Chromosome-Wide Computational Identification And Comparative Analysis Of Wheat Mirnas Using The Survey Sequences:a Case Study In Group 7 Chromosomes

MicroRNAs(miRNAs)are a class of important biological elements that regulates gene expression by translational repression or transcript degradation both in plants and animals.The origin,distribution and evolution of the miRNA genes have been systematically studies in many model plants,while they are not well understood in wheat.In current study,we have systematically identified the pre-miRNAs and mature miRNAs in wheat group 7 chromosomes(7A,7B and 7D)by computational analysis of the genomic survey sequences of the isolated chromosome.And some of the prediction miRNAs had been validation by qRT-PCR.The target sites of all the miRNAs which were first identified in wheat were also predicted.We also had done the GO annotation of miRNA targets and repeat element analysis of all the pre-miRNAs.The main results are as follows:1.After analyzing shotgun sequences from wheat group 7 chromosomes(7A,7B and 7D)of bread wheat(Triticum aestivum L.),a total of 58 conserved miRNAs were predicted in silico,of which 28 miRNAs with the proportion of 48.28(28/58)percent were identified in wheat for the first time.And 30 miRNAs with the proportion of 51.72(30/58)percent had been identified previously in wheat.2.A total of 731 pre-miRNAs belonging to 58 miRNA families were identified from the datasets,of which 204,276 and 251 pre-miRNAs distributed on 7A,7B and 7D,respectively.It was found that there were more mature miRNAs but less pre-miRNAs distributing on 7A compared to 7B and 7D chromosomes.7A chromosome was found to harbor 37 miRNAs(7BL:30;7AS:25)and representation 204 pre-miRNAs(7AL:122;7AS:82).While 7B chromosome was found to harbor 276 pre-miRNAs(7BL:115,7BS:161)and 33 miRNAs(7BL:23,7BS:26).7D chromosome was found to harbor 36 miRNAs(7DL:26,7DS:30)and representation 251 pre-miRNAs(7DL:118,7DS:133).3.Five new identified miRNAs were random selected to validation by qRT-PCR.Results showed that all the five miRNAs were expression at a different level,which supported that they were really existed in wheat.4.Targets of the new identified miRNAs were also done by psRNATarget which was a web based miRNA targets prediction tool.Finally,we got 296 target genes for the 28 new identified miRNAs excepting miR428,miR100 and miR5287,with the average of 12 targets per miRNA(296/25).205 out of the targets gene were regulated by mRNA cleavage with the proportion of 69.26 percent(205/296).And 30.74 percent(91/296)of targets genes were regulated by repression of translation.Among those target genes,including transcription factors such as Myb transcription factor which played an important role in plant development.Response to biotic stress genes such as Leucine Rich Repeat family protein,CHY zinc finger family protein and Cytochrome P450 and so on.Resistance gene such as NBS-LRR,RPG1(stem rust resistance gene)and CsAtPR5(powdery mildew resistance gene).Moreover,there were many targets gene directly involves in biological metabolism process such as Glucose-6-phosphate 1-dehydrogenase,Phosphoglycerate kinase,Glycolate oxidase and so on.5.To gain a better understanding of the functional roles of the predicted conserved miRNA target genes in wheat,predicted targets have been grouped into functional categories by BGI WEGO software.Among these target genes,genes involving in Biological Process,Molecular Function and Component could be classified into 20,9 and 9 categories respectively.Compared with 7D,target genes of miRNAs on 7A and 7B had a lower proportion involving in Biological Process,with the number of 44.56 and 44.79 percent respectively.Target gene of miRNAs on 7D was 53.44 percent.While target gene on 7A and 7B had a larger proportion involving in Component compared with 7D.And there was no difference on target genes involving in molecular function among those three chromosomes.Results showed that it was conserved on the target miRNAs involving in Molecular Function among those three chromosomes,while there was some difference between 7D with other two chromosomes on target genes involving in Biological Process and Component.In summary,this is the first study to computationally identify and comparatively analyze the miRNA in A,B and D homoeologous chromosomes of the wheat group 7.which may be beneficial to improve our understanding about the distribution of wheat miRNAs and its evolutionary role in polyploidisation.The chromosome arm-centered approaches which reducing DNA sample complexity and allows us dissect miRNAs from homeologous chromosomes.And it will establish contribution of miRNAs on each homeologous chromosomes to gene regulation during development and response to environment.