Supplementary data to Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR (doi:10.60507/FK2/UKAAO0)

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Supplementary data to Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR

doi:10.60507/FK2/UKAAO0

bonndata

2025-08-22

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Marín Recinos, María Fernanda; Pucker, Boas, 2025, "Supplementary data to Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR", https://doi.org/10.60507/FK2/UKAAO0, bonndata, V2

Supplementary data to Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR

doi:10.60507/FK2/UKAAO0

Marín Recinos, María Fernanda (University of Bonn)

Pucker, Boas (University of Bonn)

bonndata

Pucker, Boas

Marin Recinos, Maria

2025-08-15

https://doi.org/10.60507/FK2/UKAAO0

Other

This dataset contains supplementary files associated with the manuscript "Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR", which investigates the evolutionary divergence, sequence variation, promoter motif composition, and coexpression patterns of LAR1 and LAR2 genes across multiple plant lineages. Supplementary materials include statistical analysis outputs, gene expression data, polypeptide sequences, sequence conservation values, cis-regulatory element data, BAM files with aligned RNA-seq reads around the LAR1 and LAR2 loci, and synteny results.

2023-06-21-2025-08-05

<a href="http://creativecommons.org/licenses/by/4.0">CC BY 4.0</a>

Marin-Recinos M and Pucker B. (2025). Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR. bioRxiv 2025.08.06.668978

Marin-Recinos M and Pucker B. (2025). Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR. bioRxiv 2025.08.06.668978

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20251107_README_LAR_Evolution.txt

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Additional_file_1A-statistic_analysis.pdf

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PDF document with the complete results of the Linear Mixed Models (LMM) and Estimated Marginal Means (EMM) statistical analyses. Includes violin plots summarizing variation in gene expression of LAR paralogs across tissues for the following species: Taxus chinensis, Ginkgo biloba, Pinus pinaster, Picea sitchensis, Thuja plicata, Vitis vinifera, Theobroma cacao, Moringa oleifera, Gossypium hirsutum, Actinidia chinensis, Eucalyptus grandis, Populus trichocarpa, Carya illinoinensis, and Morella rubra.

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Additional_file_1B-GE_Achinensis_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Actinidia chinensis

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Additional_file_1B-GE_Cillinoinensis_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Carya illinoinensis

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Additional_file_1B-GE_Egrandis_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Eucalyptus grandis

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Additional_file_1B-GE_Gbiloba_LAR.csv

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Gene expression data for LARI and LARII genes in Ginkgo biloba

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Additional_file_1B-GE_Ghirsutum_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Gossypium hirsutum

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Additional_file_1B-GE_Moleifera_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Moringa oleifera

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Additional_file_1B-GE_Mrubra_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Morella rubra

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Additional_file_1B-GE_Ppinaster_LAR.csv

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Gene expression data for LARI and LARII genes in Pinus pinaster

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Additional_file_1B-GE_Psitchensis_LAR.csv

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Gene expression data for LARI and LARII genes in Picea sitchensis

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Additional_file_1B-GE_Ptrichocarpa_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Populus trichocarpa

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Additional_file_1B-GE_Tcacao_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Theobroma cacao

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Additional_file_1B-GE_Tchinensis_LAR.csv

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Gene expression data for LARI and LARII genes in Taxus chinensis

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Additional_file_1B-GE_Tplicata_LAR.csv

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Gene expression data for LARI and LARII genes in Thuja plicata

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Additional_file_1B-GE_Vvinifera_LAR.csv

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Gene expression data for LAR1 and LAR2 genes in Vitis vinifera

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Additional_file_1C-phylogenetic_tree.pdf

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PDF document with the complete phylogenetic tree that includes non-collapsed clades and full labels.

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Additional_file_1D-gene-positions.csv

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CSV table listing the genomic positions of LAR1 and LAR2 genes.

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Additional_file_2A_Dicots_LAR_scores.csv

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Polypeptide sequence differences and logo plot analysis containing positional scores, most common residues or codon per group, and conservation rates for dicot LAR1 and LAR2 sequences.

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Additional_file_2A_Gymnosperm_LAR_scores.csv

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Polypeptide sequence differences and logo plot analysis containing positional scores, most common residues or codon per group, and conservation rates for for gymnosperm LARI and LARII.

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Additional_file_2B_conservation_barplot.pdf

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Contains bar plots results showing the amino acid conservation values within specific LAR sequence groups: Gymnosperms and Dicots.

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Additional_file_2C_AA_gymnosperm_LARI.fasta

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Contains polypeptide sequences for LARI in gymnosperms.

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Additional_file_2D_AA_gymnosperm_LARII.fasta

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Contains polypeptide sequences for LARII in gymnosperms.

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Additional_file_2E_AA_dicot_LAR1.fasta

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Contains polypeptide sequences for LAR1 in dicots.

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Additional_file_2F_AA_dicot_LAR2.fasta

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Contains polypeptide sequences for LAR2 in dicots.

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Additional_file_3-coexp_GE_Moleifera_LAR1.csv

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Contains results of coexpression analysis for LAR1 in Moringa oleifera.

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Additional_file_3-coexp_GE_Moleifera_LAR2.csv

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Contains results of coexpression analysis for LAR2 in Moringa oleifera.

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Additional_file_3-coexp_GE_Tcacao_LAR1.csv

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Contains results of coexpression analysis for LAR1 in Theobroma cacao.

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Additional_file_3-coexp_GE_Tcacao_LAR2.csv

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Contains results of coexpression analysis for LAR2 in Theobroma cacao.

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Additional_file_3-coexp_GE_Vvinifera_LAR1.csv

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Contains results of coexpression analysis for LAR1 in Vitis vinifera.

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Additional_file_3-coexp_GE_Vvinifera_LAR2.csv

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Contains results of coexpression analysis for LAR2 in Vitis vinifera.

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Additional_file_4A-CRE_Moleifera_LAR1.csv

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Predicted cis-regulatory elements (CREs) in the promoter regions of LAR1 in Moringa oleifera.

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Additional_file_4A-CRE_Moleifera_LAR2.csv

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Predicted cis-regulatory elements (CREs) in the promoter regions of LAR2 in Moringa oleifera.

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Additional_file_4A-CRE_Tcacao_LAR1.csv

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Predicted cis-regulatory elements (CREs) in the promoter regions of LAR1 in Theobroma cacao.

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Additional_file_4A-CRE_Tcacao_LAR2.csv

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Predicted cis-regulatory elements (CREs) in the promoter regions of LAR2 in Theobroma cacao.

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Additional_file_4A-CRE_Vvinifera_LAR1.csv

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Predicted cis-regulatory elements (CREs) in the promoter regions of LAR1 in Vitis vinifera.

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Additional_file_4A-CRE_Vvinifera_LAR2.csv

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Predicted cis-regulatory elements (CREs) in the promoter regions of LAR2 in Vitis vinifera.

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Additional_file_4A-frequency_CRE_Moleifera.csv

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Frequency table summarizing the number of occurrences of each cis-element in LAR1 and LAR2 gene promoters in Moringa oleifera.

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Additional_file_4A-frequency_CRE_Tcacao.csv

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Frequency table summarizing the number of occurrences of each cis-element in LAR1 and LAR2 gene promoters in Theobroma cacao.

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Additional_file_4A-frequency_CRE_Vvinifera.csv

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Frequency table summarizing the number of occurrences of each cis-element in LAR1 and LAR2 gene promoters in Vitis vinifera.

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Additional_file_4B_SRA_accessions.csv

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Table with SRA accessions (SRR IDs) for RNA-seq datasets used in promoter validation and co-expression analysis.

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Additional_file_4C_promoters_UTR.fa

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Contains promoter and 5’ untranslated region (UTR) sequences for LAR1 and LAR2 genes from all species analyzed.

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Additional_file_4D_LAR_reads_mapping_Tcacao.bam

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Contains the RNA-seq read mapping to Theobroma cacao LAR1 and LAR2 loci for promoter analysis.

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Additional_file_4E_LAR_reads_mapping_Moleifera.bam

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Contains the RNA-seq read mapping to Moringa oleifera LAR1 and LAR2 loci for promoter analysis.

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Additional_file_5_sinteny_LAR1.csv

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Synteny connections for LAR1 (indicated with *) across five plant species (Vitis vinifera, Theobroma cacao, Moringa oleifera, Carica papaya, and Bretschneidera sinensis). A dot (.) indicates absence of a corresponding syntenic gene in that species.

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Additional_file_5_sinteny_LAR1_brassicales.csv

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Synteny connections for LAR1 in Brassicales (indicated with *), listing syntenic genes only among the Brassicales species: Moringa oleifera, Carica papaya, Bretschneidera sinensis, Capsella rubella, Boechera stricta, Arabidopsis thaliana, Arabidopsis halleri, Eutrema salsugineum, and Brassica rapa. A dot (.) indicates absence of a corresponding syntenic gene in that species.

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Additional_file_5_sinteny_LAR2.csv

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Synteny connections for LAR2 (indicated with *) across five plant species (Vitis vinifera, Theobroma cacao, Moringa oleifera, Carica papaya, and Bretschneidera sinensis). A dot (.) indicates absence of a corresponding syntenic gene in that species.

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Additional_file_6A_AA_LAR_ANR_DFR.fasta

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Contains polypeptide sequences of LAR, ANR, and DFR.

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Additional_file_6B_CDS_LAR_ANR_DFR.fasta

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Contains coding sequences (CDS) of LAR, ANR, and DFR.

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