The evolutionary history and functional specialization of microRNA genes inArabidopsis halleriandA. lyrata

Abstract

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 better understand this, we first performed a detailed annotation of miRNA genes in the closely related plants Arabidopsis halleri and A. lyrata and 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. Nucleotide polymorphism was lower in the mature miRNA sequence than in the other parts of the hairpin (stem, terminal loop), and the regions of coding sequences targeted by miRNAs also had reduced diversity as compared to their neighboring regions along the genes. These patterns were less pronounced for recently emerged than for evolutionarily conserved miRNA genes, suggesting a weaker selective constraint on the most recent miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary processes by which a small fraction of them eventually integrate into "core" biological processes.

Scenarios for the emergence of new miRNA genes in the plantArabidopsis halleri

“…Overall, we identified 104,231 TEs sequences, comprising 31.6% of the assembly (Figure 1), in line with Legrand et al (2019). The 463 miRNA precursor sequences predicted by Pavan et al (2024) collectively covered 0.04% of the genome. Among them, 310 are specific to A. halleri accessions, as they have not been observed in any of the 13 A. lyrata samples examined or any other plant species (Pavan et al, 2024).…”

“…The A. halleri reference genome (Pavan et al, 2024) comprises 34,721 predicted protein-coding genes, whose coding and non-coding fractions represent 16.7% and 20.1%…”

“…Mature miRNAs are typically 21 nucleotides long and can downregulate gene expression by binding to ARGONAUTE proteins resulting in either mRNA degradation or translation inhibition (Zhan and Meyers, 2023). In plants, while some miRNA genes are deeply conserved, the majority of miRNAs are lineage-specific and thus are evolutionarily young (Fahlgren et al, 2010;Cuperus et al, 2011;Chávez Montes et al, 2014;Guo et al, 2022a;Pavan et al, 2024). Similar to protein-coding genes, new miRNA genes can be formed from ancestral genes or have a de novo origin.…”

“…In addition, the annotation of TEs in these species has since been improved (Legrand et al, 2019), revealing a substantially higher TE content than they used, possibly leading to an underestimation of TEs as loci of origin. Finally, the miRNA annotation they used was based on a single sequencing experiment from a single accession, limiting the detection power, especially for the evolutionarily youngest miRNA genes (Pavan et al, 2024). To study more directly the process by which new miRNA genes emerge, it is thus necessary to compare species that are even more closely related.…”

“…halleri (Pavan et al, 2024), and absent from all A. lyrata accessions examined, from which it diverged less than one million years ago (Roux et al, 2011). In this study, we took advantage of this large set of very young miRNA genes to explore the mutational…”