Fournier-Leveletal_DataSEM

Input file and R scripts used to perform the SEM analysis

Fournier-Leveletal_DataQTLMapping

Input for the QTL mapping performed using the MCQTL software (Jourjon et al.,2006

Primers used for developing ILs.

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.</div

Analysis of <i>FRIGIDA</i> alleles in natural strains of <i>C</i>. <i>hirsuta</i> and <i>A</i>. <i>thaliana</i>.

Analysis of FRIGIDA alleles in natural strains of C. hirsuta and A. thaliana.</p

Natural variation at <i>SPL9</i>.

(A) Leaflet number progression of C. hirsuta Ox, the Chspl9 mutant, and the introgression line IL-LLN4_2, all in the Ox genetic background. Differences in leaflet numbers between the 3 genotypes were tested with a Dunn test and the P values, adjusted according to the Bonferroni method, are indicated by asterisks: *: P ≤ 0.05; **: P ≤ 0.01; ***: P ≤ 0.001. (B, C) Genome-wide RNA-seq analyses of entire seedlings. (B) Comparison of C. hirsuta Az1 and C. hirsuta Ox, and (C) the NILs HIF-LLN4_2 (Rec29) with Az1 and Ox alleles at the SPL9 region. Negative log base 10 transformed P values are plotted against fold change of expression and each point is a gene. Red-colored points are significantly differentially expressed, while the black ones are not. The SPL9 gene is indicated in each plot. (D) Phylogeny and homology of SPL9 genes in 16 Brassicaceae. The left panel shows the SPL9 gene tree. The top panel shows the proportion of genes harboring the most common AA. The bottom-middle panel shows the entire SPL9 protein sequence, while the bottom-right panel corresponds to the region around the SPL9 missense SNPE242Q (indicated by asterisk). The data underlying the graphs shown in the figure can be found at https://doi.org/10.5281/zenodo.7907435. AA, amino acid; Az1, Azores1; Chspl9, C. hirsuta loss-of-function allele of SPL9; Ox, Oxford; SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9. (TIFF)</p

Positions for new assembled regions of the reference chromosome 8.

Positions for new assembled regions of the reference chromosome 8.</p

Sample location and Illumina sequencing information of all 752 <i>C</i>. <i>hirsuta</i> natural strains.

Sample location and Illumina sequencing information of all 752 C. hirsuta natural strains.</p

Genetic divergence at the <i>SPL9</i> QTL cluster agrees with climatic gradient on the Azores.

(A) Reduced leaflet number in an IL carrying the SPL9Az1 locus in the Ox background (IL LLN4_2Az1) compared to the wild type when grown in a common garden on the island of Faial, Azores. The difference between the means was tested for significance with the Wilcoxon rank-sum test. (B) Genome-wide scan for selection with pcadapt. A Manhattan plot is shown with the results from the analysis of 753 C. hirsuta strains. The negative log base 10 transformed P values for SNPs are plotted against their physical positions on each chromosome. The dashed horizontal line indicates the genome-wide threshold on or above which there are only 1,000 SNPs. The functional missense SNP E242Q of SPL9 underlying QTL LLN4_2 is highlighted by a red circle. Yellow boxes in the lower part of the panel indicate the locations of QTL LLN4_1A, LLN4_1B, and LLLN4_2. (C) PCA of 753 C. hirsuta strains with pcadapt using all SNPs (minor allele frequency > = 5%) outside the pcadapt peaks at the SPL9 QTL cluster (GBG, left) and inside (SPL9 cluster, right). Each point is a strain and colors indicate whether it belongs to the Western Azores group grp1 (blue), Eastern Azores group grp2 (red), or others (gray). (D) An east–west climatic gradient on the Azorean archipelago as indicated by precipitation of the driest quarter (BIO17) and the distribution of strains grouped according to pcadapt analysis (S5A and S5B Fig). Each independent sampling is represented by a pie chart, indicated by season (S, spring; F, fall) and year (e.g., S10 –Spring 2010). Pie charts show the proportions of strains from the different groups in our sample colored according to Fig 5B (blue—grp1; red—grp2; black—recombinant in the SPL9 cluster; gray—others). The size of the pie chart is scaled to the number of strains according to the legend in the bottom left. Collection locations are indicated on the map by points colored according to BIO17 as indicated by the legend on the right. The latitudinal and longitudinal gradients for BIO17 across the collection sites on the Azores are also indicated along the upper and right margins of the figure. Map layers were made with Natural Earth and [142]. (E) Boxplots showing climatic differences between locations of C. hirsuta strains belonging to grp1 from West Azores (blue) and grp2 from East Azores (red). Only bioclimatic variables that were significantly different between both groups according to a Kruskal–Wallis test are shown. The P values of the test are indicated by asterisks: * 0.01 P ≤ 0.05, *** P ≤ 0.001. (F) Geographic locations of weather stations from which data were analyzed. Stations were chosen to represent the 4 major groups discovered with ADMIXTURE analysis (Fig 3C; AZ, IBE, BAL, NCE) based on abundance of strains at their geographical locations. Map layers were made with Natural Earth and [142]. Annual trends in temperature in local weather station data from the AZ and from locations representing the other ADMIXTURE groups (S5E Fig). Daily mean temperature is plotted against day of the year. Annual changes in temperature on the Azores are much reduced compared to the other locations primarily due to mild temperature in both winter and summer. The data underlying the graphs shown in the figure can be found at https://doi.org/10.5281/zenodo.7907435. AZ, Azores; BAL, Balkan; GBG, genomic background; IBE, Iberian; IL, introgression line; NCE, Northern Central European; Ox, Oxford; PCA, principal component analysis; QTL, quantitative trait locus; SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9. (TIFF)</p

Primers used for fine-mapping QTL LLN4_2.

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.</div

Reordering of chromosome 8.

(A) The RF of genetic markers within the Ox × Az1 RIL population reveal 2 regions on chromosome 8 that most likely belong to chromosome 7 instead of previous assignment to chromosome 8 (arrows). In addition, markers of the pericentromeric region (gray diagonal line) might be inverted. (B, C) Genetic (B) and physical (C) maps based on previous (left side) and new assembly (right side) of chromosome 8. Regions colored in red, yellow, and blue depict unchanged segments of the map, whereas the region in gray color corresponds to the inverted segment. A genetic map with inverted order of markers shows reduced genetic length supporting the inverted assembly (B). The breakpoints of the predicted inversion indicated by 1 and 2 have been previously uncovered by consistent breakpoints in Nanopore long reads mapped to the original assembly of chromosome 8 (C). (D, E) Images representing Nanopore reads (positive strand–blue; negative strand -red) that span the regions 1 (D) and 2 (E) of the reassembled chromosome 8 and confirm the correctness of the new assembly. The data underlying the graphs shown in the figure can be found at https://doi.org/10.5281/zenodo.7907435. Az1, Azores1; Ox, Oxford; RF, recombination fraction; RIL, Recombinant Inbred Line. (TIFF)</p