Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis

Abstract

Background Small RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in Hevea. Methods Genes producing microRNAs (MIR genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different Hevea tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20–22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators. Results Compared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the Argonaute and Dicer-like gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers.

Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis

“…We had previously identified 445 transcripts degraded by miRNAs [20]. In this study, we did not identify any targets that were post-transcriptionally regulated by TE-derived siRNAs, consistent with the literature, revealing only translation inhibition and miRNA mimicry.…”

“…These analyses are a valuable resource for comparative epi/genomics within the Euphorbiacae, and transposon tagging for designing clone-specific molecular markers in Hevea. We had already demonstrated that the natural rubber biosynthesis pathway is under post-transcriptional control [20]. This work shows that this biosynthesis pathway is also under transcriptional control with a major role of TEs, which are functionalized in the promoters of the genes involved in natural rubber biosynthesis.…”

“…Diagram of the bioinformatics analyses described in this study, and data origins. Numbers refer to references mentioned in the text [4,5,17,18,20,21,35,[37][38][39]. TEdenovo detected 7655 consensus sequences, which were added to the expert bank already containing the consensuses obtained by LTR_STRUCT (9448 sequences in total).…”

“…In this case, 164,180 genes were detected, with a BUSCO score of 91% complete genes (Supplementary data 3). The large number of predicted genes was probably due to gene fragmentation related to assembly errors, or to transposable element genes (the capsid Gag protein To look into possible implication of in post-transcriptional regulation, degradome data were analysed with TE-derived siRNA data sets (20-22 nt), excluding previously identified miRNAs [20]. None of the TE-derived siRNAs with a size of 20-22 nt demonstrated post-transcriptional activity as well as for 24-nt TE-derived siRNA as expected (data not shown).…”

“…Several de novo genomes of rubber clones, with contrasting latex physiology, are available such as Reyan 7-33-97 [4], RRIM 600 [18], BPM 24 [19]; PB 260 [20,21] and GT 1 [5]. The rubber tree genome is large and complex to assemble because of its high heterozygosity, whole genome duplication and transposable element (TE) content [4,5].…”