Fig. 3: The history of WGD in Azolla and Salvinia.
From: Fern genomes elucidate land plant evolution and cyanobacterial symbioses
a, MAPS analysis identified two WGD events: one specific to Azolla (orange circle) and one predating the core leptosporangiates (green circle). The blue line illustrates the percentage of subtrees indicative of a gene duplication shared by the descendants at each node. The grey lines display the gene birth–death simulation results without WGD. The species divergence dates are from Testo and Sundue129. b, Density plots from fitting Gaussian mixture models to Ks distributions estimated from pairs of syntenic paralogues within the Azolla and Salvinia genomes, as well as of syntenic orthologues between Azolla and Salvinia. c, Examples of synteny between Azolla and Salvinia genomic regions. The left and right panels display a 2:1 and 2:2 syntenic relationship between Azolla and Salvinia regions, respectively. Each subpanel represents a genomic region in Azolla or Salvinia, with gene models on both strands shown above and below the dashed line. High-scoring sequence pairs (HSPs) in protein-coding sequences are marked by short vertical bars above the gene models. Selected HSP links between genomic regions are depicted as coloured lines crossing the subpanels, whereas others (for example, the HSP links between the two Azolla genomic regions in the left panel) are left out for clarity. Collinear series of HSPs across genomic regions indicates a syntenic relationship between the regions concerned. Genomic regions conserved in duplicate after the WGD that occurred prior to the divergence between Azolla and Salvinia should show a 2:2 syntenic relationship, whereas regions conserved in duplicate after the Azolla-specific WGD should show a 2:1 syntenic relationship with Salvinia regions. The left and right panels can be regenerated at https://genomevolution.org/r/ujll and https://genomevolution.org/r/ukys, respectively.
