Data from: A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

Comparisons of flowering plant genomes reveal multiple rounds of ancient
polyploidy characterized by large intra-genomic syntenic blocks. Three
such whole genome duplication (WGD) events, designated as rho (ρ), sigma
(σ), and tau (τ), have been identified in the genomes of cereal grasses.
Precise dating of these WGD events is necessary to investigate how they
have influenced diversification rates, evolutionary innovations, and
genomic characteristics such as the GC profile of protein coding
sequences. The timing of these events has remained uncertain due to the
paucity of monocot genome sequence data outside the grass family
(Poaceae). Phylogenomic analysis of protein coding genes from sequenced
genomes and transcriptome assemblies from 35 species, including
representatives of all families within the Poales, has resolved the timing
ofrho and sigma relative to speciation events and placed tau prior to
divergence of Asparagales and the commelinids but after divergence with
eudicots. Examination of gene family phylogenies indicates that
rhooccurred just prior to the diversification of Poaceae and sigma
occurred before early diversification of Poales lineages but after the
Poales-commelinid split. Additional lineage specific WGD events were
identified on the basis of the transcriptome data. Gene families
exhibiting high GC content are underrepresented among those with duplicate
genes that persisted following these genome duplications. However, genome
duplications had little overall influence on lineage-specific changes in
the GC content of coding genes. Improved resolution of the timing of WGD
events in monocot history provides evidence for the influence of
polyploidization on functional evolution and species diversification.