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Abstract Rafflesiaceae is a family of endangered plants whose members are solely parasitic to the tropical grape vineTetrastigma(Vitaceae). Currently, the genetics of their crosstalk with the host remains unexplored. In this study, we use homology-basedin silicoapproaches to characterize micro-RNAs (miRNAs) expressed bySapria himalayanaandRafflesia cantleyifrom published omics data. Derived from secondary structures or hairpins, miRNAs are small regulators of gene expression. We found that some plant-conserved miRNA still exists in Rafflesiaceae. Out of 9 highly conserved miRNA families in plants, 7 families (156/157, 159/319, 160, 165/166, 171, 172, 390) were identified with a total of 22 variants across Rafflesiaceae. Some miRNAs were missing endogenous targets and may have evolved to target host miRNA, though this requires experimental verification. Rafflesiaceae miRNA promoters are mostly inducible by ethylene that mediates stress response in the host but could be perceived by the parasites as a signal for growth. This study provides evidence that certain miRNAs with ancient origins in land plants still exist in Rafflesiaceae, though some may have been coopted by parasites to target host genes. 

Societal Impact Statement Rafflesiais a genus of parasitic plants with the largest flowers in the world, unique to the threatened forest habitats of tropical Asia. Here, we report on genes that are active (the transcriptome) inRafflesiaseeds as part of a larger effort to understandRafflesia.Rafflesiahas never been grown successfully outside of its native range. Consequently, seed banking is not yet possible, precluding a critical management strategy for conservation. The study ofRafflesiaseed biology is a critical step to improve its cultivation, which will educate the public about unique species and the importance of conserving their habitats. SummaryRafflesiais of great interest as one of the only two plants known to have completely lost its chloroplast genome.Rafflesiais a holoparasite and an endophyte that lives inside the tissues of its host, a tropical grape vine (Tetrastigma), emerging only to bloom—with the largest flower of any plant. Here, we report the firstRafflesiaseed transcriptome and compare it with those of other plants to deepen our understanding of its extraordinary life history.We assembled a transcriptome from RNA extracted from seeds of the Philippine endemicRafflesia speciosaand compared this with those of other plants, includingArabidopsis, parasitic plantsStrigaandCuscuta, and the mycoheterotrophic orchidAnoectochilus.Genetic and metabolic seed pathways inRafflesiawere generally similar to the other plant species. However, there were some notable exceptions. We found evidence of horizontal transfer of a gene potentially involved in circumventing host defenses. Moreover, we identified a possible convergence among parasitic plants becauseRafflesia,Striga, andCuscutashared important similarities. We were unable to find evidence of genes involved in mycorrhizal symbiosis, suggesting that mycoheterotrophy is unlikely to play a role inRafflesiaparasitism.To date, ex situ propagation ofRafflesiaby seed has been mostly unsuccessful. Our research is a bold step forward in understanding the fundamentals ofRafflesiaseed biology that will inform the continued propagation and seed‐banking efforts concerning this recalcitrant plant. We discuss our findings in the broader context of the conservation of a genus in peril.