DOI: 10.6084/m9.figshare.30302547
title: Additional file 1 of Signatures in domesticated beet genomes pointing at genes under selection in a sucrose-storing root crop

description: Additional file 1: Table S1: Summary statistics of the paired-end Illumina raw reads without trimming from 290 accessions. Table S2: Summary statistics of the paired-end Illumina trimmed and cleaned reads from 290 accessions. Table S3: Summary statistics of the sample information, total mapped reads (%), sequencing depth and genome coverage (%) across 290 accessions. “NA” : Not Available. Table S4: Summary statistics of sequence variants (SNPs and INDELs) in 290 beet accessions compared to the EL10 reference genome. EL10.2_2 genome assembly comprises 568.8 Mb and is assembled into 18 pseudomolecules. In total, 564.2 Mb (99.2%) of the total genome assembly is organized into 9 main chromosomes (pseudomolecules), and the remaining 4.6 Mb of the genome is placed on 9 small unscaffolded pseudomolecules. Fig. S1: A bar plot illustrating the number of variants, including SNPs and INDELs, across all nine EL10 chromosomes in the Beta mini-core collection of 290 accessions. The Y-axis represents the total number of variants, and the X-axis corresponds to the nine EL10 chromosomes. Chromosome 9 exhibits the minimum number of variants, approximately 1.1 million, while Chromosome 5 displays the maximum number, around 1.5 million variants. On average, each chromosome harbors approximately 1.3 million variants. Table S5: Summary statistics of the number of SNPs and INDELs with their predicted effect using VEP across 290 accessions. Table S6: Summary statistics of the number of SNPs and INDELs within coding sequences with their predicted effect using VEP across 290 accessions. Fig. S2: Principal component analysis (PCA) of 290 beet accessions comparing second and third principal components. PC2 and PC3 represent the second and third components, accounting for 3.08% and 2.50% of the total variation, respectively. The colors represent different genetic clusters according to their beet type, with the following accessions: wild accession from the Atlantic (purple), Mediterranean (blue), sugar beet (dark green), table beet (red), fodder beet (orange), and leaf beet (light green). Fig. S3: Principal component analysis (PCA) of 199 cultivated beet accessions, including sugar, table, fodder, and leaf beet accessions. PC1 and PC2 denote the first and second components, explaining 4.39% and 3.25% of the total variation, respectively. Leaf beet accessions are grouped into GP1 (biennial leaf beet) and GP2 (annual leaf beet) based on phenotypic classification. Although the grouping is phenotype-based, the two groups also exhibited differing levels of sugar beet and Mediterranean sea beet ancestry at the admixture level. Fig. S4: Cross-validation errors for each K in 10 replicates tested using model-based clustering in ADMIXTURE, incorporating varying numbers of ancestral kinships (K=1 and K=10). The Y-axis represents the cross-validation error value, while the X-axis corresponds to the Kth ancestry. The plot represents the cross-validation errors from 10 replicates at each K. Notably, the minimum cross-validation error and the variation within the 10 replicates were observed at K = 4. Table S7: Summary statistics of sequence variants (SNPs and INDELs) within each sub-cluster compared to the EL10 reference genome. Table S8: Pairwise shared variants between the Mediterranean sea beet accessions and the other sub-clusters. Table S9: Pairwise shared variants between the Atlantic sea beet accessions and the other sub-clusters. Fig. S5: Linkage disequilibrium (LD) decay among distinct genetic clusters of the Beta mini-core collection across all nine chromosomes. Accessions with low admixture are depicted in black. LD is plotted across nine chromosomes (1 to 9). Within each plot, the Y-axis represents the pairwise correlation coefficient (r2) between two SNP markers, and the X-axis represents the physical distance (kb) between corresponding SNP markers. Fig. S6: Linkage disequilibrium (LD) decay comparisons among nine chromosomes within each Beta mini-core collection genetic cluster. LD decay comparisons are depicted within sugar beet, table beet, fodder beet, leaf beet, Mediterranean sea beet, Atlantic sea beet, and 245 accessions with low admixture from other genetic ancestries. LD is collectively plotted across all nine chromosomes (1 to 9) within each distinct genetic cluster. In each plot, the Y-axis represents the pairwise correlation coefficient (r2) between two SNP markers, and the X-axis represents the physical distance (kb) between corresponding SNP markers. The colors marked in the legend represent nine chromosomes. Table S10: Summary statistics of the percentage of heterozygous SNPs in each accession. Fig. S7: The frequency distribution plots of the percentage of heterozygous SNPs within distinct genetic clusters. The frequency distribution of heterozygous SNPs within each genetic cluster, such as Mediterranean sea beet, leaf beet, fodder beet, sugar beet, table beet, and Atlantic sea beet, is plotted. Six classes were calculated, ranging from 5-10%, 10-15%, 15-20%, 20-25%, 25-30% and 30-35%. In each plot, the Y-axis represents the frequency of individual accessions belonging to the representative classes, plotted on the X-axis. The colors distinguish between the six different classes. Table S11: Summary statistics of pairwise comparisons of population differentiation (FST) between the Atlantic sea beet accessions and the other sub-clusters. Table S12: Summary statistics of nucleotide diversity within each genetic sub-cluster. Fig. S8: XP-CLR revealed selection sweeps in sugar beets across all nine EL10 chromosomes. XP-CLR across the nine EL10 chromosomes using 10 kb sliding window size and 1 kb step size while comparing sugar beet accessions with the Mediterranean sea beet accessions. The blue dots indicate XP-CLR values along the nine EL10 chromosomes, while the horizontal red line denotes the empirical 95th percentile threshold. According to XP-CLR, genomic regions above this threshold are considered putative regions under selection. The Y-axis represents the XP-CLR values ranging from 0 to 1000, and the X-axis illustrates the chromosome length in Mb. Fig. S9: Population differentiation using fixation index (FST) between sugar beet and Mediterranean sea beet accessions across all nine EL10 chromosomes. The FST calculations employed 10 kb sliding window size and 1 kb step size while comparing sugar beet accessions with the Mediterranean sea beet accessions. The blue dots on the graphs indicate FST values along the nine EL10 chromosomes, while the horizontal red line represents the empirical 95th percentile threshold. Genomic regions above this threshold are considered highly differentiated regions between sugar beet and Mediterranean sea beet, as indicated by FST. The Y-axis represents FST values ranging from 0 to 1, where 0 signifies no genetic differentiation and 1 indicates complete genetic differentiation between the two populations. The X-axis illustrates the chromosome length in Mb. Fig. S10: Nucleotide diversity values within various genetic clusters, including leaf and fodder beets, in the regions of interest encompassing selective sweeps, with a specific focus on genes involved in cold tolerance during post-harvest storage and the vernalization pathway in flowering time control. The colors represent different genetic clusters based on beet type, representing the wild accession from the Atlantic (purple) and the Mediterranean (blue), sugar beet (dark green), table beet (red), fodder beet (orange), and leaf beet (light green) accessions. The Y-axis illustrates the nucleotide diversity value, while the X-axis denotes the location along the chromosome. The vertical red lines represent the gene boundaries of the predicted gene models. The nucleotide diversity values across different clusters are graphically represented for (A) inositol transporter 1 on chromosome 2, (B) raffinose synthase 5 on chromosome 1, (C) FLOWERING LOCUS C (FLC) on chromosome 6, and (D) SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) on chromosome 1. Fig. S11: Nucleotide diversity values within various genetic clusters, including leaf and fodder beets, in the regions of interest encompassing selective sweeps, with a specific focus on genes associated with earthy flavor and plant immunity. The colors represent different genetic clusters based on beet type, representing the wild accession from the Atlantic (purple) and the Mediterranean (blue), sugar beet (dark green), table beet (red), fodder beet (orange), and leaf beet (light green) accessions. The Y-axis illustrates the nucleotide diversity value, while the X-axis denotes the location along the chromosome. The vertical red lines represent the gene boundaries of the predicted gene models. The nucleotide diversity values across different clusters are graphically represented for (A) terpene synthase on chromosome 7, (B) terpene synthase on chromosome 8, (C) WUSCHEL-RELATED HOMEOBOX 4 (WOX4) gene on chromosome 1. Fig. S12: Estimated historical effective population size (Ne) of genetic clusters in the Beta mini-core collection using the program MSMC2. The X-axis represents the years on a logarithmic scale, while the Y-axis represents the effective population size. A mutation rate of 1.25e-8 was used. The colors represent different genetic clusters according to their beet type: wild accession from the Atlantic (purple), wild accession from the Mediterranean (blue), sugar beet (dark green), table beet (red), fodder beet (orange), and leaf beet (light green) accessions. Table S13: Description of sea beet and cultivated beet accessions used in this study. “NA” indicates data that is Not Available. Fig. S13: Overview of the bioinformatics workflow used in the study. The Illumina short-reads were mapped to the EL10.2_2 genome assembly using BWA-MEM. Note S1: Custom R script used for calculating and plotting PCA and heterozygosity. The script includes data processing steps, calculation of heterozygosity percentages, and the complete ggplot2 code used to visualize the results.