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

The New Phytologist
Yushuai WangTian Tang

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 contin...Continue Reading

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Citations

Mar 18, 2020·The New Phytologist·Mimmi C ErikssonOvidiu Paun
Jan 30, 2021·Journal of Applied Genetics·Agata TyczewskaTomasz Twardowski
May 19, 2021·Heredity·Ajinkya Bharatraj Patil, Nagarjun Vijay
Sep 8, 2021·Frontiers in Plant Science·Rahman EbrahimzadeganGhader Mirzaghaderi

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