Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most rapid and spectacular phenotypic changes, which are often repeated, thus offering a unique chance to characterise its genomic basis. These repeated patterns of evolutionary change in plants on oceanic archipelagos, or the ‘plant island syndrome’, include changes in leaf phenotypes, acquisition of perennial life-style, flowering period and self-compatibility, and ancestral ploidy. Here, we describe the genome of the critically endangered and Scalesia atractyloides Arnot., type species for this Galápagos-endemic genus, obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence, and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galápagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in one of Darwin’s giant daisies. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterises the quick and pronounced genomic changes in an iconic group of island plants.

See Cerca et al.