Transcriptionally active LTR retroelement-related sequences and their relationship with small RNA in moso bamboo (Phyllostachys edulis)

Abstract

Many different cultivars or forms with diverse phenotypes of moso bamboo have been produced during its long cultivation history. The diverse phenotypes of moso bamboo are mainly reversible and unpredictable during cultivation, which lead to the hypothesis of their epigenetic origin. Earlier studies have shown that transposable elements might be involved in the different expression patterns of moso bamboo genes. LTR (long terminal repeat) retroelement populations are the main components of moso bamboo genomes. In the present study, a genome-wide analysis addressing their potential impact on host gene expression and the regulatory network was carried out. The results show that LTR retroelements are usually inserted far away from the gene regions. Transcriptional activity appears to be common in some moso bamboo retroelement-related sequences. The expression level and number of retroelement-related sequences tend to decrease with increasing distance from the closest genes, indicating that the interaction between retroelement-related sequences and near genes might play a role in the expression pattern of retroelement-related sequences. Retroelement-related sequences generate more than 30% of the siRNAs in moso bamboo. Both 21-nt siRNA and 24-nt siRNA mainly target within LTR regions of the bamboo LTR retroelements. Given the high copy number of LTR retroelements, the transcriptional activity of LTR retroelements, and the high number of siRNAs derived from the LTR retroelements, moso bamboo LTR retroelements might be involved in the transcriptional regulation of host genes, and this may be responsible for the diverse phenotypes of moso bamboo.