Fig. 1: Paspalum (Paspalum vaginatum) genome and evolution.
a Properties of the paspalum genome. Layers in circos plots are (I): TE (transposable element) coverage per 100 Kb, (II): gene density (proportion of sequence covered by annotated genes) per 1 Mb (megabase), (III): GC content per 10 kb (kilobase) region, (IV): transcription represented by log2(TPM (transcripts per million)) per 100 kb. Green lines indicate inter- and intra- chromosomal synteny. b Phylogeny and estimated divergence times among maize (Zea mays), sorghum, paspalum, foxtail millet (Setaria italica), Oropetium (Oropetium thomaeum), Brachypodium (Brachypodium distachyon), and rice (Oryza sativa). Numbers in black indicate the estimated divergence time in millions of years before present (Myr) for each node. Numbers in blue and red indicate the number of gene families predicted to have experienced copy number expansion or contraction along each branch of the phylogeny, respectively. c Distribution of the estimated lineage-specific synonymous substitution rates for syntenically conserved genes in each of the seven species shown in panel a (see Methods). d Distribution of the estimated lineage-specific ratios of nonsynonymous substitution rates to synonymous substitution rates for syntenically conserved genes among each of the seven species shown in panel a. N = 16,633 distinct genes. For box plots in this figure and all subsequent box plots shown in this paper center lines indicate medians, box limits indicate 25th and 75th percentiles if the data distribution and whiskers the closer to the median of the minimum and maximum values or 1.5x the interquartile range, with data points outside this range plotted as individual points. Colors correspond to the legend provided in panel c. Source data are provided as a Source Data file.
