| Gene duplication is a prevalent phenomenon in living things, among the modelspecies that has been sequenced in the genome level, the existence of duplicate genehas covered the both prokaryote and eucaryon, especially during the evolution ofangiosperm, it has underwent several rounds of polyploidization process andcontribute to the formation of abundant duplicate genes, the polyploidization is themost important driving force that promote the higher plant evolution and is also theimportant source of novelties. Duplicate genes result in diverse gene expressionpatterns to satisfy requirements for the development and evolution of species.Therefor, it is of significant meaning to clarify architectural varation as well asfunction divergence of duplicate gene. However, in the genome level, few reportsexist in the literature that dissects the characterization, divergence, and function ofeach family in the mesopolyploid species Brassica rapa. In the present study, the48duplicate gene families (387genes) of the B. rapa genome were used to reveal theprinciple of divergence in duplicate genes. The characteristic analysis of duplicategenes shows that the specific repetitive elements, such as tandem repeats (TRs), invertrepeats (IRs), simple repeat sequences, and transposons, are preferentially distributedin the introns and untranslated regions (UTRs) rather than in the exons. The variationin the duplicate genes in each family was mainly reflected in the promoter regions aswell as in the5-and3-UTRs. However, their coding regions exhibited a variation ofhigher number and longer fragments. The Tajima's D test results show that mostduplicate genes are subjected to negative selection. The variation in the regulatoryelements of duplicate genes plays a remarkable role in driving the divergence ofduplicate genes. The birth or divergence of duplicate genes increased the plasticity ofthe gene regulatory network and the adjusted capability of polyploid species towardthe environment. Gene duplication optimizes the gene architecture and function tofacilitate species evolution. In addition, the expression level prediction result showedthat about70.80%of the nascent duplicate genes maintain higher expression level.The duplicate genes were mainly involved in metabolic processes (29.71%), response to the environment (14.48%), These genes principally participated in binding function(57.71%), molecular biological function(21.14%) as well as catalytic activity (10.02%)and were expressed in the organelle (37.98%) and cell(21.93).In order to further investigate the divergence characteristic of duplicate gene inB.rapa, we analyzed the structure and express pattern in the defensin gene family. Theresult indicated that each member has eight conserved cysteine residues, the length ofintron in each copy is various and signal peptide sequences have been diverged inpartial members. The expression pattern may diverged in the process of evolutionsuch as selective expression differences. We cloned three defensin genes in theB.rapa in the genome level and lay the foundation for the investigation of expressdifferences among the copies members.In addition we developed a novel promoter molecular marker technology basedon ATG conserved region of CDS sequences in Brassica rapa and core elements ofpromoter region. Among16accessions of Brassica species were detected abundantpolymorphism. The results showed that a total of124loci were detected with15pairsof primers in the tested Brassica accessions,116of which were polymorphic withaverage polymorphism of90.81%. The average amplification loci of each pairs ofprimer was8.27. We randomly extracted bands to sequencing and analyzed thecis-acting elements, the results indicated that there were a great quantity of cis-actingelements in the amplification sequences. Therefor, the primers based on thistechnology can be used to detect DNA interval region polymorphism and is importantfor identification of germplasm resources as well as molecular marker assistedbreeding. |
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