Sonneratia alba DNA methylation and small RNA sequencing

Transposable elements (TEs) are an important source of genetic diversity and can be co-opted or exapted for the regulation of host genes. Despite their capacity to be responsive to internal and external stimuli, the evolution and regulatory activities of TEs in plants that grow in challenging environments remain poorly understood. Sonneratia alba is a pioneer mangrove that is more salt tolerant than its relative S. caseolaris. S. alba possesses more TEs than S. caseolaris. Particularly, much more young Gypsy LTR (long terminal repeat) retrotransposons have been accumulated in S. alba than in S. caseolaris, albeit purifying selection against TE insertions is stronger in the former. The top two abundant Gypsy families in S. alba exhibited preferential insertion in gene-poor regions together with relaxation of epigenetic repression, probably associated with the CHROMO domain in their 3'-ends. Although considerable TEs in S. alba showed differential expression under salt stress, only two copies were positively correlated with their nearby genes in expression levels. One such TE-gene pair involves Abscisic acid 8'-hydroxylase 3 functioning in absisic acid catabolism. This study shed light on the evolutionary dynamics and potential function of TEs in an extremophile. Our results suggest that co-option of TEs is rare even though activation of TEs by stress might be prevalent.