The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach

The plant genus Oenothera has played an important role in the study of
genome evolution and plant defense and reproduction. Here, we built on the
1kp transcriptomic dataset and developed a molecular resource of 63
transcriptomes and present a large-scale comparative study across 29
Oenothera species. We produced 2.3 million transcripts and 25.4 Mb of
total length assembly per individual. We used this transcriptome resource
to examine genome-wide evolutionary patterns and functional
diversification by searching for orthologous genes and performed gene
family evolution analysis. We found wide heterogeneity in gene family
evolution across the genus, with section Oenothera exhibiting the most
pronounced evolutionary changes. Overall, more significant expansions
occurred than contractions. We also analyzed the molecular evolution of
phenolic metabolism by retrieving proteins annotated for phenolic
enzymatic complexes. We identified 1,568 phenolic genes arranged into 83
multigene families that varied widely across the genus. All taxa
experienced rapid phenolic evolution involving 33 gene families, which
exhibited large expansions, gaining about 2-fold more genes than they
lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl:
CoA ligase (4CL) accounted for most of the significant expansions and
contractions. Our results suggest that adaptive responses to environmental
stress coupled with non-adaptive evolutionary forces have contributed to
Oenothera diversification and rapid gene family evolution.