Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 173 Figure 2 Pangenome analysis of 149 representative wild and cultivated rice accessions (Adopted from Guo et al., 2025) Image captions: a, Geographical distribution of 133 wild rice accessions, with dots coloured by group. Inset maps show enlarged views of West Africa and Australia. Positive values indicate east longitude (°E) and north latitude (°N). b, Schematic representation of p-contigs and a-contigs, showing gene models and variant information from HiFi genome assemblies. c–e, Violin plots comparing O. sativa (Os; n = 16) and O. rufipogon (Or; n = 129) varieties for nuclear genome size (c), gene number (d) and gene density (gene number per Mb) (e). The box edges mark the 25% and 75% quartiles and the central line marks the median. Whiskers extend to 1.5 times the interquartile range (IQR). Statistical significance was determined by two-sided Wilcoxon test; Pvalues are shown at the top. f, Distribution of genes on a-contigs across 133 HiFi genomes, including O. longistaminata (Ol). g, Heat map showing RGA loci that have a higher average copy number in wild rice than in cultivated rice, normalized using a row-wise z-score method. Each row indicates an RGA locus, and each column indicates a variety. h, Local synteny plot of Pi5 loci (chr. 9: 9.65–9.79 Mb in the Nipponbare reference genome) from 41 accessions. Pi5 genes (Pi5-1, Pi5-2and Pi5-3) are shown in green with collinearity represented by lines of different colours; adjacent genes are shown in blue with grey collinearity lines. i, Accumulation curve of the number of pan-genes (uptrend lines) and core genes (downtrend lines) across O. sativa (green; n = 16) and O. rufipogon (purple; n = 129) varieties. The pie chart shows the gene proportions in the combined wild–cultivated pangenome (n = 145). j, Phylogenetic tree of the 180 Oryzavarieties, on the basis of single-copy genes. Diverse groups are denoted by colour-coded labels (Adopted from Guo et al., 2025)
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