Fig 1.
Intragenic duplicate pairs retrival.
Schematic overview of the pipeline used to identify putative intragenic ohno-miRNA and SSD-derived miRNA pairs. The number of putative pairs retained at each step is reported.
Fig 2.
Schematic representation of how the alignment score is assigned to miRNA gene pairs, leveraging mature miRNA alignments. Mature miRNAs are aligned using the modified version of the Needleman-Wunsch algorithm. The represented case would see the pair MIRxxx and MIRyyy assigned an alignment score of 34.
Fig 3.
Comparative analysis of regulatory motifs among WGD and SSD miRNA pairs.
V-Motif (A1-A2), Bifan (B1-B2), PPI-Bifan (C1-C2), and PPI-Delta (D1-D2). Panels A1-D1 show the distribution of enrichment scores computed for each miRNA-target pair (WGD pairs on the left, SSD pairs on the right). Panels A2-D2 display the number of motif instances collected in classes: For V-motifs (A2), pairs are binned by the number of motifs (0, 1–50, >50); for all other motifs (B2, C2, D2), pairs (or single miRNAs in D2) are separated in two classes, corresponding to being involved in 0 or motif. An enrichment signal relative to WGD pairs is observed for V-Motifs, Bifan, and PPI-Bifan. In contrast, PPI-Delta motifs show minimal differences, with nearly all miRNAs showing no enrichment.
Fig 4.
Outdegree distributions of ohno-miRNAs compared with SSD-derived miRNAs, and miRNAs that didn’t undergo any duplication (singlets), in the TarBase network. (***: p < 0.001, Kolmogorov-Smirnov test).
Fig 5.
Subgenome identity affects miRNA retention but not motif enrichment or expression correlation.
(A) Distribution of WGD-derived miRNA pairs across subgenomes. Pairs derived from the first (1R) and second (2R) rounds of whole-genome duplication are grouped by subgenome identity. As expected from Peterson et al. (2022), β–β pairs from the 1R are underrepresented due to reduced conservation on the β subgenome. (B-C) Enrichment score for simple bifans (B) and PPI-bifans (C) in 1R- and 2R-derived pairs. No significant difference is observed, suggesting that motif enrichment is a general feature of WGD-derived miRNA pairs. (D) Distribution of expression correlations between 1R- and 2R- derived pairs. Expression correlation is measured as 1-Cosine similarity (see Methods), filtering pairs involved in different motifs. No significant differences in correlations are observed; a slight increase in expression correlation is observed when considering only pairs involved in PPI-bifans. (E) Schematic representation of the 2 WGD events. The scheme is based on [19] and [43], used to classify 1R- and 2R-derived WGD pairs into α–α, β–β, α–β classes.
Table 1.
Intragenic ohno-miRNA pairs recognized as duplicates by Ensembl.
Table 2.
The only pair of intragenic SSD-derived paralogue miRNAs recognized as duplicates by Ensembl.
Fig 6.
Sequence similarity and target similarity.
(A, B) Sequence similarity (A) and target similarity (B); Sørensen–Dice coefficient on TarBase targets for putative intragenic miRNA pairs. (C, D) Sequence similarity (C) and target similarity (D) for the full set of ohno-miRNA pairs and SSD-derived miRNA pairs, as annotated in [19,20]. WGD-associated miRNA pairs consistently show higher scores than SSD-derived pairs across both metrics. (***: p < 0.001, Kolmogorov-Smirnov test).
Fig 7.
Expression of ohno-miRNAs (blue) and SSD-derived miRNAs (orange) across multiple human tissues, based on two independent datasets: MirGeneDB (A1–A4) and MiRNATissueAtlas (B1–B4). Each panel shows the distribution of miRNA expression within a tissue. Across all tissues, WGD-derived miRNAs consistently exhibit higher median expression levels than SSD-derived miRNAs. MiRNAs that both underwent WGD and SSD are included exclusively in the WGD set.
Fig 8.
Evolution of MIR499A, MIR208A and MIR208B.
Suggested evolutionary history linking MYH7B, MYH7 and MYH6 and their intronic miRNAs (MIR499A, MIR208A, MIR208B). As explained in the Discussion, the duplication times suggested by Ensembl are considered to be errors in the annotations.