Rapid copy number expansion and recent recruitment of domains in S-receptor kinase-like genes contribute to the origin of self-incompatibility

More than half of flowering plants have a sophisticated mechanism for self-pollen rejection, named self-incompatibility. In the Brassicaceae family, the recognition specificity of a self-incompatibility system is achieved by the interaction of the stigmatic S-receptor kinase and its ligand S-locus cysteine-rich protein, which are encoded by two tightly linked polymorphic genes. During the last two decades, many studies have explored their functions, although their origin and evolutionary history have still not been elucidated clearly. In the present study, an extensive survey in nine whole-genome sequenced plants, including one moss, one fern and seven flowering plants, was conducted to clarify these issues. The data obtained showed that S_locus_glycop domain-related genes, which are land plant specific, have an ancient origin that can be traced back to early land plants and also have a significantly expansion in flowering plants. In the four predominant domain architectures (Types I to IV) of these proteins, Type III genes had absolute predominance and appeared to be raw materials for diversification of the S_locus_glycop domain-related genes by frequent domain re-organizations. S-receptor kinase-like sequences (Type IV) might have originated from Type III genes by domain gains, and S-locus glycoprotein-like sequences (Type I) might have arisen by partial duplication of its linked S-receptor kinase genes. Although similar topologies were detected in S-receptor kinase and S-locus cysteine-rich protein trees, their physical linkage were found only in Brassicaceae, suggesting that the strong linkage disequilibrium and their co-evolution may be a key factor for the origin and maintenance of the S-receptor kinase-based self-incompatibility system in Brassicaceae.