Data from: Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers

Polyploidy is common and an important evolutionary factor in most land
plant lineages, but it is rare in gymnosperms. Coast redwood (Sequoia
sempervirens) is one of just two polyploid conifer species and the only
hexaploid. Evidence from fossil guard cell size suggests that polyploidy
in Sequoia dates to the Eocene. Numerous hypotheses about the mechanism of
polyploidy and parental genome donors have been proposed, based primarily
on morphological and cytological data, but it remains unclear how Sequoia
became polyploid and why this lineage overcame an apparent gymnosperm
barrier to whole-genome duplication (WGD). We sequenced transcriptomes and
used phylogenetic inference, Bayesian concordance analysis and paralog age
distributions to resolve relationships among gene copies in hexaploid
coast redwood and close relatives. Our data show that hexaploidy in coast
redwood is best explained by autopolyploidy or, if there was
allopolyploidy, it happened within the Californian redwood clade. We found
that duplicate genes have more similar sequences than expected, given the
age of the inferred polyploidization. Conflict between molecular and
fossil estimates of WGD can be explained if diploidization occurred very
slowly following polyploidization. We extrapolate from this to suggest
that the rarity of polyploidy in gymnosperms may be due to slow
diploidization in this clade.