Analysis of divergence of annual and perennial crucifers by genome comparisons and interspecific genetics reveals contribution of reproductive assurance

Life history evolves rapidly in plants. In stable environments, polycarpic perennials predominate and live for many years, reproducing each year. By contrast, monocarpic annuals, that reproduce only once are favoured in unstable environments. Annuals have evolved strategies termed reproductive assurance to ensure that they reproduce successfully during their short life-cycle, and these have arisen independently many times. However, the genetic basis of the divergence of annuals from ancestral perennials is poorly understood. Here, we analyse the genetics of life-history divergence in a clade of the Brassicaceae family containing the model perennial Arabis alpina. We compare the A. alpina genome to the newly assembled genome of its sister annual, and functionally characterize differences between them by analysing an introgression population made by hybridizing the species. We show that the markedly smaller genome of the annual is due to the presence of fewer and older retrotransposons. The occurrence of this difference correlates with the divergence of the species and the emergence of self-fertilization in the annual. Also, utilizing the introgression lines, we identify loci from the annual that confer rapid flowering or more flowering branches on the perennial. We propose that reproductive assurance contributes to shaping the genome and genetics of the annual.