| Flavonoids are plant secondary metabolites. They involved in various biological processes during plant growth and development, including pigment accumulation, resistance against pathogenic microorganisms and insect pests, and pollen development. Chalcone isomerase (CHI, EC 5.5.1.6) is an important enzyme in the flavonoid biosynthesis pathway, and exists extensively in angiosperm. The genes encoded Chalcone isomerase belong to a multiple gene family. The copy numbers and expression patterns of the genes in the family are diverse among different plants. In order to further understand the general evolutionary regulation of chi gene family in angiosperm and specific evolutionary patterns in three allopolyploids Oryza species with CD genome (O. alta Swallen., O. grandiglumis (Doell) Prod.and O. latifolia Desv.), the methods of bioinformation, cloning and sequencing were used in the present study. Addtionally, in order to understand the evolutionary dynamics of duplicate homoeologous loci in polyploid plants, the levels and patterns of nucleotide diversity for triosephosphate isomerase (rict) gene was estimated.The main results are summarized as follows:1. Phylogeny and evolution of chalcone isomerase gene family in angiospermFive hundred and twenty two amino acid sequences were retrieved from NCBI and TAIR databases, and 113 was used for phylogenetic analysis after removing redundancies and fragments. The NJ tree grouped the 113 sequences to 5 clusters. ClusterⅠinclude many of plants in angiosperm. ClusterⅡhad only plants in family Leguminaceae. The less genetic distance between the former clusters suggested the clusterⅡmight derived from gene duplication with functional diversely in Leguminaceae.ClusterⅢto Cluster V possessed fewer plants with obvious sequence differences with the former two Clusters, suggesting that CHI family had experienced complicated divergence among genes copies during the long evolutionary history of angiosperm. Additionally, these genes still shares higher homology with corresponding sequences in fungi and bacilli. The result implied that chi genes had an old origin and experienced a dynamic process with duplication and deletion.2. Molecular evolution of chalcone isomerase gene family in Oryza allotetrapoids with CD genomeIn present study, two copies of chi gene grouped to ClusterⅠand the ClusterⅢin the former angiosperm's phylogenetic tree were obtained. The gene of chi1 in the American allopolyploids shares higher homology with the locus of Os03g0819600 located in the third chromosome of O. saliva. One homologue was found in three allotetraploids with genome CD. All of sequences are highly consistent. Only a 8bp insertion in the fourth intron differentiated O. latifolia from the other two species. Based on the comparison with diploid O. officinalis with genome C, we estimated that the present homologues in these allopolyploids possible derived from their paternal D genomic ancestors.The gene of chi2 shares higher homology with the locus of Os11g0116300 and Os12g0115700 located in the 11 and 12 chromosomes of O. sativa. In contrast to chi1, bi-parental homologues of C and D genomic types were all retained in three allopolyploids.Inconsistent expression patterns between chi1 and chi2 were also revealed in this study. The single homologue of chi1 could express normally in three allopolyploids, different homologues of chi2, however, experienced a bias expression patterns among the three species. The paternal lineage homologues were expressed in O. alta and O. latifolia, whereas the maternal lineage homologue was expressed in O. grandiglumis.3 Nucleotide diversity of the homoeologous rict loci in the American allotetraploid Oryza speciesIn the present study, a low level of nucleotide diversity for Triosephosphate isomerase (rict) loci in three American allotetraploid Oryza species:O. alta, O. grandiglumis, and O. latifolia were revealed, and a different evolutionary dynamics of homoeologous rict loci in these allotetraploid was also been found. |
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