Fig. 2: Dioscoreaceae chromosome evolution.
From: Chromosome evolution and the genetic basis of agronomically important traits in greater yam
a Ribbon diagram demonstrating conserved chromosomal synteny and large-scale segmental collinearity (semi-transparent gray ribbons) between Dioscorea alata (black horizontal bars), D. rotundata (gold), and D. zingiberensis (cyan) one-to-one orthologous gene pairs. Only D. rotundata sequences with five or more collinear genes are shown. To improve visual clarity, some chromosomes, marked with asterisks, were reverse complemented with respect to their assembled sequences. Chromosome sizes are proportional to the number of annotated genes. b Dot plot showing evidence of two whole-genome duplications exposed by TDa95/00328 intragenomic comparison. Each point represents a mutual best-hit (MBH) gene pair and each white box (outlined in grey) represents the intersection of two chromosomes. Homoeology from the recent Dioscoreaceae delta duplication is shown in black and the ancient, core monocot tau duplication can be seen as clusters in blue (see also, Supplementary Fig. 9). c The synonymous substitution rate (KS) histograms for orthologous (solid lines) or homoeologous (dotted lines) gene pairs between D. alata and select species comparators are shown: D. rotundata (n = 14,889), T. zeylanicus (n = 9013), D. alata delta (n = 1578), A. comosus (n = 6405), D. alata tau (n = 404), and S. polyrhiza (n = 4973). The D. alata–D. rotundata ortholog density was rescaled by 0.25 to emphasize other comparisons. d Shared segmental homoeology (semi-transparent gray) between D. alata chromosomes (black horizontal bars) resulting from the delta duplication is depicted with a ribbon diagram, as in panel a, but with putative centromere positions now included as gold circles (Supplementary Data 2). Source data are provided as a Source Data file.
