Data from: Ancestral polyploidy in seed plants and angiosperms

Whole-genome duplication (WGD), or polyploidy, followed by gene loss and
diploidization has long been recognized as an important evolutionary force
in animals, fungi and other organisms1, 2, 3, especially plants. The
success of angiosperms has been attributed, in part, to innovations
associated with gene or whole-genome duplications4, 5, 6, but evidence for
proposed ancient genome duplications pre-dating the divergence of monocots
and eudicots remains equivocal in analyses of conserved gene order. Here
we use comprehensive phylogenomic analyses of sequenced plant genomes and
more than 12.6 million new expressed-sequence-tag sequences from
phylogenetically pivotal lineages to elucidate two groups of ancient gene
duplications—one in the common ancestor of extant seed plants and the
other in the common ancestor of extant angiosperms. Gene duplication
events were intensely concentrated around 319 and 192 million years ago,
implicating two WGDs in ancestral lineages shortly before the
diversification of extant seed plants and extant angiosperms,
respectively. Significantly, these ancestral WGDs resulted in the
diversification of regulatory genes important to seed and flower
development, suggesting that they were involved in major innovations that
ultimately contributed to the rise and eventual dominance of seed plants
and angiosperms.