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

Wu Shuangqing, Guyot Romain, Bocs Stéphanie, Droc Gaëtan, Oktavia Fetrina, Hu Songnian, Tang Chaorong, Montoro Pascal, Leclercq Julie. 2020. 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. International Journal of Molecular Sciences, 21 (12):4220, 21 p.

Quartile : Q1, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY / Quartile : Q2, Sujet : CHEMISTRY, MULTIDISCIPLINARY

Résumé : 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.

Mots-clés Agrovoc : Hevea brasiliensis, biosynthèse, transposon, caoutchouc, épigénétique, arn, Transcription génique

Mots-clés libres : Transposable elements, SiRNA, Rubber tree, Transcriptional regulation, Epigenomics

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Auteurs et affiliations

• Wu Shuangqing, Academy of Agricultural Sciences (CHN)
• Guyot Romain, IRD (FRA)
• Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
• Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-1849-1269
• Oktavia Fetrina, IRRI [International Rice Research Institute] (THA)
• Hu Songnian, CAS (CHN)
• Tang Chaorong, Hainan University (CHN)
• Montoro Pascal, CIRAD-BIOS-UMR AGAP (FRA)
• Leclercq Julie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8110-3762 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/597543/)

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