Scalesia atractyloides genome assembly

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.