Divergence in Gene Expression Is Uncoupled from Divergence in Coding Sequence in a Secondarily Woody Sunflower

Abstract

Premise of research. The transition from herbaceous annual to woody perennial has occurred numerous times during angiosperm evolution, but the suite of genetic changes that accompanies this life history shift remains poorly understood. Here we analyze genetic sequence and gene expression divergence between the annual Helianthus annuus and a recently diverged woody perennial ecotype from California.Methodology. We grew plants from populations of typical H. annuus and the woody perennial ecotype in a common garden and measured days to flower, mature height, and basal stem density. We looked for evidence of genome size evolution in the woody ecotype using flow cytometry and conducted anatomical observations of stem development in seedlings. We sequenced the aboveground seedling transcriptomes of six individuals of each ecotype and identified genes with high fixation index (FST) and significant divergence in gene expression. Finally, we examined the gene ontology annotation of differentiated genes and assesse...