Supplementary data to Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LARdoi:10.60507/FK2/UKAAO0bonndata2025-08-222Marín 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, V2Supplementary data to Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LARdoi:10.60507/FK2/UKAAO0Marín Recinos, María FernandaPucker, BoasbonndataPucker, BoasMarin Recinos, Maria2025-08-15OtherThis 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.2023-06-212025-08-05<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 2025.08.06.668978Marin-Recinos M and Pucker B. (2025). Evolutionary Dynamics of the Proanthocyanidin Biosynthesis Gene LAR. bioRxiv 2025.08.06.66897820251107_README_LAR_Evolution.txttext/plainAdditional_file_1A-statistic_analysis.pdfPDF 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.application/pdfAdditional_file_1B-GE_Achinensis_LAR.csvGene expression data for LAR1 and LAR2 genes in Actinidia chinensistext/csvAdditional_file_1B-GE_Cillinoinensis_LAR.csvGene expression data for LAR1 and LAR2 genes in Carya illinoinensistext/csvAdditional_file_1B-GE_Egrandis_LAR.csvGene expression data for LAR1 and LAR2 genes in Eucalyptus grandistext/csvAdditional_file_1B-GE_Gbiloba_LAR.csvGene expression data for LARI and LARII genes in Ginkgo bilobatext/csvAdditional_file_1B-GE_Ghirsutum_LAR.csvGene expression data for LAR1 and LAR2 genes in Gossypium hirsutumtext/csvAdditional_file_1B-GE_Moleifera_LAR.csvGene expression data for LAR1 and LAR2 genes in Moringa oleiferatext/csvAdditional_file_1B-GE_Mrubra_LAR.csvGene expression data for LAR1 and LAR2 genes in Morella rubratext/csvAdditional_file_1B-GE_Ppinaster_LAR.csvGene expression data for LARI and LARII genes in Pinus pinastertext/csvAdditional_file_1B-GE_Psitchensis_LAR.csvGene expression data for LARI and LARII genes in Picea sitchensistext/csvAdditional_file_1B-GE_Ptrichocarpa_LAR.csvGene expression data for LAR1 and LAR2 genes in Populus trichocarpatext/csvAdditional_file_1B-GE_Tcacao_LAR.csvGene expression data for LAR1 and LAR2 genes in Theobroma cacaotext/csvAdditional_file_1B-GE_Tchinensis_LAR.csvGene expression data for LARI and LARII genes in Taxus chinensistext/csvAdditional_file_1B-GE_Tplicata_LAR.csvGene expression data for LARI and LARII genes in Thuja plicatatext/csvAdditional_file_1B-GE_Vvinifera_LAR.csvGene expression data for LAR1 and LAR2 genes in Vitis viniferatext/csvAdditional_file_1C-phylogenetic_tree.pdfPDF document with the complete phylogenetic tree that includes non-collapsed clades and full labels.application/pdfAdditional_file_1D-gene-positions.csvCSV table listing the genomic positions of LAR1 and LAR2 genes.text/csvAdditional_file_2A_Dicots_LAR_scores.csvPolypeptide 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.text/csvAdditional_file_2A_Gymnosperm_LAR_scores.csvPolypeptide 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.text/csvAdditional_file_2B_conservation_barplot.pdfContains bar plots results showing the amino acid conservation values within specific LAR sequence groups: Gymnosperms and Dicots.application/pdfAdditional_file_2C_AA_gymnosperm_LARI.fastaContains polypeptide sequences for LARI in gymnosperms.application/octet-streamAdditional_file_2D_AA_gymnosperm_LARII.fastaContains polypeptide sequences for LARII in gymnosperms.application/octet-streamAdditional_file_2E_AA_dicot_LAR1.fastaContains polypeptide sequences for LAR1 in dicots.application/octet-streamAdditional_file_2F_AA_dicot_LAR2.fastaContains polypeptide sequences for LAR2 in dicots.application/octet-streamAdditional_file_3-coexp_GE_Moleifera_LAR1.csvContains results of coexpression analysis for LAR1 in Moringa oleifera.text/csvAdditional_file_3-coexp_GE_Moleifera_LAR2.csvContains results of coexpression analysis for LAR2 in Moringa oleifera.text/csvAdditional_file_3-coexp_GE_Tcacao_LAR1.csvContains results of coexpression analysis for LAR1 in Theobroma cacao.text/csvAdditional_file_3-coexp_GE_Tcacao_LAR2.csvContains results of coexpression analysis for LAR2 in Theobroma cacao.text/csvAdditional_file_3-coexp_GE_Vvinifera_LAR1.csvContains results of coexpression analysis for LAR1 in Vitis vinifera.text/csvAdditional_file_3-coexp_GE_Vvinifera_LAR2.csvContains results of coexpression analysis for LAR2 in Vitis vinifera.text/csvAdditional_file_4A-CRE_Moleifera_LAR1.csvPredicted cis-regulatory elements (CREs) in the promoter regions of LAR1 in Moringa oleifera.text/csvAdditional_file_4A-CRE_Moleifera_LAR2.csvPredicted cis-regulatory elements (CREs) in the promoter regions of LAR2 in Moringa oleifera.text/csvAdditional_file_4A-CRE_Tcacao_LAR1.csvPredicted cis-regulatory elements (CREs) in the promoter regions of LAR1 in Theobroma cacao.text/csvAdditional_file_4A-CRE_Tcacao_LAR2.csvPredicted cis-regulatory elements (CREs) in the promoter regions of LAR2 in Theobroma cacao.text/csvAdditional_file_4A-CRE_Vvinifera_LAR1.csvPredicted cis-regulatory elements (CREs) in the promoter regions of LAR1 in Vitis vinifera.text/csvAdditional_file_4A-CRE_Vvinifera_LAR2.csvPredicted cis-regulatory elements (CREs) in the promoter regions of LAR2 in Vitis vinifera.text/csvAdditional_file_4A-frequency_CRE_Moleifera.csvFrequency table summarizing the number of occurrences of each cis-element in LAR1 and LAR2 gene promoters in Moringa oleifera.text/csvAdditional_file_4A-frequency_CRE_Tcacao.csvFrequency table summarizing the number of occurrences of each cis-element in LAR1 and LAR2 gene promoters in Theobroma cacao.text/csvAdditional_file_4A-frequency_CRE_Vvinifera.csvFrequency table summarizing the number of occurrences of each cis-element in LAR1 and LAR2 gene promoters in Vitis vinifera.text/csvAdditional_file_4B_SRA_accessions.csvTable with SRA accessions (SRR IDs) for RNA-seq datasets used in promoter validation and co-expression analysis.text/csvAdditional_file_4C_promoters_UTR.faContains promoter and 5’ untranslated region (UTR) sequences for LAR1 and LAR2 genes from all species analyzed.application/octet-streamAdditional_file_4D_LAR_reads_mapping_Tcacao.bamContains the RNA-seq read mapping to Theobroma cacao LAR1 and LAR2 loci for promoter analysis.application/gzipAdditional_file_4E_LAR_reads_mapping_Moleifera.bamContains the RNA-seq read mapping to Moringa oleifera LAR1 and LAR2 loci for promoter analysis.application/gzipAdditional_file_5_sinteny_LAR1.csvSynteny 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.text/csvAdditional_file_5_sinteny_LAR1_brassicales.csvSynteny 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.text/csvAdditional_file_5_sinteny_LAR2.csvSynteny 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.text/csvAdditional_file_6A_AA_LAR_ANR_DFR.fastaContains polypeptide sequences of LAR, ANR, and DFR.application/octet-streamAdditional_file_6B_CDS_LAR_ANR_DFR.fastaContains coding sequences (CDS) of LAR, ANR, and DFR.application/octet-stream