Supplementary data supporting the study: "Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae"

Name: Supplementary data supporting the study: "Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae"
Published: 2025-12-18
License: http://creativecommons.org/licenses/by/4.0

Open this dataset in the live repository

Important usage condition: Use and redistribution are governed by CC BY 4.0. Review and comply with the license before using the data.

Persistent identifier: doi:10.60507/FK2/ZNVSLA
Published version: 1.0
Publication date: 2025-12-18
License: CC BY 4.0

Description

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 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.

Creators

Choudhary, Nancy
Hagedorn, Marie
Pucker, Boas

Keywords

flavonoids, pigmentation, gene loss, phylogenomics, carotenoids, comparative genomics, Cucurbitaceae

Files

Before downloading: Use and redistribution are governed by CC BY 4.0. Review and comply with the license before using the data.

File	Type	Bytes	Checksum
Gene_Annotation_dataset.tar.gz	application/gzip	2192069456	MD5 7b79b7bf905e7e72c5b234a3968b2971
BUSCO_genes_for_species_phylogeny.csv	text/csv	51652	MD5 6349019a3d9a25b2d52db69957243d10
Gene_annotation_stats.csv	text/csv	7705	MD5 8b6e314c149aa413049e66e977c863cb
Coding_seq_gene_trees_dataset.tar.gz	application/gzip	6056086	MD5 76582297191abb036adfb1cd7d07c96c
Expression_datasets.tar.gz	application/gzip	1227781722	MD5 1fa4521900ba3fbab3d589936a2c3849
Bait_sequences_gene_trees.csv	text/csv	49864	MD5 5e1581a14a019d45774fe557a1e12a8d
Kraken_classification.csv	text/csv	35465	MD5 d03c4330afa93ae046f183653f66d1c6
Fruit_flower_colour_sources.csv	text/csv	13899	MD5 0d2e5292f31213e8b98d08d54fde165b
README.txt	text/plain	17406	MD5 09efa63aa55dec812e8d28aa1037efac
Dataset_sources.csv	text/csv	37277	MD5 3e5fd89ec0b5c62d0b40ec9e8097a8ff

Citation

Choudhary, Nancy; Hagedorn, Marie; Pucker, Boas, 2025-12-18, Supplementary data supporting the study: "Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae", doi:10.60507/FK2/ZNVSLA, V1.0

Additional Dataverse fields

Id	527
Dataset Type	dataset
Internal Version Number	26
Latest Version Publishing State	RELEASED
Production Date	2025-12-15
Release Time	2025-12-18T14:00:01Z
Create Time	2025-12-01T13:22:29Z
Citation Date	2025-12-18
File Access Request	True

Export metadata

Static metadata exports available for this published dataset version:

Complete Dataverse metadata

Citation Metadata

Title title

Supplementary data supporting the study: "Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae"

Author author

Author Name
Choudhary, Nancy
Author Affiliation
IZMB, University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0000-0002-2562-7905
Expandedvalue
Person Name
Choudhary, Nancy
@id
https://orcid.org/0000-0002-2562-7905
Scheme
ORCID
@type
https://schema.org/Person
Author Name
Hagedorn, Marie
Author Affiliation
IZMB, University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0009-0009-1312-0531
Expandedvalue
Person Name
Hagedorn, Marie
@id
https://orcid.org/0009-0009-1312-0531
Scheme
ORCID
@type
https://schema.org/Person
Author Name
Pucker, Boas
Author Affiliation
IZMB, University of Bonn
Author Identifier Scheme
ORCID
Author Identifier
Type Name
authorIdentifier
Multiple
False
Type Class
primitive
Value
https://orcid.org/0000-0002-3321-7471
Expandedvalue
Person Name
Pucker, Boas
@id
https://orcid.org/0000-0002-3321-7471
Scheme
ORCID
@type
https://schema.org/Person

Dataset Contact datasetContact

Dataset Contact Name
Choudhary, Nancy
Dataset Contact Affiliation
University of Bonn
Dataset Contact Email
nchoudha@uni-bonn.de

Ds Description dsDescription

Ds Description Value
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 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.
Ds Description Date
2025-12-15

Subject subject

Medicine, Health and Life Sciences

Subject Refinement subjectRefinement

Subject Refinement Value
Plant Sciences [202]

Free Keyword freeKeyword

Free Keyword Value
flavonoids
Free Keyword Value
pigmentation
Free Keyword Value
gene loss
Free Keyword Value
phylogenomics
Free Keyword Value
carotenoids
Free Keyword Value
comparative genomics
Free Keyword Value
Cucurbitaceae

Publication publication

Publication Relation Type
IsSupplementTo
Publication Citation
Nancy Choudhary, Marie Hagedorn, Boas Pucker (2025). Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae
Publication IDType
doi
Publication URL
https://doi.org/10.1101/2025.10.06.680802

Language language

English

Production Date productionDate

2025-12-15

Production Place productionPlace

Bonn

Contributor contributor

Contributor Type
Supervisor
Contributor Name
Boas Pucker

Depositor depositor

Choudhary, Nancy

Date Of Deposit dateOfDeposit

2025-12-15

Date Of Collection dateOfCollection

Date Of Collection Start
2024-12-26
Date Of Collection End
2025-07-31

Software software

Software Name
GeMoMa
Software Version
1.9
Software Name
BUSCO
Software Version
5.8.1
Software Name
Kraken
Software Version
2.1.3
Software Name
Bracken
Software Version
2.9
Software Name
kallisto
Software Version
0.44
Software Name
Python
Software Version
3.11.8

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