Figure 3: Carrot genome evolution.
(a) Evolutionary relationships of the eudicot lineage (Supplementary Fig. 12). Circles indicate the ages of WGD (red) or WGT (blue) events. Age estimates for the A. thaliana, kiwifruit, lettuce, and Solanaceae WGD and WGT events and for the γ WGT event were obtained from the literature30,65,66. The polyploidization level of the kiwifruit WGDs (purple circles) awaits confirmation. Mya, million years ago. (b) Age distribution of fourfold-degenerate sites for genes from the D. carota, A. thaliana, and Solanum lycopersicum genomes. The x axis shows fourfold-degenerate transversion rates; the y axis shows the percentage of gene pairs in syntenic or collinear blocks. The γ peak represents the ancestral γ WGT shared by core eudicots; Dc-α and Dc-β represent carrot-specific WGD and WGT events, respectively. (c) The distribution of remaining carrot duplicated blocks derived from the seven eudicot protochromosomes. (d) Synteny of carrot protochromosome A19 with corresponding blocks on grape, coffee, tomato, and kiwifruit chromosomes. Vertical bars indicate the depth of primary correspondence to carrot protochromosome A19. Of the 110 syntenic blocks identified in comparison of carrot and grape protochromosome A19, a substantial portion (43; 39.1%) correspond to 6 grape blocks. A similar pattern was observed for the carrot–coffee, carrot–kiwifruit, and carrot–tomato comparisons, indicating that carrot has experienced either 3 × 2 or 2 × 3 WGD events. (e) Representation of carrot-specific genome duplications. The tracks, from outermost to innermost, show GC content (%), density of tandem duplications (number per 0.5-Mb window), genes retained in the carrot Dc-α (cyan) and Dc-β (blue) events, chromosomal blocks descending from the seven ancestral core eudicot protochromosomes (colored as in c), and duplicated segments derived from the Dc-α (dashed links; duplicates) and Dc-β (solid links; triplicates) events.
