BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

Abstract

We characterized a Brassica miniature inverted repeat transposable element (MITE) from the Stowaway superfamily, designated BraSto (Bra ssica Sto waway). BraSto copy number was assessed using real-time quantitative PCR in the two diploid species B. rapa (genome A) and B. oleracea (genome C) and the corresponding allotetraploid species B. napus (genome AC). Phylogenetic relationships among a set of 131 BraSto copies were then analyzed. BraSto appears to have been only moderately amplified in the Brassica genome and was still active recently with marks of proliferation in both diploid Brassica species, which diverged 3.75 million years ago, but also in the allotetraploid species after reuniting of the two differentiated genomes. We characterized insertion sites for low-divergence BraSto copies among the gene space of the B. rapa genome using bioinformatics approaches. For BraSto copies localized nearby or within genes, we observed frequent associations of BraSto with putative promoters and regulatory regions of genes, but exclusion from coding regions. In addition, BraSto was significantly similar to several Brassica expressed sequence tags (ESTs), including stress-induced ESTs. We also demonstrated the enrichment of BraSto sequences in binding sites for transcription factors and other regulatory elements. Our results lead to the question of a role for BraSto in the regulation of gene expression: this putative role, if further confirmed experimentally, would help to obtain a new insight into the significance of MITEs in the functional plant genome.

Miniature Transposable Elements (mTEs): Impacts and Uses in the Brassica Genome

“…The TIRs are more conserved than their respective internal sequences, and act as a recognition site for endonucleases for integration of TEs via transposition (Casacuberta and Santiago 2003). The TIRs are complementary to each other, leading to the formation of a secondary loop structure, which can be a source of small RNA and may act in gene regulation (Mo et al 2012;Sampath et al 2013;Sarilar et al 2011). The internal sequences of MITEs have sequence diversity due to the influence of unrelated autonomous TEs during transposition (Sampath et al 2013;.…”

“…Transposition of MITEs into genes have been found to modify gene structure and function by deletion, point mutation, and affecting the transcriptional activity Mo et al 2012;Sarilar et al 2011;Shirasawa et al 2012). Specifically, MITE transposition into introns in triplicated B. rapa genes appears to underlie their differential expression patterns (Sampath et al 2013) (Fig.…”

Mechanisms of Transposable Element Evolution in Plants and Their Effects on Gene Expression

“…Although some LTR retrotransposons show no insertional preference [107], TE families with a preference towards euchromatic regions include miniature inverted repeat elements (MITEs), SINEs, helitrons, CACTAs, and MULEs [19,96,[108][109][110][111]. Likewise, the Ds/Spm family preferentially inserts in GC-rich regions around translational initiation sites [112], with a similar insertion pattern noted for the BraSto MITE family in Brassica species [113]. With higher mutagenic potential, the Tos17 and Ac/Ds TE families in rice show an insertion preference towards exons [114][115][116].…”

“…Where they have a positive effect, they can confer stress-inducible expression on the adjacent genes, thereby contributing to new gene-regulatory networks [104]. Similarly, the BraSto elements in Brassica species may provide new transcription factor-binding sites, thereby regulating gene expression, particularly under stress [113]. Through high insertion rates in heterochromatic regions, TEs may be also be functionally domesticated to provide centromeres (e.g., in potatoes [217,218]) or matrix attachment regions (e.g., in rice and sorghum [219]).…”

The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications

“…), these long-term effects are likely to be similar in autopolyploids and in the long run we can expect the initial differences in transposition burst triggered by the two modes of polyploidization to be less important compared to the relaxation of purifying selection shared by both systems. Indeed, in the allotetraploid Capsella bursa-pastoris, an increase in TE content was observed around genes compared to its two parental diploid species, C. grandiflora and C. orientalis, which was attributed primarily to a relaxation of purifying selection and not to any change in TE activity (Ågren et al, 2016), and there is accumulating evidence of TE proliferation over long timespans following polyploidization (Sarilar et al, 2011;Yaakov and Kashkush, 2012;Piednoël et al, 2015). However, this doesn't seem to apply to all TE families equally.…”