Molecular Evolutions For Functional Transition Of P34and Legume Traits

Legumes (Fabaceae or Leguminosae) are the third largest family of angiosperms, and widely distributed and cultivated. The legumes have unique ability of symbiotic nitrogen fixation in nodules, and their seeds are rich in oil and proteins, alkaloids and flavonoids and other secondary metabolites, having very high economic value. Therefore, the studies on the legumes have theoretical importance and economic significance.Whole genome duplication (WGD) has long been recognized as an important driving force of species evolution, especially in plants. Previous studies show that, about58million years ago (Mya), soon after the origin of legumes, a WGD event occurred in most legumes. Note that P34is a storage protein, a major allergen and a syringolide receptor in soybean, but its ancestor is a cysteine peptidase, indicating a functional transition. Therefore, we hypothesize that the greatest mutation in legume history may contribute to gene diversity and these special traits in the legumes. To prove this viewpoint, the evolutionary details for functional transition of P34was firstly studied in order to understand the evolutionary patterns of genes in legumes; and the association between this WGD and the evolution of legume traits was further explored under genome-wide framework. The results are as follows.1) Using syntenic relationships from the Plant Genome Duplication Database, homologous genes of P34were identified, these homologous genes along with SPE31were used to construct the gene tree of P34, and the gene tree along with gene expression and crystal structure data was used to investigate the functional transition of P34. Results show that multiple gene duplications, exon-shuffling and following granulin domain loss, some critical point mutations are associated with the transition. Although the evidence of positive selection is observed from positive selection test, the possibility that random fixation under the relaxation of purifying selection results in the functional transition is supported as well in this study. In addition, a new sub-group including Glyma08g12340and Medtr8g086470within the papain family is found. This study describes a typical and complex case of studying functional transition and aids in understanding the formation of a storage protein and an allergen.2) Using four legumes(Cajanus cajan, Glycine max, Lotus japonicus and Medicago truncatuld) and three non-legume species (Populus trichocarpa Arabidopsis thaliana and Vitis vinifera) as materials, the phylogenies of the genes from the above seven species were reconstructed. These gene trees reconciled with their species tree were used to identify the ancestral nodes representing the early legume WGD event. Results show that26.5%of duplicate genes are retained in the four legumes when ignoring bootstrap values on duplicate branches and only considering their topologies of the gene trees, the retained proportion varies from legume to legume, and expression patterns for most duplicates vary from gene to gene. GO enrichment analysis shows that legumes prefer to retain WGD-derived duplicates relative to environment response and molecular transport. The association between biological processes and special traits in the legumes is also observed in this study. This study provides clues to further exploration of molecular mechanisms underling the legume traits.