Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

Ancient duplication events and retained gene duplicates have contributed
to the evolution of many novel plant traits and, consequently, to the
diversity and complexity within and across plant lineages. While mounting
evidence highlights the importance whole-genome duplication (WGD;
polyploidy) and its key role as an evolutionary driver, gene duplication
dynamics and mechanisms, both of which are fundamental to our
understanding of evolutionary process and patterns of plant diversity,
remain poorly characterized in many clades. We use newly available
transcriptomic data and a robust phylogeny to investigate the prevalence,
occurrence, and timing of gene duplications in Lamiaceae (mints), a
species-rich and chemically diverse clade with many ecologically,
economically, and culturally important species. We also infer putative
WGDs—an extreme mechanism of gene duplication—using large-scale data sets
from synonymous divergence (KS), phylotranscriptomic, and divergence time
analyses. We find evidence for widespread but asymmetrical levels of gene
duplication and ancient polyploidy in Lamiaceae that correlate with
species richness, including pronounced levels of gene duplication and
putative ancient WGDs (7–18 events) within the large subclade Nepetoideae
and up to 10 additional WGD events in other subclades. Our results help
disentangle WGD-derived gene duplicates from those produced by other
mechanisms and illustrate the non-uniformity of duplication dynamics in
mints, setting the stage for future investigations that explore their
impacts on trait diversity and species diversification. Our results also
provide practical context for evaluating the benefits and limitations of
transcriptome-based approaches to inferring WGD, and we offer
recommendations for researchers interested in investigating ancient WGDs
in other plant groups.