep.fa Begonia_darthvaderiana/ Begonia_darthvaderiana.cds.fa Begonia_darthvaderiana.gff3 Begonia_darthvaderiana.pep.fa Begonia_fimbristipula/ Begonia_fimbristipula.cds.fa Begonia_fimbristipula.gff3 Begonia_fimbristipula.pep.fa Begonia_fuchsioides/ Begonia_fuchsioides.cds.fa Begonia_fuchsioides.gff3 Begonia_fuchsioides.pep.fa Begonia_loranthoides/ Begonia_loranthoides.cds.fa Begonia_loranthoides.gff3 Begonia_loranthoides.pep.fa Begonia_masoniana/ Begonia_masoniana.cds.fa Begonia_masoniana.gff3 Begonia_masoniana.pep.fa Begonia_peltatifolia/ Begonia_peltatifolia.cds.fa Begonia_peltatifolia.gff3 Begonia_peltatifolia.pep.fa Benincasa_fistulosa/ Benincasa_fistulosa.cds.fa Benincasa_fistulosa.gff3 Benincasa_fistulosa.pep.fa Borneosicyos_simplex/ Borneosicyos_simplex.cds.fa Borneosicyos_simplex.gff3 Borneosicyos_simplex.pep.fa Bryonia_dioica1/ Bryonia_dioica1.cds.fa Bryonia_dioica1.gff3 Bryonia_dioica1.pep.fa Cayaponia_prunifera/ Cayaponia_prunifera.cds.fa Cayaponia_prunifera.gff3 Cayaponia_prunifera.pep.fa Citrullus_lanatus4/ Citrullus_lanatus4.cds.fa Citrullus_lanatus4.gff3 Citrullus_lanatus4.pep.fa Citrullus_naudinianus/ Citrullus_naudinianus.cds.fa Citrullus_naudinianus.gff3 Citrullus_naudinianus.pep.fa Coriaria_nepalensis/ Coriaria_nepalensis.cds.fa Coriaria_nepalensis.gff3 Coriaria_nepalensis.pep.fa Cucumis_cinereus/ Cucumis_cinereus.cds.fa Cucumis_cinereus.gff3 Cucumis_cinereus.pep.fa Cucumis_hirsutus/ Cucumis_hirsutus.cds.fa Cucumis_hirsutus.gff3 Cucumis_hirsutus.pep.fa Cucumis_queenslandicus/ Cucumis_queenslandicus.cds.fa Cucumis_queenslandicus.gff3 Cucumis_queenslandicus.pep.fa Cucumis_sagittatus/ Cucumis_sagittatus.cds.fa Cucumis_sagittatus.gff3 Cucumis_sagittatus.pep.fa Cucumis_sativus10/ Cucumis_sativus10.cds.fa Cucumis_sativus10.gff3 Cucumis_sativus10.pep.fa Cucumis_sativus8/ Cucumis_sativus8.cds.fa Cucumis_sativus8.gff3 Cucumis_sativus8.pep.fa Cucumis_sativus9/ Cucumis_sativus9.cds.fa Cucumis_sativus9.gff3 Cucumis_sativus9.pep.fa Cucumis_umbellatus/ Cucumis_umbellatus.cds.fa Cucumis_umbellatus.gff3 Cucumis_umbellatus.pep.fa Cucumis_variabilis/ Cucumis_variabilis.cds.fa Cucumis_variabilis.gff3 Cucumis_variabilis.pep.fa Cucurbita_ficifolia/ Cucurbita_ficifolia.cds.fa Cucurbita_ficifolia.gff3 Cucurbita_ficifolia.pep.fa Cyclanthera_cordifolia/ Cyclanthera_cordifolia.cds.fa Cyclanthera_cordifolia.gff3 Cyclanthera_cordifolia.pep.fa Datisca_glomerata/ Datisca_glomerata.cds.fa Datisca_glomerata.gff3 Datisca_glomerata.pep.fa Dendrosicyos_socotranus/ Dendrosicyos_socotranus.cds.fa Dendrosicyos_socotranus.gff3 Dendrosicyos_socotranus.pep.fa Diplocyclos_schliebenii/ Diplocyclos_schliebenii.cds.fa Diplocyclos_schliebenii.gff3 Diplocyclos_schliebenii.pep.fa Gerrardanthus_grandiflorus/ Gerrardanthus_grandiflorus.cds.fa Gerrardanthus_grandiflorus.gff3 Gerrardanthus_grandiflorus.pep.fa Gurania_insolita/ Gurania_insolita.cds.fa Gurania_insolita.gff3 Gurania_insolita.pep.fa Gurania_lobata/ Gurania_lobata.cds.fa Gurania_lobata.gff3 Gurania_lobata.pep.fa Gynostemma_guangxiense/ Gynostemma_guangxiense.cds.fa Gynostemma_guangxiense.gff3 Gynostemma_guangxiense.pep.fa Gynostemma_pentaphyllum1/ Gynostemma_pentaphyllum1.cds.fa Gynostemma_pentaphyllum1.gff3 Gynostemma_pentaphyllum1.pep.fa Gynostemma_pentaphyllum2/ Gynostemma_pentaphyllum2.cds.fa Gynostemma_pentaphyllum2.gff3 Gynostemma_pentaphyllum2.pep.fa Gynostemma_pentaphyllum3/ Gynostemma_pentaphyllum3.cds.fa Gynostemma_pentaphyllum3.gff3 Gynostemma_pentaphyllum3.pep.fa Lagenaria_breviflora/ Lagenaria_breviflora.cds.fa Lagenaria_breviflora.gff3 Lagenaria_breviflora.pep.fa Lagenaria_siceraria5/ Lagenaria_siceraria5.cds.fa Lagenaria_siceraria5.gff3 Lagenaria_siceraria5.pep.fa Luffa_acutangula2/ Luffa_acutangula2.cds.fa Luffa_acutangula2.gff3 Luffa_acutangula2.pep.fa Marah_fabacea1/ Marah_fabacea1.cds.fa Marah_fabacea1.gff3 Marah_fabacea1.pep.fa Microsechium_compositum/ Microsechium_compositum.cds.fa Microsechium_compositum.gff3 Microsechium_compositum.pep.fa Momordica_foetida1/ Momordica_foetida1.cds.fa Momordica_foetida1.gff3 Momordica_foetida1.pep.fa Momordica_subangulata/ Momordica_subangulata.cds.fa Momordica_subangulata.gff3 Momordica_subangulata.pep.fa Muellerargia_jeffreyana/ Muellerargia_jeffreyana.cds.fa Muellerargia_jeffreyana.gff3 Muellerargia_jeffreyana.pep.fa Neoalsomitra_pilosa/ Neoalsomitra_pilosa.cds.fa Neoalsomitra_pilosa.gff3 Neoalsomitra_pilosa.pep.fa Polyclathra_cucumerina/ Polyclathra_cucumerina.cds.fa Polyclathra_cucumerina.gff3 Polyclathra_cucumerina.pep.fa Psiguria_triphylla1/ Psiguria_triphylla1.cds.fa Psiguria_triphylla1.gff3 Psiguria_triphylla1.pep.fa Psiguria_umbrosa/ Psiguria_umbrosa.cds.fa Psiguria_umbrosa.gff3 Psiguria_umbrosa.pep.fa Pteropepon_parodii/ Pteropepon_parodii.cds.fa Pteropepon_parodii.gff3 Pteropepon_parodii.pep.fa Ruthalicia_longipes/ Ruthalicia_longipes.cds.fa Ruthalicia_longipes.gff3 Ruthalicia_longipes.pep.fa Sechiopsis_diptera/ Sechiopsis_diptera.cds.fa Sechiopsis_diptera.gff3 Sechiopsis_diptera.pep.fa Sechiopsis_laciniata/ Sechiopsis_laciniata.cds.fa Sechiopsis_laciniata.gff3 Sechiopsis_laciniata.pep.fa Sechium_chinantlense/ Sechium_chinantlense.cds.fa Sechium_chinantlense.gff3 Sechium_chinantlense.pep.fa Sechium_mexicanum/ Sechium_mexicanum.cds.fa Sechium_mexicanum.gff3 Sechium_mexicanum.pep.fa Sechium_panamensis/ Sechium_panamensis.cds.fa Sechium_panamensis.gff3 Sechium_panamensis.pep.fa Sechium_pittieri1/ Sechium_pittieri1.cds.fa Sechium_pittieri1.gff3 Sechium_pittieri1.pep.fa Sechium_tacaco/ Sechium_tacaco.cds.fa Sechium_tacaco.gff3 Sechium_tacaco.pep.fa Sechium_venosa/ Sechium_venosa.cds.fa Sechium_venosa.gff3 Sechium_venosa.pep.fa Sechium_villosa/ Sechium_villosa.cds.fa Sechium_villosa.gff3 Sechium_villosa.pep.fa Sicydium_synantherum/ Sicydium_synantherum.cds.fa Sicydium_synantherum.gff3 Sicydium_synantherum.pep.fa Sicyocaulis_pentagonus/ Sicyocaulis_pentagonus.cds.fa Sicyocaulis_pentagonus.gff3 Sicyocaulis_pentagonus.pep.fa Sicyos_baderoa/ Sicyos_baderoa.cds.fa Sicyos_baderoa.gff3 Sicyos_baderoa.pep.fa Sicyos_bulbosus/ Sicyos_bulbosus.cds.fa Sicyos_bulbosus.gff3 Sicyos_bulbosus.pep.fa Sicyos_chiriquensis/ Sicyos_chiriquensis.cds.fa Sicyos_chiriquensis.gff3 Sicyos_chiriquensis.pep.fa Sicyos_galeottii/ Sicyos_galeottii.cds.fa Sicyos_galeottii.gff3 Sicyos_galeottii.pep.fa Sicyos_hispidus/ Sicyos_hispidus.cds.fa Sicyos_hispidus.gff3 Sicyos_hispidus.pep.fa Sicyos_lanceoloideus/ Sicyos_lanceoloideus.cds.fa Sicyos_lanceoloideus.gff3 Sicyos_lanceoloideus.pep.fa Sicyos_macrophyllus/ Sicyos_macrophyllus.cds.fa Sicyos_macrophyllus.gff3 Sicyos_macrophyllus.pep.fa Sicyos_mawhai/ Sicyos_mawhai.cds.fa Sicyos_mawhai.gff3 Sicyos_mawhai.pep.fa Sicyos_pachycarpus/ Sicyos_pachycarpus.cds.fa Sicyos_pachycarpus.gff3 Sicyos_pachycarpus.pep.fa Sicyosperma_gracile/ Sicyosperma_gracile.cds.fa Sicyosperma_gracile.gff3 Sicyosperma_gracile.pep.fa Sicyos_undara/ Sicyos_undara.cds.fa Sicyos_undara.gff3 Sicyos_undara.pep.fa Sinobaijiania_yunnanensis1/ Sinobaijiania_yunnanensis1.cds.fa Sinobaijiania_yunnanensis1.gff3 Sinobaijiania_yunnanensis1.pep.fa Telfairia_occidentalis1/ Telfairia_occidentalis1.cds.fa Telfairia_occidentalis1.gff3 Telfairia_occidentalis1.pep.fa Thladiantha_angustisepala/ Thladiantha_angustisepala.cds.fa Thladiantha_angustisepala.gff3 Thladiantha_angustisepala.pep.fa Thladiantha_cordifolia1/ Thladiantha_cordifolia1.cds.fa Thladiantha_cordifolia1.gff3 Thladiantha_cordifolia1.pep.fa Thladiantha_medogensis/ Thladiantha_medogensis.cds.fa Thladiantha_medogensis.gff3 Thladiantha_medogensis.pep.fa Thladiantha_pustulata/ Thladiantha_pustulata.cds.fa Thladiantha_pustulata.gff3 Thladiantha_pustulata.pep.fa Trichosanthes_cucumerina2/ Trichosanthes_cucumerina2.cds.fa Trichosanthes_cucumerina2.gff3 Trichosanthes_cucumerina2.pep.fa Trichosanthes_truncata1/ Trichosanthes_truncata1.cds.fa Trichosanthes_truncata1.gff3 Trichosanthes_truncata1.pep.fa Ulmus_minor/ Ulmus_minor.cds.fa Ulmus_minor.gff3 Ulmus_minor.pep.fa Xerosicyos_decaryi/ Xerosicyos_decaryi.cds.fa Xerosicyos_decaryi.gff3 Xerosicyos_decaryi.pep.fa Xerosicyos_perrieri1/ Xerosicyos_perrieri1.cds.fa Xerosicyos_perrieri1.gff3 Xerosicyos_perrieri1.pep.fa Xerosicyos_pubescens1/ Xerosicyos_pubescens1.cds.fa Xerosicyos_pubescens1.gff3 Xerosicyos_pubescens1.pep.fa Description: Structural annotation of various datasets generated in the study using GeMoMa v1.9. Each subfolder contains the structural annotations in GFF3 (.gff3) format, predicted coding sequences as FASTA file (.cds.fa), and the predicted polypeptide sequences as FASTA file (.pep.fa) for the corresponding dataset. File names are based on the plant species name. Expression_datasets/ Benincasa_hispida1/ Benincasa_hispida1.cds.fa Benincasa_hispida1.pep.fa Benincasa_hispida1.tpms.txt Carya_illinoinensis/ Carya_illinoinensis.cds.fa Carya_illinoinensis.pep.fa Carya_illinoinensis.tpms.txt Castanea_mollissima/ Castanea_mollissima.cds.fa Castanea_mollissima.pep.fa Castanea_mollissima.tpms.txt Citrullus_lanatus2/ Citrullus_lanatus2.cds.fa Citrullus_lanatus2.pep.fa Citrullus_lanatus2.tpms.txt Cucumis_sativus1/ Cucumis_sativus1.cds.fa Cucumis_sativus1.pep.fa Cucumis_sativus1.tpms.txt Cucurbita_moschata1/ Cucurbita_moschata1.cds.fa Cucurbita_moschata1.pep.fa Cucurbita_moschata1.tpms.txt Cucurbita_pepo1/ Cucurbita_pepo1.cds.fa Cucurbita_pepo1.pep.fa Cucurbita_pepo1.tpms.txt Fragaria_vesca/ Fragaria_vesca.cds.fa Fragaria_vesca.pep.fa Fragaria_vesca.tpms.txt Gynostemma_pentaphyllum2/ Gynostemma_pentaphyllum2.cds.fa Gynostemma_pentaphyllum2.pep.fa Gynostemma_pentaphyllum2.tpms.txt Hippophae_rhamnoides/ Hippophae_rhamnoides.cds.fa Hippophae_rhamnoides.pep.fa Hippophae_rhamnoides.tpms.txt Juglans_regia/ Juglans_regia.cds.fa Juglans_regia.pep.fa Juglans_regia.tpms.txt Luffa_aegyptiaca1/ Luffa_aegyptiaca1.cds.fa Luffa_aegyptiaca1.pep.fa Luffa_aegyptiaca1.tpms.txt Malus_domestica/ Malus_domestica.cds.fa Malus_domestica.pep.fa Malus_domestica.tpms.txt Momordica_charantia2/ Momordica_charantia2.cds.fa Momordica_charantia2.pep.fa Momordica_charantia2.tpms.txt Quercus_robur/ Quercus_robur.cds.fa Quercus_robur.pep.fa Quercus_robur.tpms.txt Ulmus_minor/ Ulmus_minor.cds.fa Ulmus_minor.pep.fa Ulmus_minor.tpms.txt Description: Gene expression data of selected datasets used for expression analysis. File names are based on the plant species name. Each sub-folder contains the reference sequence (*.cds.fa & *.pep.fa), and a count table with the expression data (*.tpms.txt). Coding_seq_gene_trees_dataset/ 2ODD.cds.fasta arGST.cds.fasta bHLH.cds.fasta CHI.cds.fasta CHS.cds.fasta CYP450.cds.fasta MYB.cds.fasta SDR.cds.fasta UGT.cds.fasta WD40.cds.fasta Descriptions: Coding sequences used for constructing individual gene phylogenetic trees in FASTA format. C SHARING/ACCESS INFORMATION 1. Was data derived from another source? : No 2. Licenses/restrictions placed on the data: CC BY 4.0 3. Links to publications that cite or use the data: https://doi.org/10.1101/2025.10.06.680802 D METHODOLOGICAL INFORMATION Data collection, structure, and processing: All input datasets are publicly available. Sources of data can be found in Dataset_sources.csv. Gene models were predicted using GeMoMa v1.9 using 10 high-quality reference genome sequences. All datasets (coding sequences) were taxonomically classified using Kraken v2.1.3 and Bracken v2.9. RNA-seq data sets were retrieved from the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) via fastq-dump (https://github.com/ncbi/sra-tools). Reference sequences were manually collected from different sources and processed as described. Gzip-compressed FASTQ files were processed via kallisto v0.44 (https://github.com/pachterlab/kallisto) to quantify gene expression based on annotated coding sequences. The individual count tables produced by kallisto were merged into one count table per species using a Python script (https://github.com/bpucker/CoExp). Samples with a low total number of reads or with a read distribution that does not match RNA-seq expectations were excluded. 'Additional_file1.csv' lists the sources of coding sequence data sets that were used as reference for the gene expression analysis. Note: Detailed methods used for collection and analysis of the data can be found in the methods section of: https://doi.org/10.1101/2025.10.06.680802 People involved in sample collection, processing, analysis and/or submission: all authors File formats: CSV, TXT, FASTA, GFF