Domestication of Transposable Elements into MicroRNA Genes in Plants

Abstract

Transposable elements (TE) usually take up a substantial portion of eukaryotic genome. Activities of TEs can cause genome instability or gene mutations that are harmful or even disastrous to the host. TEs also contribute to gene and genome evolution at many aspects. Part of miRNA genes in mammals have been found to derive from transposons while convincing evidences are absent for plants. We found that a considerable number of previously annotated plant miRNAs are identical or homologous to transposons (TE-MIR), which include a small number of bona fide miRNA genes that conform to generally accepted plant miRNA annotation rules, and hairpin derived siRNAs likely to be pre-evolved miRNAs. Analysis of these TE-MIRs indicate that transitions from the medium to high copy TEs into miRNA genes may undergo steps such as inverted repeat formation, sequence speciation and adaptation to miRNA biogenesis. We also identified initial target genes of the TE-MIRs, which contain homologous sequences in their CDS as consequence of cognate TE insertions. About one-third of the initial target mRNAs are supported by publicly available degradome sequencing data for TE-MIR sRNA induced cleavages. Targets of the TE-MIRs are biased to non-TE related genes indicating their penchant to acquire cellular functions during evolution. Interestingly, most of these TE insertions span boundaries between coding and non-coding sequences indicating their incorporation into CDS through alteration of splicing or translation start or stop signals. Taken together, our findings suggest that TEs in gene rich regions can form foldbacks in non-coding part of transcripts that may eventually evolve into miRNA genes or be integrated into protein coding sequences to form potential targets in a “temperate” manner. Thus, transposons may supply as resources for the evolution of miRNA-target interactions in plants.

Identification of microRNA elements from genomic data of European hazelnut (Corylus avellana L.) and its close relatives

“…Those young miRNAs may have some species-specific regulatory roles inside the organisms (Sun et al 2012;Fahlgren et al 2007). On the other hand, the highest number of hits might be also TE-derived microRNAs because most of the transposable elements were domesticated into microRNA genes (Li et al 2011).…”

MiRNAs’ Function and Role in Evolution: Under the View of Genomic Enhancement Phenomena

“…Recently, strong evidence was published for similar procedures in plants [ 32 , 36 , 43 ]. The very detailed bioinformatic analysis by Li et al [ 32 ] gave results supporting the notion that TEs in gene rich regions in plants can form foldbacks in non-coding part of transcripts that may eventually evolve into miRNA gene s or be integrated into protein coding sequences to form potential targets in a "temperate" manner. A similar work by Sun et al [ 36 ] in four plant species confi rmed that a signifi cant number of miRNAs in plants derived from TEs.…”

In silico Analysis of MicroRNAs in Spinacia oleracea Genome and Transcriptome

“…Low representations of miRNA families are also included in the analysis because they might be 'young-miRNAs'. On the other hand, the highest number of hits might be repetitive elements since most of the transposable elements have been domesticated into microRNA genes and they have high number of copies throughout the genome [19]. Fig.…”