Background: Alternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year ("on-year"), followed by a low-yield or even no crop the following year ("off-year"). Several factors may affect the balance between such developmental phase-transition processes. Among them are the microRNA (miRNA), being gene-expression regulators that have been found to be involved as key determinants in several physiological processes. Results: Six olive (Olea europaea L. cv. Ayvalik variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves (”on year” and ”off year” leaves in July and in November, respectively) and sequenced by high-throughput Illumina sequencing. The RNA was retrotranscribed and sequenced using the high-throughput Illumina platform. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in the olive. In addition, 38 putative novel miRNAs were discovered in the datasets. Expression of olive tree miRNAs varied greatly among the six libraries, indicating the contribution of diverse miRNA in balancing between reproductive and vegetative phases. Predicted targets of miRNA were categorized into 108 process ontology groups with significance abundance. Among those, potential alternate bearing-associated processes were found, such as development, hormone-mediated signaling and organ morphogenesis. The KEGG analyses revealed that the miRNA-targeted genes are involved in seven main pathways, belonging to carbohydrate metabolism and hormone signal-transduction pathways. Conclusion: A comprehensive study on olive miRNA related to alternate bearing was performed. Regulation of miRNA under different developmental phases and tissues indicated that control of nutrition and hormone, together with flowering processes had a noteworthy impact on the olive tree alternate bearing. Our results also provide significant data on the miRNA-fruit development interaction and advance perspectives in the miRNA profile of the olive tree.

DNA methylation is one of the major epigenetic modifications influencing the regulation of gene expression. The opium poppy is an important medicinal plant. Its latex contains opium, which is a rich source of pharmaceutical benzyisoquinoline alkaloids (BIA). Here, the methylation-sensitive amplification polymorphism (MSAP) profiling technique using 21 MSAP molecular markers was applied in order to compare levels of DNA methylation between 6 opium poppy varieties. MSAP profiling reflected the different methylation statuses among opium poppy varieties having divergent BIA content. Moreover, different organ-specific epigenetic profiles were observed between the samples. Differential epigenetic profiles of capsules and shoots from the leaves pointed to the impact of methylation on BIA biosynthesis. The data implied that the different DNA methylation status may have important biological significance, in the case of alkaloid content in opium poppy in particular.

Papaver somniferum is a medicinal plant of the Papaveraceae family that has traditionally been used for diet or its therapeutic value for thousands of years. Mainly, morphine and noscapine alkaloids exhibit anti-analgesic and anti-cancer effects. However, gene expression patterns and regulatory elements, such as transcription factors between different tissues, still need to be detected. In this study, comparative in silico transcriptome analyses were conducted to examine the tissue-specificity of the benzylisoquinoline alkaloids (BIAs) biosynthetic genes and transcription factors (TFs) between morphine and noscapine cultivars. Analysis showed that BIA biosynthetic genes are expressed in a different pattern between two varieties. Results showed that some members of plant-specific secondary metabolites related to TF families, such as MYB, MADS-box, bHLH, NAC, and WRKY, are differentially expressed between tissues and varieties.

We examined the proteomic profiles of three registered opium poppy cultivars (Papaver somniferum L.) having different alkaloid contents. The study was conducted on both the stem and capsule organs. A high number of differentially expressed proteins (DEPs) were identified between the cultivars and the organs. We analyzed DEPs for their contribution in GO terms and KEGG pathways. The up-regulated DEPs were significantly enriched in photosynthesis and translation, for morphine-rich and noscapine-rich cultivars, respectively. The data depicted that photosynthesis is crucial for Benzylisoquinoline alkaloid (BIA) biosynthesis, but different processes are also effective on morphine and noscapine biosynthesis, which occur at different branches in the biosynthetic pathway. The protomic profiles revealed that energy demand is more effective in morphine biosynthesis, while translational control has a leading role in noscapine biosynthesis. This is the first report demonstrating the organ-based and cultivar-based protein expression differences in mature poppy plant.

Background: Papaver somniferum (opium poppy) is a major source of benzylisoquinoline alkaloids (BIAs), including pharmaceutically important compounds such as morphine and noscapine. While the enzymatic pathways underlying BIA biosynthesis are well-characterized, the epigenetic mechanisms that govern tissue- and genotype-specific alkaloid accumulation remain poorly understood. Results: This study presents a comparative DNA methylation analysis of stem and capsule tissues from P. somniferum cultivars with distinct alkaloid profiles. High-alkaloid-yielding cultivars exhibited hypomethylation of genomic regions involved in photosynthesis, carbon metabolism, protein phosphorylation, and intracellular transport, particularly in stem tissues. DNA methylation patterns revealed tissue- and compound-specific epigenetic signatures: morphine-rich cultivars showed enrichment of differentially methylated regions (DMRs) associated with membrane-related functions, whereas noscapine-rich cultivars exhibited DMR enrichment in nuclear regulatory components and ribosome-associated pathways. Genes encoding cytochrome P450 enzymes, F-box proteins, and ABC transporters were differentially expressed and epigenetically modulated, reflecting a multi-layered regulatory network coordinating biosynthesis, transport, and detoxification of alkaloids. Conclusions: Our findings suggest that noscapine biosynthesis is under strict, evolutionarily conserved regulatory control, while morphine production is supported by transcriptional and metabolic enhancements in photosynthesis and carbohydrate metabolism. This study provides the first integrative epigenomic perspective on alkaloid biosynthesis in the opium poppy and highlights DNA methylation as a key determinant of metabolic specialization.