Fig. 1: Genome features of three Papaver species.
a Karyotyping shows P. setigerum is diploid (2n = 44). b Intraspecies synteny analysis reveals two rounds of whole-genome duplications (WGD) in P. setigerum genome. The tracks a, b, and c of the circos plot represent the distribution of gene density, repeat density, and GC density, respectively (calculated in 2 Mb windows). Track d shows genome-wide syntenic blocks detected by MCScanX87 where an example of duplications involving four chromosomes as a result of two WGDs was highlighted. Bandwidth is proportional to syntenic block size. c Dotplots of interspecies syntenic blocks reveal the 1:2:4 syntenic block ratio of P. rhoeas, P. somniferum, and P. setigerum. Each dot indicates a syntenic gene pair detected by MCScanX. Synteny blocks were colored by MCScanX. d Synonymous substitution rate (Ks) density distributions of syntenic paralogs and orthologs, with colored lines representing comparisons among four plant species: P. set. (P. setigerum), P. rho. (P. rhoeas), P. som. (P. somniferum) and A. coerulea (Aquilegia coerulea)89. For P. setigerum, only the reciprocal best matches among the syntenic gene pairs were considered as the pairs from WGD-2 while other syntenic gene pairs were grouped as the pairs from WGD-1. e Inferred maximum likelihood phylogenetic tree by RAxML94. Divergence timings and the supported bootstrap values were labeled on the tree. Estimated WGD-1 and WGD-2 timings and the reported whole-genome triplication (WGT)/WGD timings were superimposed on the phylogenetic tree. MRCA most recent common ancestor, Mya million years ago. Source data underlying b–e are provided as a Source Data file.
