Fig. 1: The assemblies and evolution of five Flaveria genomes.

a Summary of phylogeny and timescale of the five Flaveria species and the three indicated outgroup species, i.e., Arabidopsis thaliana (Atha), Helianthus annuus (Hann, sunflower), Lactuca sativa (Lsat, lettuce). Bars represent 95% confidence intervals of the estimated divergence time. Whole genome duplications are shown at the corresponding node/branch. The plant image of Atha, Hann and Lsat were created in BioRender. b The circular representation of pseudochromosomes. From outer to inner side: blue: long terminal repeats density per million base pair (Mb), purple: exon density per Mb, pink: transcript abundance per gene in log10 TPM (transcript per kilobase per million mapped reads). Lines in the inner circle represent links between synteny-selected paralogs. c Fluorescence in situ hybridization images to assess the chromosome numbers in Ftri, Flin, and Frob. This experiment was conducted in three biological replicates and one representative result (c) was shown. d Ks between different species and within species. Ks of Frob vs. Hann and Ftri vs. Hann are shown to represent a speciation between Flaveria and Hann. Ks of Lsat vs. Hann, Frob vs. Lsat are shown to represent the speciation of Asteraceae and Lsat, and Ks of Hann vs. Atha, Lsat vs. Atha are shown to represent the speciation of Asterids II with Atha. Ks of paralogs in Frob and Hann are shown representing a whole genome duplication event (WGD). Frob and Hann shared the WGD2 indicated as the second peak in orange “WGD2”. The first peak for Ks curves for either Frob or Hann represents tandem duplication found in each species. (Frob F. robusta, Fson F. sonorensis, Flin F. linearis, Fram F. ramosissima, Ftri F. trinervia).