Systems-level transcriptomics reveals the regulatory architecture of the post-pollination syndrome in Vanilla planifolia

In many angiosperms, reproductive development depends on pollination-induced reprogramming of ovary and ovule growth; however, the mechanisms coordinating this development remain poorly understood, particularly in non-model species. In orchids such as Vanilla planifolia Andrews, this process involves a distinctive post-pollination syndrome in which ovule development is reactivated following pollination and proceeds through a prolonged, environmentally responsive developmental program. To characterize the organization of this syndrome, we integrated developmental anatomical analyses with systems-level transcriptomics, combining orthology inference, differential expression analysis, co-expression network reconstruction, and a bioinformatic labeling framework that encompasses structural and functional dimensions of gene regulation. Co-expression analysis identified nine transcriptional modules associated with reproductive development, metabolism, chromatin organization, and gene expression regulation, with enrichment in hormone signaling pathways. By intersecting structural and functional labels, we prioritized 88 candidate regulators associated with the post-pollination syndrome and classified them according to their roles within the architecture and function of the system. Our results define a molecular framework for the post-pollination syndrome and the flower-to-fruit transition in Vanilla planifolia , linking transcriptional organization with anatomical development and supporting its interpretation as an integrated regulatory system. This approach provides a reproducible and generalizable strategy for identifying and prioritizing key regulators in non-model plants with complex reproductive transitions.