Whole-Genome Doubling Affects Pre-miRNA Expression in Plants

Area of Science:

• Plant biology
• Genomics
• Molecular genetics

Background:

• Whole-genome doubling (polyploidy) is a frequent event in angiosperms, often linked to significant biological changes.
• MicroRNAs (miRNAs) are increasingly recognized for their role in regulating gene expression, particularly in response to polyploidization.
• A comprehensive comparative analysis of miRNA expression across different polyploid species was previously lacking.

Purpose of the Study:

• To investigate the role of microRNAs (miRNAs) in whole-genome doubling (polyploidy) across multiple plant species.
• To identify conserved and species-specific miRNA precursor (pre-miRNA) expression patterns in diploid (2x) versus tetraploid (4x) plants.
• To understand the regulatory functions of differentially expressed pre-miRNAs in response to polyploidization.

Main Methods:

• Re-analysis of publicly available RNA sequencing datasets from five plant species: *Arabidopsis thaliana*, *Morus alba*, *Brassica rapa*, *Isatis indigotica*, and *Solanum commersonii*.
• Identification and quantification of microRNA precursor (pre-miRNA) sequences in diploid (2x) and tetraploid (4x) samples.
• Bioinformatic prediction of target messenger RNA (mRNA) transcripts for identified pre-miRNAs.

Main Results:

• 3568 pre-miRNAs were identified across all species.
• Three specific pre-miRNAs (pre-miR414, pre-miR5538, pre-miR5141) were highly abundant in diploids but absent or low in tetraploids, targeting transcription factors, DNA repair, and stress-related genes.
• Sixteen pre-miRNAs showed altered expression in tetraploids, including pre-miRNA482, pre-miRNA2916, and pre-miRNA167.
• A conserved ploidy-dependent response involving DNA repair, ATP synthesis, terpenoid biosynthesis, and stress-responsive transcripts was observed in all studied species.
• In *S. commersonii*, ploidy-dependent pre-miRNAs appear to regulate nucleotide metabolism, potentially supporting increased DNA replication demands.

Conclusions:

• MicroRNA-mediated responses play a critical role in plant adaptation following autopolyploidization.
• Conserved miRNA expression patterns suggest a common regulatory strategy for coping with whole-genome doubling across diverse angiosperms.
• Differential regulation of nucleotide metabolism by miRNAs in polyploids highlights their importance in managing genomic changes.