Identification And Analysis Of Spliceosomal Genes In Wheat

Spliceosome is an evolutionarily conserved and highly dynamic polyribonucleoprotein complex,which catalyze the process from precursor m RNA to mature m RNA and is a key element of transcription and post-transcriptional regulation in organisms.A large number of studies have found that spliceosome plays an important role in regulating plant growth and development and response to stress.Wheat is one of the most important food crops in China and even in the world.The sustained steady and increased production of wheat is a major demand for ensuring Chinese food security.Therefore,identification of wheat spliceosome-related genes and analysis of their key regulatory roles in wheat growth and development and stress response are not only necessary to further understand the necessary requirements of wheat growth and development and stress resistance regulation network,but also provide newly important gene resources for wheat genetic improvement.Therefore,based on the newly released reference genome information of "Chinese spring" wheat,to identify and analyze the spliceosomal protein-related genes in wheat at the genome-wide level,and to clarify the composition of spliceosomal protein-related genes in wheat genome.Then,codon usage bias,chromosome distribution,collinearity analysis,GO functional enrichment analysis were also studied.In addition to,we analyzed the expression pattern and co-expression network of the spliceosomal protein,using the second-generation transcriptome data of "Chinese Spring" wheat.The 14 SM/LSM genes of the spliceosome were studied,including their chromosome distribution,collinearity analysis,the ratio of nonsynonymous to synonymous substitution rates,gene structure,cis-acting regulation elements,preliminary verification of gene function by RT-PCR in wheat and its ancestor Triticum urartu,Triticum dicoccoides,Aegilops tauschii.1.Identification and correlation analysis of wheat spliceosomal proteinsBased on the updated reference genome information of wheat,1017 spliceosomal proteins’ sequences were identified,and they were named and classified according to the name of the rice spliceosomal genes’.The wheat spliceosomal genes are rough uniformly distributed in the A,B,and D subgenomes,most genes are distributed on chromosome 4 and the least on chromosome 1.Collinearity analysis of A,B,and D subgenomes revealed that 8genes are located in the 4AL-5AL-7BS chromosome model.The relative synonymous codon usage of spliceosomal proteins was studied according to our classification,and it was found that the top2 of relative synonymous codon usage were the Arg codon AGG and the stop codon UGA.The GO enrichment of spliceosomal genes revealed that some spliceosomal genes have the functions of response to stimulus besides of composing spliceosome.2.Analysis of expression patterns of wheat spliceosomal proteinsUsing 39 RNA-seq data of "Chinese Spring" wheat analysis the expression patterns of spliceosomal proteins according to three tissues of root,leaf,and ear,and six stages of germination,seedling,heading,booting,flowering,and filling,showed that the spliceosomal proteins are more highly expressed in the spike than in the leaf,and in the leaf more than in the root.The spliceosomal proteins are more highly expressed in the flowering stage than at the heading stage,the heading stage more than booting stage,booting stage more than seedling stage,and the seedling stage more than filling stage,and the germination stage are the least.Analyzing the expression levels of spliceosomal genes under drought stress,heat stress,and salt stress,it was identified that three genes may be related to three stresses at the same time.3.Construction of wheat gene co-expression networkUsing 39 RNA-seq data of "Chinese Spring" wheat to construct a co-expression network and analyzed the spliceosomal proteins in the co-expression network,it was found that Ta Prp40 a,Traes CS3A02G440000.1,and Ta HSP73 may have a certain relationship in the regulation of stress resistance.4.Bioinformatics analysis of spliceosomal SM/LSM genes in wheat and its ancestorAccording to the Arabidopsis spliceosomal SM/LSM gene and the LSM hidden Markov model to identify the spliceosomal SM/LSM gene.Totally,57 spliceosomal SM/LSM genes were obtained in wheat,together with 41,17 and 19 found in Triticum dicoccoides,Triticum urartu,Aegilops tauschii,respectively.Chromosome distribution,collinearity analysis and analysis of non-synonymous substitutions and synonymous substitutions d N/d S of spliceosomal SM/LSM genes in the wheat and its ancestor,found that the distribution of SMD2 gene in 5A,4B and 4D was caused by translocation.Form the result of d N/d S,we found that most of the SM genes were purifily selected during polyploidization except in the first stage of polyploidization SMD1 were positively selected and in the second stage of polyploidization SMB were positively selected,while spliceosomal LSM genes mostly undergo positive selection except for LSM3 and LSM7 genes.Through RNA-seq data and RT-PCR analysis,we found that LSM7-7A,SMD1-2A and LSM8-1A are highly expressed under salt and drought stress.These genes may be related to drought resistance and salt tolerance.This study laid a foundation for the further study on the function of wheat spliceosomal proteins,and also provided ideas for the study of the normal growth and development and resistance.