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

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.

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

“…It has been well established that TEs are abundant in the rubber tree genome, and the proportion of TE types found in our study was similar to those found by other authors (Liu et al, 2020b; Tang et al, 2016; Wu et al, 2020). Responsible for major changes in the genetic architecture (e.g., rearrangements, duplication, gene breaking, and the origin of new genes) (Bennetzen, 2005; Flagel and Wendel, 2009; Lisch, 2013), TEs are usually neutral.…”

“…Responsible for major changes in the genetic architecture (e.g., rearrangements, duplication, gene breaking, and the origin of new genes) (Bennetzen, 2005; Flagel and Wendel, 2009; Lisch, 2013), TEs are usually neutral. However, such elements possess mutagenic potential due to epigenetic mechanisms and are able to alter regulatory networks and confer genetic adaptations, leading to important phenotypic variations (Lisch, 2013; Wei and Cao, 2016; Wu et al, 2020); this has currently received great attention in genetic improvement programs for several species (Domínguez et al, 2020; Lee et al, 2006; Wang et al, 2020). In Hbr, Wu et al (2020) showed that TEs located in gene regulatory regions in Hbr were involved in latex production through cis regulation, which would explain the differential gene expression among contrasting genotypes.…”

“…However, such elements possess mutagenic potential due to epigenetic mechanisms and are able to alter regulatory networks and confer genetic adaptations, leading to important phenotypic variations (Lisch, 2013; Wei and Cao, 2016; Wu et al, 2020); this has currently received great attention in genetic improvement programs for several species (Domínguez et al, 2020; Lee et al, 2006; Wang et al, 2020). In Hbr, Wu et al (2020) showed that TEs located in gene regulatory regions in Hbr were involved in latex production through cis regulation, which would explain the differential gene expression among contrasting genotypes. The incidence of PKs close to TEs pinpoints the importance of such elements on PK functionality, as already demonstrated by other studies describing TE-mediated regulation in kinases Fan et al (2019); Zayed et al (2007).…”

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

“…These TEs have already been described as being involved in gene expression, responses to external stimuli and plant development (Kashkush et al, 2003;Matsunaga et al, 2015;Traylor-Knowles et al, 2017;Tran and Choi, 2020). In rubber trees, TEs may be related to the differential expression observed in some commercial clones, affecting important processes such as rubber production (Wu et al, 2020a). As pointed out by Wang et al (2020), the identification of TEs associated with functional genes related to important characteristics suggest that they can be used as molecular markers in MAS, contributing significantly to the genetic improvement of woody trees.…”

“…This approach has become increasingly common in humans (Wu et al, 2018), animals (Fonseca et al, 2018), microorganisms (Wang et al, 2019), and combinations of species (Pinu et al, 2019). However, for plants, such integrated methodologies are still a great challenge, especially for nonmodel species with elevated genetic diversity and complex genomes (Jamil et al, 2020), which is the case for H. brasiliensis (Tang et al, 2016;Liu et al, 2020c, Wu et al, 2020a. Despite its economic importance, no study incorporating multiomics has been carried out on H. brasiliensis.…”