Phylogenomic Study Of Self-Incompatibility S-locus In Rosaceae Fruit Trees

Self-incompatibility(SI)is a kind of phenomenon formed in the long-term evolution of flowering plants after self-pollination cannot produce zygote,which reduces the production efficiency of Rosaceae fruit trees such as apple and pear to a certain extent.Gametophytic selfincompatibility(GSI)mechanism mediated by S-RNase gene is determined by a single locus(S-locus)containing style determinant(S-RNase)and pollen determinant(SLF,S-locus F-box),which is common in Rosaceae,Solanaceae,Plantaginaceae and Rutaceae plants.The functions of the two determinants of S-locus have been reported to some extent by predecessors,however,the phylogenetic relationships and evolutionary history of S-RNase and SLF genes in eudicots and Rosaceae plants remain unclear.Many representative genomes of Rosaceae species have been sequenced at present.In our work,from the perspective of phylogenetic genomics,the phylogenetic relationship and evolutionary characteristics of S-RNase and SLF genes were systematically analyzed in S-locus across Rosaceae species by combining phylogenetic reconstruction and genomic collinearity information.The duplication,loss,linkage and specific translocation of S-locus genes were dissected,which laid the foundation for further function studies.The main results are as follows:1.The S-RNase based GSI mechanism of Rosaceae has a single evolutionary origin,originated from eudicots plants.Phylogenetic analysis showed that the RNase T2 gene family was divided into three classes(Class I,Class II,Class III),S-RNase genes belonged to Class III,and S-like RNase genes were distributed in Class I and Class II,respectively.2.The Class III clade RNase T2 genes was derived from the Class I clade.Class I genes showed relatively conserved collinearity relationships in angiosperms.And our used of synteny network analysis allowed us to identify the relationships of Class III S-RNase and Class I S-like RNase genes,which confirmed the phylogenetic relationship and can be further used as direct evidence that Class III is derived from Class I gene duplication.3.Several lineage-specific genomic transpositions of S-RNase genes have been identified in eudicots species,such as Rosaceae,Solanaceae and Rutaceae.S-RNase genes from Maleae(apple,pear,loquat)and Prunus(peach,Japanese apricot,Chinese plum)has a high sequence homology,but with specific transposition in genomic position.4.Whole genome duplication and a large number of tandem duplication events of SLF genes occurred in Rosaceae species and originated from basal Rosaceae group Fairy wood.According to the phylogeny,SLF genes were divided into four classes(Class I-IV),in which functional SLF genes of Maleae,part of Pruns,Solanaceae and Rosaceae were located in Class I,while SLF functional genes of most Pruns plants was located in Class II.The duplication and diversification of SLF genes may appear in Prunus plants before species diversification.5.The S-locus could be traced back to the basal Rosaceae group Fairy wood and showed diverse collinearity trends in Maleae,Prunus and Rosoideae,corresponding to the changes of synteny genomic positions.Most Rosaceae genomes contain S-locus.For instance,S-locus of Maleae(apple,pear and loquat,etc)is located on Chr17,S-locus of Bowman’s root and Fairy wood are located on Chr5 and Drydscaffold226,respectively.S-locus of peach is located in Chr6.The results of macrosynteny and microsynteny analysis revealed that S-locus showed the specific translocations occurred in S-locus of Maleae species: ancient S-locus may exist on Chr4 and Chr12 in Maleae,then were translocated on Chr9 and Chr17,and the present existing S-locus was only retained on Chr17.We speculated that the whole genome duplication event shared by Maleae species may lead to S-locus appearing specific genomic position in this subfamily.