Comparative Analysis of the Gene Space in the Plant Family Asteraceae Reveals Gene Families Showing Lineage-Specific Differential Rates of Evolution and Selective Constraint

The Asteraceae is the largest family of flowering plants and contains many agronomically important crop and ornamental species. Given a global distribution and adaptation to many different environments, the Asteraceae represent an important system for investigating the relative importance of different evolutionary forces that contribute to adaptive radiations. In this study, we generated de novo genome assemblies for sunflower, safflower, lettuce, and gerbera from repeat-reduced whole-genome shotgun libraries with each species being from one of the four major subfamilies in the Asteraceae. We inferred orthologous and paralogous gene relationships between these species based on similarity from an all-vs-all BLAST followed by MCL clustering. By employing a novel phylogenomic approach we were able to analyze the proportional rate of evolution for each gene family and statistically evaluate these rates among gene families for each species. Here, we show that Gene Ontology categories showing proportionally slower rates of evolution were related to transcription, RNA biosynthesis and cellular processes while those showing proportionally higher rates of evolution across species were related to nucleic acid metabolism and DNA binding. While some divergent patterns appear to be driven by differences in synonymous substitution rates, we also found evidence of elevated nonsynonymous substitution in genes related to plant defense or DNA binding.