Abstract
Long terminal repeat (LTR) retrotransposons constitute the majority of the content of angiosperm genomes, but their evolutionary dynamics remain poorly understood. Here, we report the isolation and characterization of a putative full-length (~9550 bp) Ty1/copia-like retrotransposon in Excoecaria agallocha and its evolution in Euphorbiaceae. The so-called EARE-1 is phylogenetically closely related to RIRE-1 from Oryza australiensis, and has proliferated recently (~7.19 Mya) in the E. agallocha genome. An RT-PCR analysis revealed substantial transcription of EARE-1 in all examined organs (leaves, staminate flowers, pistillate flowers, seeds, and roots) in unstressed E. agallocha plants and indications of elevated expression under stress. We conducted sequence analyses of 256 RT-RH fragments (~860 bp) of EARE-1 from 34 species representing four subfamilies of Euphorbiaceae that exist in China. EARE-1 copies from two Excoecaria species and Phyllanthus urinaria showed incongruent phylogeny with the host species and exhibited high sequence similarity to the host genes, suggesting a horizontal transfer from P. urinaria to the common ancestor of Excoecaria. However, SSAP analysis detected no new insertions of EARE-1 among full-sibling progeny plants of E. agallocha, despite considerable SSAP polymorphisms among half-siblings. EARE-1 is the first transcriptionally active Ty1/copia-like retrotransposon isolated from E. agallocha. Our results provide empirical evidence of the horizontal transfer of LTR retrotransposons in plants, and may suggest a significant role of post-transcriptional host control in the life cycles of transposable elements.
Highlights
Long terminal repeat (LTR) retrotransposons are ubiquitous transposable elements (TEs) that constitute the majority of the content of higher plant genomes (Lee and Kim, 2014)
The observed low ratio of LTR to the internal region (2.16–2.48) of EARE-1 indicates either that the efficiency of removal of EARE-1 by unequal intra-strand homologous recombination (UHR) is low or that a recent burst of transposition has occurred that outpaces DNA removal by recombination. We considered the latter scenario more plausible, since EARE-1 has long LTRs approximately 1900 bp in length that should be readily subject to UHR
horizontal transfer (HT) has been shown to preferentially occur in several TE types (Schaack et al, 2010). Consistent with this notion, we found that EARE-1 is phylogenetically close to RIRE1, which is extremely successful in the wild rice O. australiensis (Noma et al, 1997; Piegu et al, 2006)
Summary
Long terminal repeat (LTR) retrotransposons are ubiquitous transposable elements (TEs) that constitute the majority of the content of higher plant genomes (Lee and Kim, 2014). The retrotransposon life cycle has been shown to involve multiple steps that are inherently error-prone and mutagenic (Sabot and Schulman, 2006). This leads to numerous remnant elements that are incapable of transposition due to accumulated mutations. Studies have shown that the transposition of retrotransposons is under strict host control by small RNA-mediated gene silencing at the transcriptional and posttranscriptional levels, which further limits their replication and transmission (Slotkin and Martienssen, 2007; Rigal and Mathieu, 2011). High sequence similarity between TEs from distantly related taxa, tree incongruence between TEs and the host species and/or patchy distributions of TEs in phylogenies are three lines of evidence commonly used to infer HT (Daniels et al, 1990; Syvanen, 1994; Roulin et al, 2009)
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