Constant conflict between Gypsy LTR retrotransposons and CHH methylation within a stress‐adapted mangrove genome

Abstract

The evolutionary dynamics of the conflict between transposable elements (TEs) and their host genome remain elusive. This conflict will be intense in stress-adapted plants as stress can often reactivate TEs. Mangroves reduce TE load convergently in their adaptation to intertidal environments and thus provide a unique opportunity to address the host-TE conflict and its interaction with stress adaptation. Using the mangrove Rhizophora apiculata as a model, we investigated methylation and short interfering RNA (siRNA) targeting patterns in relation to the abundance and age of long terminal repeat (LTR) retrotransposons. We also examined the distance of LTR retrotransposons to genes, the impact on neighboring gene expression and population frequencies. We found differential accumulation amongst classes of LTR retrotransposons despite high overall methylation levels. This can be attributed to 24-nucleotide siRNA-mediated CHH methylation preferentially targeting Gypsy elements, particularly in their LTR regions. Old Gypsy elements possess unusually abundant siRNAs which show cross-mapping to young copies. Gypsy elements appear to be closer to genes and under stronger purifying selection than other classes. Our results suggest a continuous host-TE battle masked by the TE load reduction in R. apiculata. This conflict may enable mangroves, such as R. apiculata, to maintain genetic diversity and thus evolutionary potential during stress adaptation.

The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth

“…This suggests that while very high TE body methylation confirms preferential suppression of the transposable elements, the dynamics of non-CG methylation at the edges of TEs must have a distinct role. A dramatic increase in CHG and CHH methylation at the boundaries of TEs has been discussed before (Li et al, 2015;Noshay et al, 2019;Wang, Liang, & Tang, 2018;Zemach et al, 2013). However, barley LTRs (borders are targeted by CHH methylation) are mostly located in heterochromatin and do not show lowered CG and CHG methylation (quite the opposite).…”

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

“…Since all land plants and green algae possess the small RNA-generating RNAi machinery ( You et al, 2017 ), it is conceivable that gymnosperms, ferns and club mosses can potentially accumulate siRNAs derived from endogenous caulimovirids and/or their extant not-yet-identified episomal counterparts. Likewise, genomes of all land plants contain long terminal repeat (LTR) retrotransposons of the families Metaviridae (Ty3/Gypsy) and Pseudoviridae (Ty1/Copia) which can give rise to siRNAs as has been reported for the angiosperms A. thaliana ( Creasey et al, 2014 ; Masuta et al, 2017 ), strawberry ( Šurbanovski et al, 2016 ), mangrove ( Wang Y. et al, 2018 ), maize ( Alejandri-Ramírez et al, 2018 ) and wheat ( Sun et al, 2013 ); transposon-derived small RNAs were also reported for gymnosperms such as Picea glauca ( Liu and El-Kassaby, 2017 ) and Cryptomeria japonica ( Ujino-Ihara et al, 2018 ).…”

Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

“…However, such stressful conditions can activate transposable elements (TEs; Lyu et al , 2017). Recently, Wang et al (2018) were able to show that stress‐induced reactivations of TEs become epigenetically controlled by siRNAs‐mediated CHH methylation in the mangrove Rhizophora apiculata , but the short active windows of TEs can trigger genetic variation, possibly facilitating adaptation to new conditions.…”