Supplementary datasets for: Dinámica transcripcional de la transición de flor a fruto en Vanilla planifolia Andrews (Orchidaceae): una aproximación desde la fenología molecular y las redes de coexpresión

Supplementary datasets description This repository contains the supplementary digital datasets supporting the doctoral thesis “Dinámica transcripcional de la transición de flor a fruto en Vanilla planifolia Andrews (Orchidaceae): una aproximación desde la fenología molecular y las redes de coexpresión”. The study investigates the flower-to-fruit transition (FFT) in Vanilla planifolia, a species characterized by a post-pollination syndrome (PPS), in which ovule development is reactivated only after pollination and proceeds through an extended, environmentally sensitive developmental program. This condition makes reproductive success highly dependent on external factors and requires integrative approaches to understand its regulation. To address this, a systems-level transcriptomic framework was implemented, integrating RNA-seq analysis, differential gene expression, orthology inference, functional enrichment, and weighted gene co-expression network analysis (WGCNA). This approach enabled the identification of transcriptional modules, regulatory cores, and candidate genes associated with developmental transitions across four stages: pre-pollination (Pre-pol), pollination (Pol), post-pollination (Post-pol), and fertilization (Fer). The supplementary files include processed datasets derived from these analyses, encompassing differential expression results, functional enrichment analyses, stage-specific transcriptional signatures, gene classification based on structural and functional labels, and network-derived gene prioritization. Additionally, they support a comparative orthology framework across angiosperms and the identification of candidate regulators associated with PPS. Together, these datasets provide a reproducible and integrative resource for studying complex reproductive developmental processes in non-model plant species and establish a transferable strategy for candidate gene prioritization using coexpression networks. Contents of supplementary files 1. Differential expression analyses 2_Table S2_DEGs.csv: Global list of differentially expressed genes (DEGs) 3_Table S3_DEGs_Pre-pol_vs_Pol.csv: Pre-pol vs Pol comparison 4_Table S4_DEGs_Pre-pol_vs_Post-pol.csv: Pre-pol vs Post-pol comparison 5_Table S5_DEGs_Pre-pol_vs_Fer.csv: Pre-pol vs Fer comparison 6_Table S6_DEGs_Pol_vs_Post-pol.csv: Pol vs Post-pol comparison 7_Table S7_DEGs_Pol_vs_Fer.csv: Pol vs Fer comparison 8_Table S8_DEGs_Post-pol_vs_Fer.csv: Post-pol vs Fer comparison 2. Functional enrichment analyses 9_Table S9_GO_enrichment_C1.csv: GO enrichment for cluster C1 10_Table S10_GO_enrichment_C2.csv: GO enrichment for cluster C2 11_Table S11_GO_enrichment_C3.csv: GO enrichment for cluster C3 12_Table S12_GO_enrichment_C4.csv: GO enrichment for cluster C4 17_Table S17_GO_enrichment_Pre-pol.csv: GO enrichment for Pre-pol 18_Table S18_GO_enrichment_Pol.csv: GO enrichment for Pol 19_Table S19_GO_enrichment_Post-pol.csv: GO enrichment for Post-pol 20_Table S20_GO_enrichment_Fer.csv: GO enrichment for Fer 3. Stage-specific transcriptional signatures 13_Table S13_Pre-pol_functional_signatures.csv 14_Table S14_Pol_functional_signatures.csv 15_Table S15_Post-pol_functional_signatures.csv 16_Table S16_Fer_functional_signatures.csv 4. Label integration and intersections Tabla S21_intersecciones_entre_etiquetas.csv: Intersections among all labels Tabla S22_interseccion_estructural_y_funcional.csv: Structural vs functional intersections 5. Network-based classification Tabla S23_GNM_OCDT.csv Tabla S24_GNM_FT.csv Tabla S26_GED_OCDT.csv Tabla S27_GED_FT.csv Tabla S28_GED_RE.csv Tabla S29_GED_Pol.csv Tabla S30_GED_Post-pol.csv Tabla S31_GED_Fer.csv 6. Candidate gene prioritization Tabla S32_Candidatos_Info.xlsx: Integrated list of prioritized candidate genes