1 3 Mol Genet Genomics DOI 10.1007/s00438-014-0969-3 ORIGINAL PAPER Diversification and distinctive structural features of S-RNase alleles in the genus Solanum Lauís Brisolara-Corrêa · Claudia Elizabeth Thompson · Cláudia Lemelle Fernandes · Loreta Brandão de Freitas Received: 11 September 2014 / Accepted: 27 November 2014 © Springer-Verlag Berlin Heidelberg 2014 of the positively selected residues was identified adjacent to a conserved strand that is crucial for enzymatic cataly- sis. Additionally, we have shown significant differences in the electrostatic potential among the predicted molecular surfaces in S-RNases. The structural results indicate that local changes in the three-dimensional structure are pre- sent in some regions of the molecule, although the general structure seems to be conserved. No previous study has described such structural variations in S-RNases. Keywords Allele diversification · Solanum · S-RNase · Molecular modeling · Structural biology · Phylogenetics Introduction Several mechanisms have been identified as responsible for stigma and style recognition (Golz et al. 1999). The major- ity of flowering plants have organs with male and female structures simultaneously in the flower. Consequently, genetic self-incompatibility (SI) systems evolved to prevent the detrimental effects of self-fertilization and inbreeding depression. SI occurs when a pollen grain lands on its own stigma or on the stigma of a genetically related plant. In these cases, the pollen will fail to germinate or will germi- nate to produce a pollen tube that grows through the style but does not reach the embryonic sac in the ovary (de Net- tancourt 1977). In general, SI is a phenomenon in which pistils spe- cifically reject pollens with which they share some alleles. Basically, there are two distinct strategies, sporophytic self-incompatibility (SSI) and gametophytic self-incom- patibility (GSI), the latter of which will be discussed in more detail because it is the mechanism found in Sola- num. GSI is controlled by a multigenic, multiallelic locus Abstract The multigenic and multiallelic S-locus in plants is responsible for the gametophytic self-incompati- bility system, which is important to prevent the detrimen- tal effects of self-fertilization and inbreeding depression. Several studies have discussed the importance of punctual mutations, recombination, and natural selection in the gen- eration of allelic diversity in the S-locus. However, there has been no wide-ranging study correlating the molecular evolution and structural aspects of the corresponding pro- teins in Solanum. Therefore, we evaluated the molecular evolution of one gene in this locus and generated a statisti- cally well-supported phylogenetic tree, as well as evidence of positive selection, helping us to understand the diversifi- cation of S alleles in Solanum. The three-dimensional struc- tures of some of the proteins corresponding to the major clusters of the phylogenetic tree were constructed and sub- sequently submitted to molecular dynamics to stabilize the folding and obtain the native structure. The positively selected amino acid residues were predominantly located in the hyper variable regions and on the surface of the protein, which appears to be fundamental for allele specificity. One Communicated by C. Gebhardt. Electronic supplementary material The online version of this article (doi:10.1007/s00438-014-0969-3) contains supplementary material, which is available to authorized users. L. Brisolara-Corrêa · L. B. de Freitas (*) Department of Genetics, Laboratory of Molecular Evolution, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil e-mail: loreta.freitas@ufrgs.br L. Brisolara-Corrêa · C. E. Thompson · C. L. Fernandes Unit of Theoretical and Computational Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil