Scenarios for the emergence of new microRNA genes in the plant Arabidopsis halleri

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Pavan, Flavia | Lacoste, Eléanore | Castric, Vincent | Legrand, Sylvain

Edité par CCSD ; Oxford University Press (OUP) -

International audience. Abstract MicroRNAs (miRNAs) are central players in the regulation of gene expression in eukaryotes. The repertoires of miRNA genes vary drastically even among closely related species, indicating that they are evolutionarily labile. However, the processes by which they originate over the course of evolution and the nature of their progenitors across the genome remain poorly understood. Here, we analyzed miRNA genes in Arabidopsis halleri, a plant species where we recently documented a large number of species-specific miRNA genes, likely to represent recent events of emergence. Analysis of sequence homology across the genome indicates that a diversity of sources contributes to the emergence of new miRNA genes, including inverted duplications from protein-coding genes, rearrangements of transposable element (TE) sequences, and duplications of preexisting miRNA genes. Our observations indicate that the origin from protein-coding genes was less common than was previously considered. In contrast, we estimate that almost half of the new miRNA genes likely emerged from TEs. Miniature inverted-repeat TEs (MITEs) seem to be particularly important contributors to new miRNA genes, with the Harbinger and Mariner TE superfamilies representing disproportionate sources for their emergence. We further analyzed the recent expansion of a miRNA family derived from MuDR elements and the duplication of miRNA genes formed by two hAT transposons. Overall, our results illustrate the rapid pace at which new regulatory elements can arise from the modification of preexisting sequences in a genome and highlight the central role of certain categories of TEs in this process.

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