LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots

Abstract

RNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in mammals. By contrast, long terminal repeat (LTR) retrotransposons appear to be the major player in plants, although an L1-like mechanism has also been hypothesized to be involved in retroposition. We tested this hypothesis by searching for young retrocopies, as these still retain the sequence features associated with the underlying retroposition mechanism. Specifically, we identified polymorphic retrocopies (retroCNVs) by analyzing public Arabidopsis (Arabidopsis thaliana) resequencing data. Furthermore, we searched for recently originated retrocopies encoded by the reference genome of Arabidopsis and Manihot esculenta. Across these two datasets, we found cases with L1-like hallmarks, namely, the expected target site sequence, a polyA tail and target site duplications. Such data suggest that an L1-like mechanism could operate in plants, especially dicots.

LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans

“…Our previous work in plants has found that LTR-and non-LTR-mediated retroposition appear to occur with roughly equal rates in dicots (Arabidopsis thaliana and Manihot esculenta) (Zhu et al 2016). In this work, we confirm that L1-mediated retroposition is the dominant mechanism of retroposition in human and mouse (Kaessmann et al 2009).…”

The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

“…This observation (Ohshima 2013) has prompted additional studies including a recent work in Arabidopsis thaliana and cassava (Zhu et al 2016), two dicots harboring both LINE and SINE sequences in their genome. Zhu and colleagues found that some retroCNVs maintain the footprints of reverse transcription and insertion mechanisms (see section “Evolutionary insights from retroCNVs”) and that a few young retrocopies were likely generated by LINE retroelements.…”

“…Discoveries of LTR retroelement sequences flanking single genes in maize (Bureau et al 1994; Jin and Bennetzen 1994) have been followed by genome-wide investigations of LTR elements involved in retrogenes formation in rice (Wang et al 2006), Arabidopsis (Zhu et al 2016) and more recently of retroCNVs in animals (Tan et al 2016). It does seem that, as initially observed for the Ty1 element in yeast (fig.…”

“…They have also been recently analyzed in Arabidopsis and cassava (Zhu et al 2016). As mentioned above, the identification of retroCNVs depends on mapping short reads or paired reads from multiple individuals onto an available reference genome.…”

PlantRGDB: A Database of Plant Retrocopied Genes

“…Retrocopies have been identified in the genomes of Drosophila melanogaster (Schrider et al 2011), nematode (Zou et al 2012), human (Ohshima et al 2003, Zhang et al 2003, Vinckenbosch et al 2006, mammals (Pan andZhang 2009, Carelli et al 2016) and fish (Fu et al 2010, Du andHe 2015). In plants, hundreds of retrocopies have been found in Arabidopsis (Zhang et al 2005, Benovoy and Drouin 2006, Zhu et al 2016, rice (Wang et al 2006, Sakai et al 2011, Populus (Zhu et al 2009) and green algae (Jakalski et al 2016) via genome-wide analysis. These studies provide further support for the importance of retroposition in genome evolution (Zhang et al 2014).…”