The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
Bibliographical noteFunding Information:
The work conducted by the DoE JGI is supported by the Office of Science of the DoE under contract number DE-AC02-05CH11231. We thank J. Bergelson, J. Borevitz, A. Hall, C. Langley, K. Mayer, J. Nasrallah, B. Neuffer, Y. Van de Peer and O. Savolainen for contributing to the initial sequencing proposal submitted to the Community Sequencing Program at JGI. We also thank T. Bureau, D. Schoen, P. Harrison, J. Stinchcombe, A. Moses and E. Harmsen for their contributions to the Value-directed Evolutionary Genomics Initiative (VEGI) grant (Genome Quebec/Genome Canada), which funded C. grandiflora genomic and mRNA sequencing, and G. Coupland (Max Planck Institute for Plant Breeding Research) and colleagues for information on Arabis alpina repeats. The work was supported by the Max Planck Society (D.W.), the Genome Quebec and Genome Canada VEGI grant (S.I.W. and M.B.), the Natural Sciences and Engineering Research Council of Canada (NSERC) (S.I.W.), the Swedish Research Council (T.S.), the Carl Trygger and Erik Philip-Sörensen foundations (T.S.), National Science Foundation (NSF) grant 0929262 (J. Steffen and R.M.C.), the French National Research Agency (ANR-08-KBBE-012-02 to H.Q.), the Czech Science Foundation (excellence cluster P501/12/G090 to M.A.L.) and the European Regional Development Fund (CZ.1.05/1.1.00/02.0068 to M.A.L.). D.K. was supported by a Human Frontiers in Science Program Long-Term Fellowship, and G.C. was supported by the Alfred P. Sloan Foundation. Population genetics analyses were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) through the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) under project b2012122. L.M.S. was supported by a European Community FP7 Marie Curie Fellowship (PIEF-GA-2008-221553) and an EMBO Long-Term fellowship.