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. 2020 Apr 29:8:e8932.
doi: 10.7717/peerj.8932. eCollection 2020.

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

Julie Leclercq #  1   2 , Shuangyang Wu #  3 , Benoît Farinas  1   2 , Stéphanie Pointet  1   2 , Bénédicte Favreau  1   2 , Hélène Vignes  1   2 , Kuswanhadi Kuswanhadi  4 , Enrique Ortega-Abboud  1   2 , Jean-François Dufayard  1   2 , Shenghan Gao  3 , Gaëtan Droc  1   2 , Songnian Hu  3 , Chaorong Tang  5 , Pascal Montoro  1   2
Affiliations

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

Julie Leclercq et al. PeerJ. .

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.

Keywords: Abiotic stress; Crop epigenomics; Degradome; Latex; Rubber tree; Small RNA; miRNA.

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Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Scheme representing the analysis process fordeciphering post-transcriptional regulations in Hevea by miRNAs.
Each step is commented on the ‘Results’ section. The pipelines or tools used for the detection, classification and functional identification of miRNAs and their targets are shown in italic styling.
Figure 2
Figure 2. Scheme representing the exploration of degradome libraries.
CleaveLand pipeline is used in order to detect miRNA-mediated cleaved targets, with transcriptome and small RNA dataset as input. The abundance of reds starting at the cleavage site is define by the degradome category (see ‘Materials & Methods’).
Figure 3
Figure 3. Scheme representing the analyses process for deciphering post-transcriptional regulations in Hevea by ta-siRNAs.
Each step is commented on the ‘Results’ section. The pipelines or tools used for the detection, classification and functional identification of ta-siRNAs and their targets are shown in italic styling.
Figure 4
Figure 4. Length distribution of unique miRNA accessions.
MiRNAs were annotated by the MITP pipeline for Hevea brasiliensis plant tissues leaf, bark, root (black, Gébelin et al., 2012) and latex from healthy (dark grey) and TPD-affected (light grey) trees (Gébelin et al., 2013b).
Figure 5
Figure 5. Five prime base preference for small RNA of 20–22 nt in each small RNA data set.
Each base preference is indicated by a specific color.
Figure 6
Figure 6. T-plots generated by CleaveLand.
Alignments show the cleavage site experimentally validated (Gébelin et al., 2012), corresponding exactly to the cleavage site predicted by the degradome analysis showed by a red point on the T-plot. (A) SBP (CL2120Contig2)/miR156 (acc_480780). (B) ARF (CL6582Contig1)/miR160 (acc_370). (C) Chloroplastic CuZnSOD (CL4308Contig 2)/miR398 (acc_420).
Figure 7
Figure 7. Venn diagram built with sRNA accessions withslicing activity.
Six tissue-derived degradome libraries were tested (leaf, bark, root, reproductive tissues, latex, embryo).
Figure 8
Figure 8. T-plots generated by CleaveLand pipeline for miRNA/transcription factor pairs with a degradome category 0 (many readsstarting at the cleavage site). (A) HbMYC. (B) HbRAV-03. (C) HbERF-VIIa8. (D) HbERF-VIIa5.
Figure 9
Figure 9. Phylogenetic tree for Hevea and other plants of AGO andDCL proteins.
The Hevea amino acid sequences were aligned with the full-length amino acid sequences of genes in Populus trichocarpa Ricinus communis and Arabidopsis thaliana to construct a phylogenetic tree by MrBayes (v3.2.6 x64). (A) AGO proteins. (B) DCL proteins.
Figure 10
Figure 10. Analysis of miRNA biogenesis in Hevea brasiliensis.
Transcripts encoding miRNA biogenesis genes were identified by BLASTX analysis [DCL: Ribonuclease III-like DICER; SE: SERRATE (SE = mRNA00000153; SE-X2 = mRNA00000144-X2); HYL: Hyponastic leaves; AGO: ARGONAUTE; SDN: Small RNA degrading nuclease (SDN.1 = mRNA00000175; SDN.2 = mRNA00000202 and SDN.3 = mRNA00000068); HST: HASTY (HST = mRNA00000162; HST variant X2 = mRNA00000150-X2); HEN: Hua enhancer].
Figure 11
Figure 11. A simplified natural rubber biosynthesis pathway showing the miRNA cleaving the target transcripts.
miRNAs found only in latex are shown in bold.
See this image and copyright information in PMC

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Grants and funding

Shuangyang Wu benefited a scholarship from the UCAS Joint PhD Training Program. Julie Leclercq and Shuangyang Wu benefited a mobility program in 2018 from Campus France (Xu Guangqi Program no 41241QJ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.