Identification And Evolutionary Characteristics Of Maize Duplication Genes

Gene duplication is an important event in evolution,which provides a genetic basis for the evolution of species.There are three main types of replication events,including non-reciprocal associations of chromosomes,transposon duplication,and genome-wide duplication.The duplication gene will eventually move toward three outcomes,new functionalization,sub-functionalization,and loss.In particular,new functionalization and sub-functionalization has an important impact on the evolution of species.The maize genome size is centered in flowering plants,and the genome-wide duplication events can partly explain the increase in the maize genome relative to the sorghum genome.Current studies have speculated that maize has undergone at least three whole-genome duplication events,before the divergence of the monocotyledonous plant,before the divergence of grass,and a whole genome-wide duplication after the divergence of maize and sorghum,occurring about 110 million years ago,50 million years ago,and 12 million years ago.In order to comprehensively identify the duplication genes in the maize genome,to clarify the way of duplication and the time of genome-wide duplication gene production,and to identify the differential differentiation between the duplication gene pairs,especially the differences in expression and function.Furthermore,we investigated the effects of duplication genes,especially the genes generated by different genome-wide duplication events on the formation and evolution of maize traits.In this study,we identified the replication genes in the maize genome by homology clustering,collinearity analysis and phylogenetic analysis of maize,sorghum,rice and Arabidopsis genes,and clarified the way of its production and analyzed the differences.The differences between different duplication methods and genes generated by different whole genome duplication events,including sequence differences,expression and functional differences,and the effects of these replication genes on the evolution of key traits were analyzed.The results can reveal the composition and structure of the maize genome,the origin and function of the genes related to the importance traits,lay the foundation for further exploration of the formation of important economic traits and the evolution of the genome.The main findings are as follows:First,Maize duplication genes were identified at the genome-wide level by gene homology analysis,cluster analysis,chromosomal collinearity analysis,Ks distribution analysis,and phylogenetic analysis.There are 28,911 duplication genes in the maize genome,accounting for 73%of the maize genes.Among them,21,654 genes in the maize genome-retained genes were identified to be associated with genome-wide duplication,accounting for 55%of the total number of genes.Maize WGD(whole genome duplication after divergence of maize and sorghum),Pre-grasses WGD(whole genome duplication before grass)and Pre-monocots WGD(whole genome duplication before monocotyledon)related genes were 9606,5917,and 2922,respectively,accounting for 24%,15%,and 7%,respectively.Second,sequence difference analysis found that maize genome-wide duplication genes have more gene components.Including the length of the gene,coding region,exon,non-coding region,intron and the number of transcripts is higher than the average length and number in the whole genome duplication gene,and same result in the singleton gene.The average gene length of maize gene was 3995 bp,the mean value of whole genome duplication gene was 4495 bp,the average value of singleton gene was 5364 bp,the average length of coding region of maize gene was 1096 bp,and the mean value of whole genome duplication gene and singleton is 1314 bp and 1206 bp.Pre-monocots WGD,Pre-grasses WGD,Sorghum-Maize and Maize WGD comparisons between different event revealed that the Pre-monocots WGD gene has a higher transcripts number,average gene length,average CDS length,and average Intron length.The GC distribution of maize genome-wide duplication gene contributes significantly to the bimodal peak of maize GC distribution;the Pre-grasses WGD event contributes the most to the high GC content between genes.Single nucleotide polymorphism analysis revealed that maize duplication genes have fewer average SNP sites.Third,Analysis of expression and function differences revealed that the maize duplication gene has a higher average gene expression level,and the function of the retained duplication gene is enriched to development and stress response.The mean expression value(log2(FPKM))in the whole genome duplication gene was 4.1,and the average was 4.6 in the singleton gene;the values in the Noparalogs,Tandem,and Other duplication genes were1.22,1.57,and 1.66,respectively.Most of the tissue-specific expression genes are derived from the duplication gene,and there are 9902 genome-wide duplication genes,accounting for 61%of the number of tissue-specific genes.Analysis of the distribution of tissue-specific genes between different genome-wide duplication events,including Maize WGD,Maize-Sorghum,Pre-grasses WGD,and Pre-monocot WGD replication events,the numbers accounted for 37%,16%,33%and 12%respectively.Gene Ontology analysis found that maize genome-wide duplication genes are mainly involved in development and response to stress;the ontology annotation of Maize WGD genes enrichment includes nuclear,plasma membrane,DNA binding,transcription factor activity and abiotic stimulation.The earlier Pre-grasses WGD genes was enriched in a functional type similar to the most recent duplication gene,enriched in response to biotic or abiotic stress,cell death,flower development,and pollen-pistil interaction.Metabolic pathway analysis found that maize genome-wide duplication genes are involved in developmental and stress-relevant functions.In the Maize WGD genes,metabolic pathways are enriched in ribosomes,m RNA monitoring pathways,splices,MAPK signaling pathways,plant hormone signaling,autophagy,protein processing in the endoplasmic reticulum circadian rhythm.Pre-grasses WGD genes are enriched in amino acid metabolism-related pathways,metabolic pathways related to sugars and fatty acids,and synthesis of metabolites,starch and sucrose metabolism.Fourth,genetic analysis of key traits in maize revealed that the maize starch metabolism,C₄ photosynthesis,and MAPK family-related genes all experienced multiple genome-wide duplication events,and the replicated genes showed tissue specificity of expression.A total of 29 maize starch metabolism-related genes were analyzed,with 8,3,8,and 10 related to Maize WGD,Maize-Sorghum,Pre-grasses WGD,and Pre-monocot WGD events,respectively.Among them,adenosine diphosphate glucose pyrophosphorylase(ADPG)is a key enzyme in starch synthesis.Gene SH2 and AGPLS2 are replicated in the Pre-grasses WGD,and these two genes are associated with AGPLS3 and AGPLS4 genes from Pre-monocots WGD.Small subunits AGPS1a,AGPS1b,and AGPS genes are all formed by a recent duplication,and all three genes have very close evolutionary relationships.And these three genes divergence with AGPS2 during the Pre-grasses WGD.The duplicated maize starch metabolism gene shows the specificity of tissue expression.For example,in the key enzyme ADGP,AGPLS2 is mainly expressed in embryos,SH2 is mainly expressed in endosperm,AGPLS3 is highly expressed in embryo and endosperm,and AGPLS4 gene is mainly expressed in leaves.The same phenomenon occurs in the small subunit of ADPG:AGPS1b is abundantly expressed in maize leaves,and its replication genes AGPS,AGPS1a and AGPS2 genes are mainly expressed in embryos or endosperm.The C₄photosynthesis genes retained in maize are mainly derived from large fragment duplication.A total of 33genes were analyzed in the maize genome,three of which were derived from non-linear replication,one from tandem repeats and 29 from whole genome duplication.The key enzyme is phosphoenolpyruvate carboxylase(PEPC),in which the PEPC3 is formed after pre-grasses WGD and retains two copies of pepc3-a and PEPC3-b.also PEPC1 and the PEPC2 were differentiated into two copies after pre-grasses WGD.And PEPC2 gene formed two copies after Maize WGD,namely PEPC2-a and PEPC2-b.The duplicated gene shows tissue specificity of expression.The key enzyme PEPC has a significant difference between the PEPC1 and PEPC2s genes produced by pre-grasses WGD.The former is highly expressed in leaves,while the latter two gene copies formed after undergoing maize WGD are expressed in each tissue.The maize MAPK genes mainly originates from genome-wide duplication.In our study,A total of 22 genes were aggregated in the same clusters,14 of which went through Maize WGD and 22 of which experienced earlier Pre-monocots WGD.It was also found that the genes from different duplication events also had tissue specificity of expression.In summary,more than 70%of the genes in the maize genome are duplication genes and are mainly derived from several WGD.The WGD gene is rich in components,produces GC content differentiation,and has high expression level,showing tissue expression specificity.Therefore,the main form of functional differentiation is tissue expression differentiation.The key genes of maize endosperm starch metabolism and C₄ photosynthetic metabolism are mainly derived from genome-wide duplication.Therefore,the generation and functional differentiation of duplication genes determine the evolution of corresponding traits in maize.