Fig. 2: Subgenomes and evolutionary history of Scalesia.
From: The genomic basis of the plant island syndrome in Darwin’s giant daisies
A Circos plots displaying the 34 chromosome models in the assembly. Pairs are organised to the left and right from the top, and have the same colour coding. B Selected families of transposable elements (TEs) that are differently represented on each subgenome (17 pairwise comparisons; each TE is labelled after the assembly (scaAtr), round and family number (2–95) after RepeatMasker). These TE families were likely active while the two subgenomes were separated, being thus unevenly represented. These highlight subgenome identification. Each data point corresponds to a chromosome in a subgenome (subgenome A in blue and B in orange). Chromosome pairs are linked by grey lines. C Single-copy ortholog phylogeny of the studied Asteraceae genome assemblies. Node ages are provided to the right of each node, as well as the predicted time for the polyploidization event. D Pairwise sequentially Markovian coalescent (PSMC) estimation of the demographic history of Scalesia atractyloides, two other Scalesia species, and two members of the Pappobolus genus, which is the sister taxon to Scalesia using bootstrapping (100 replicates). PSMC runs for the whole genome and subgenomes yielded similar results (Supplementary Fig. 03).
