Abstract
Similarly to other plant genomes of similar size, more than half of the genome of P. patens is covered by Transposable Elements (TEs). However, the composition and distribution of P. patens TEs is quite peculiar, with Long Terminal Repeat (LTR)-retrotransposons, which form patches of TE-rich regions interleaved with gene-rich regions, accounting for the vast majority of the TE space. We have already shown that RLG1, the most abundant TE in P. patens, is expressed in non-stressed protonema tissue. Here we present a non-targeted analysis of the TE expression based on RNA-Seq data and confirmed by qRT-PCR analyses that shows that, at least four LTR-RTs (RLG1, RLG2, RLC4 and tRLC5) and one DNA transposon (PpTc2) are expressed in P. patens. These TEs are expressed during development or under stresses that P. patens frequently faces, such as dehydratation/rehydratation stresses, suggesting that TEs have ample possibilities to transpose during P. patens life cycle. Indeed, an analysis of the TE polymorphisms among four different P. patens accessions shows that different TE families have recently transposed in this species and have generated genetic variability that may have phenotypic consequences, as a fraction of the TE polymorphisms are within or close to genes. Among the transcribed and mobile TEs, tRLC5 is particularly interesting as it concentrates in a single position per chromosome that could coincide with the centromere, and its expression is specifically induced in young sporophyte, where meiosis takes place.
Highlights
Mosses are one of the oldest groups of land plants, forming a sister clade with vascular plants (Leebens-Mack et al, 2019)
A single retrotransposon family, RLG1 accounts for almost half (47.44%) of the genome space occupied by class I elements (Lang et al, 2018)
RLG1 is actively expressed in nonstressed protonema cells, and it may have transposed recently during P. patens evolution, as some of its copies are polymorphic between P. patens Gransden and Villersexel ecotypes (Vives et al, 2016; Lang et al, 2018)
Summary
Mosses are one of the oldest groups of land plants, forming a sister clade with vascular plants (Leebens-Mack et al, 2019). Transposable Elements (TEs) account for the 57% of the 462,3 Mb of the assembled P. patens genome This TE coverage is not very different from that of other plant genomes of similar size (Tenaillon et al, 2010). The RLG1 retrotransposon is transcribed in P. patens protonema cells, suggesting that it can transpose during P. patens development (Vives et al, 2016; Lang et al, 2018) These data suggest that TE activity may have shaped the genome of P. patens and may continue to generate variability that potentially impact P. patens evolution, the global analysis of the capacity of P. patens TEs to be expressed and transpose is still lacking. The data presented here reinforce the idea that TEs have shaped the genome of P. patens and show that they continue to drive its evolution
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