The evolutionary history and functional specialization of microRNA genes in <i>Arabidopsis halleri</i> and <i>A. lyrata</i>
MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To address this question, we first performed a detailed annotation of miRNA genes in the closely related Arabidopsis halleri and A. lyrata, then evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of "canonical" miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Analysis of nucleotide polymorphism distribution along the hairpin sequence (stem, mature miRNA, terminal loop) revealed that the selective constraints on recently emerged miRNA genes were initially weak, gradually increasing toward evolutionarily conserved miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary progression toward canonical miRNAs by which a small fraction of de novo formed miRNA genes eventually integrate into "core" biological processes.
Authors
- Karine Labadie (ORCID: https://orcid.org/0000-0001-7467-8509)
- Mathieu Genête (ORCID: https://orcid.org/0000-0002-9640-8793)
- Rita A. Batista (ORCID: https://orcid.org/0000-0002-2083-4622)
- Chloé Ponitzki (ORCID: https://orcid.org/0009-0007-0766-9451)
- Chloé Beaumont (ORCID: https://orcid.org/0009-0002-3291-6753)
- Corinne Cruaud (ORCID: https://orcid.org/0000-0002-4752-7278)
- Éléonore Durand (ORCID: https://orcid.org/0000-0002-0912-9252)
- Vincent Castric (ORCID: https://orcid.org/0000-0002-4461-4915)
- Sophie Gallina (ORCID: https://orcid.org/0000-0002-6194-3649)
- Christelle Blassiau
- Jean‐Marc Aury (ORCID: https://orcid.org/0000-0003-1718-3010)
- Sylvain Legrand (ORCID: https://orcid.org/0000-0002-7098-0273)
- Ute Kraemer (ORCID: https://orcid.org/0000-0001-7870-4508)
- Jacinthe Azevedo (ORCID: https://orcid.org/0000-0002-2096-0805)
- Eléanore Lacoste
- Claire Patiou
- Laurence Debacker
- Flavia Pavan (ORCID: https://orcid.org/0009-0007-9884-9553)
- Esther Houzé
- Vinod Kumar (ORCID: https://orcid.org/0000-0003-0843-1342)
- Firas Louis
Institutions
- Centre National de la Recherche Scientifique (FR)
- Université de Lille (FR)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Université Paris-Saclay (FR)
- Genoscope (FR)
- CEA Paris-Saclay (FR)
- Laboratoire Génome et Développement des Plantes (FR)
- Unité Évolution, Écologie et Paléontologie (FR)
- Ruhr University Bochum (DE)
Publication Details
- Journal
- The Plant Cell
- Published
- 2025-06-27
- DOI
- https://doi.org/10.1093/plcell/koaf168
- Citations
- 3
- Primary Topic
- Plant Molecular Biology Research
- Type
- article
- Field-Weighted Citation Impact
- 5.25
Funders
- Université de Lille
- Agence Nationale de la Recherche
- Ministry of Minority Affairs