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. 2020 Jun 13;21(12):4220.
doi: 10.3390/ijms21124220.

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

Shuangyang Wu  1   2   3   4 , Romain Guyot  5   6 , Stéphanie Bocs  1   2   7 , Gaëtan Droc  1   2   7 , Fetrina Oktavia  8 , Songnian Hu  4   9 , Chaorong Tang  10 , Pascal Montoro  1   2 , Julie Leclercq  1   2
Affiliations

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

Shuangyang Wu et al. Int J Mol Sci. .

Abstract

The natural rubber biosynthetic pathway is well described in Hevea, although the final stages of rubber elongation are still poorly understood. Small Rubber Particle Proteins and Rubber Elongation Factors (SRPPs and REFs) are proteins with major function in rubber particle formation and stabilization. Their corresponding genes are clustered on a scaffold1222 of the reference genomic sequence of the Hevea brasiliensis genome. Apart from gene expression by transcriptomic analyses, to date, no deep analyses have been carried out for the genomic environment of SRPPs and REFs loci. By integrative analyses on transposable element annotation, small RNAs production and gene expression, we analysed their role in the control of the transcription of rubber biosynthetic genes. The first in-depth annotation of TEs (Transposable Elements) and their capacity to produce TE-derived siRNAs (small interfering RNAs) is presented, only possible in the Hevea brasiliensis clone PB 260 for which all data are available. We observed that 11% of genes are located near TEs and their presence may interfere in their transcription at both genetic and epigenetic level. We hypothesized that the genomic environment of rubber biosynthesis genes has been shaped by TE and TE-derived siRNAs with possible transcriptional interference on their gene expression. We discussed possible functionalization of TEs as enhancers and as donors of alternative transcription start sites in promoter sequences, possibly through the modelling of genetic and epigenetic landscapes.

Keywords: epigenomics; rubber tree; siRNA; transcriptional regulation; transposable elements.

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Conflict of interest statement

The authors declare no conflict of interest and the funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
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].
Figure 2
Figure 2
Detailed diagram of the transposable element annotation process implemented by the LTR_STRUCT, REPET pipeline, MUST and Sine_finder.
Figure 3
Figure 3
Quantitative representation, on a genome scale, of LTR retrotransposon RT domains in the H. brasiliensis PB 260genomic sequences. The phylogenetic analysis was carried out with reverse transcriptase (RT) domains (19,151) having a length > 200 aa and amino-acid identity > 70% compared to the RT reference domains downloaded from GyDB. The Gypsy LTR retrotransposon clades are represented in different green and yellow colours. The Copia LTR retrotransposon clades are represented in purple.
Figure 4
Figure 4
Timing of full-length LTR retrotransposon insertions into the H. brasiliensis clone PB 260 genomic sequence. (A) Blue and red lines represent, respectively, the number of Ty1/copia (RLC) and Ty3/gypsy (RLG) full-length LTR retrotransposons per bins of 0.5 Million Years (MY). (B) Coloured lines represent the number of full-length Ty3/gypsy (RLG) LTR retrotransposon lineages per bins of 0.5 MY. (C) Coloured lines represent the number of full-length Ty1/copia (RLC) LTR retrotransposon lineages per bins of 0.5 MY. Only the full-length LTR retrotransposons found by LTR_STRUC were used here. An average substitution rate of 3.89 × 10−9 was used.
Figure 5
Figure 5
Length distribution of unique TE-derived small RNA accessions from Hevea tissues: (young trees (•), latex fromhealthy trees (•) and latex from TPD-affected trees (•)).
Figure 6
Figure 6
24-nt siRNA production by transposable element order and superfamilies (%).
Figure 7
Figure 7
Phylogenetic analysis of the nucleotide sequences of the REF/SRPP genes present on scaffold 1222 (Reyan 7-33-97 in red and PB 260 in blue). Manihot esculenta SRPP genes were added, as well as a superoxide dismutase gene (SOD) as an out-group. Local gene duplication in Reyan 7-33-97 when compared to PB 260 were shaded in light grey.
Figure 8
Figure 8
Scaffold 1222 sequence comparison between clones PB 260, Reyan 7-33-97, RRIM 600 and GT 1 by Dot-Plot and genomic DNA read abundance, gene, transposable elements and small RNA density (for PB 260 only). Genomic DNA reads are represented in dark blue, genes in black, transposable elements in light blue, and small RNA in red associated with their density profile. Regions of interest were zoomed in and displayed at the right.
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