How broad is the selfing syndrome? Insights from convergent evolution of gene expression across species and tissues in the Capsella genus

Abstract

The shift from outcrossing to selfing is one of the main evolutionary transitions in plants. It is accompanied by profound effects on reproductive traits, the so-called selfing syndrome. Because the transition to selfing also implies deep genomic and ecological changes, one also expects to observe a genomic selfing syndrome. We took advantage of the three independent transitions from outcrossing to selfing in the Capsella genus to characterize the overall impact of mating system change on RNA expression, in flowers but also in leaves and roots. We quantified the extent of both selfing and genomic syndromes, and tested whether changes in expression corresponded to adaptation to selfing or to relaxed selection on traits that were constrained in outcrossers. Mating system change affected gene expression in all three tissues but more so in flowers than in roots and leaves. Gene expression in selfing species tended to converge in flowers but diverged in the two other tissues. Hence, convergent adaptation to selfing dominates in flowers, whereas genetic drift plays a more important role in leaves and roots. The effect of mating system transition is not limited to reproductive tissues and corresponds to both adaptation to selfing and relaxed selection on previously constrained traits.

Keywords: Capsella; convergent adaptation; gene expression; genomic and selfing syndromes; mating system change; relaxed selection.

Fig. 1

Overall gene expression clusters by tissue, and by mating system in flower and phylogeny in root and leaf. (a) Evolutionary history of four species in Capsella genus. Species are labeled with specific colors: pink, C. grandiflora (CG); purple, C. rubella (CR); sky‐blue, C. orientalis (CO). (b) Principal component analysis. Different tissues are represented by different colors and species by different shapes: orange, flower; dark green, leaf; light green, root. The zoomed‐in plot for flowers is shown at the bottom left. (c) Heatmaps based on TMM normalized reads counts for 17 307 transcripts of CR (selfer), CG (outcrosser) and CO (selfer) for the three tissues: ‘Root’, left panels, ‘Leaf’, middle panels and ‘Flower’, right panels. For each heatmap, each row represents a transcript and each column represents the mean expression value of a species. The higher the expression value the darker the red, and conversely the lower the blue the lower the expression. The upper dendrogram shows the hierarchical relationships among species, and the row dendrogram shows the hierarchical relationships of gene expression for a specific tissue. Species are labeled with specific colors: pink, CG; purple, CR; sky‐blue, CO.

Fig. 2

Global effect of mating system transition and phylogeny on gene expression. (a, c) The D _CR index compares gene expression difference between Capsella rubella (CR) and C. orientalis (CO) (black line in the upper schematic plot), on the one hand, and the difference between C. rubella (CR) and C. grandiflora (CG) (gray line in the upper schematic plot), on the other (see Eqn 2 in the text). D _CR  < 0 indicates that CR expression is closer to that of CO than to that of CG, D _CR  > 0 is the opposite (CR closer to CG than to CO), D _CR  ≈ 0 indicates that CR expression is equidistant from CG and CO. Dotted lines are the median of the distribution of the D _CR index for the three tissues. (a) all genes; (c) differentially expressed (DE) genes between CG and CO. Both D _CO and D _CR value ranges from −1 to 1. (b, d) The D _CO index compares gene expression difference between C. orientalis (CO) and C. rubella (CR) ¦CO–CR¦ (black line in the upper schematic plot), on the one hand, and the difference between C. orientalis (CO) and C. grandiflora (CG) (gray line in the upper schematic plot), on the other (see Eqn 1 in the text). D _CO  < 0 indicates that CO expression is closer to that of CR than to that of CG, D _CO  > 0 is the opposite (CO closer to CG than to CR), D _CO  ≈ 0 indicates that CO expression is equidistant from CG and CR. Flower, yellow; leaf, dark green; root, light green. Dotted lines are the median of the distribution of the D _CO index for the three tissues. (b) All genes; (d) DE genes between CG and CR.

Fig. 3

π_N : π_S ratios for different categories of D _CO index. The distribution of π_N : π_S ratios is compared between D _CO  ≤ − 0.5 and D _CO  ≥ 0.5 for the different species (Capsella grandiflora, CG, left column; C. rubella, CR, middle column; C. orientalis, CO, right column) and for the different tissues (flowers, top row; leaves, middle row; roots, bottom row). Within each box plot, the bold horizontal line represents the median value; box region means values within interquartilie range (IQR) from first quartile (Q1) to third quartile (Q3); up and down whiskers indicate 1.5 IQR above the Q3 (Q3 + 1.5 IQR) and 1.5 IQR below the Q1 (Q1 − 1.5 IQR), separately; circles representative outliers. Wilcoxon test: ns, P > 0.05; **, P < 0.01; ***, P < 0.001.

Fig. 4

Differentially expressed (DE) genes analysis and mating system transition (MST) related candidate genes identification. (a) Venn diagrams showing the number of detected DE (FDR < 0.05) genes in flower from groups of species pairwise comparison (i.e. between CR and CG, CO and CG, CR and CG), as well as overlaps between groups in number and in percentage. The orange highlighted overlap represents co‐differentially‐expressed genes (coDEGs) of CR and CO in flower. The coDEGs of CR and CO were defined as being differentially expressed between CG and CR and between CG and CO, but not between CR and CO. The gray highlighted overlap represents the coDEGs of CG and CO in flower. (b) In leaf (dark green), the same role as (a). (c) In root (light green), the same role as (a). (d) Identification of MST‐related candidate genes. Each coDEGs of CR and CO should be flower‐specific (orange highlighted) to be an MST‐related candidate. (e) Summary of DE genes of CR/CG and CO/CG across tissues. ‘++’ and ‘−−’ means genes either upregulated in both CR/CG and CO/CG, or downregulated in both comparisons. ‘+−‘ and ‘−+’ means genes upregulated in one comparison but downregulated in another. CG, Capsella grandiflora; CO, C. orientalis; CR, C. rubella.

Fig. 5

Similarity indices of subgenomes of Capsella bursa‐pastoris (Cbp) to different ‘parental’ species. In a given pair of diploid species, for each tissue and each subgenome, the median of similarity indices for each subgenome, either inherited from CO (S _CO ) or from CG (S _CG ), are presented as well as the difference between the two indices (ΔS) (see the Materials and Methods section for definitions). ΔS measures the dominance of one parental genetic background. Gray dotted line (S = 0) corresponds to an absence of bias. Phylogenetic trees on the top of each panel represent the phylogenetic relationships of Cbp with the diploid species used for the comparison. CG, Capsella grandiflora; CO, C. orientalis; CR, C. rubella.