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Constant conflict between Gypsy LTR retrotransposons and CHH methylation within a stress‐adapted mangrove genome
Author(s) -
Wang Yushuai,
Liang Weiqi,
Tang Tian
Publication year - 2018
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.15209
Subject(s) - retrotransposon , genome , biology , mangrove , genetics , methylation , constant (computer programming) , evolutionary biology , ecology , transposable element , gene , computer science , programming language
Summary The evolutionary dynamics of the conflict between transposable elements ( TE s) and their host genome remain elusive. This conflict will be intense in stress‐adapted plants as stress can often reactivate TE s. 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 (si RNA ) 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 si RNA ‐mediated CHH methylation preferentially targeting Gypsy elements, particularly in their LTR regions. Old Gypsy elements possess unusually abundant si RNA s 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.