Genome-wide Analysis Of Transposable Elements In Bread Wheat

Transposable elements(TEs)are a type of DNA sequences which have the jumping ability,distributed widely in plant and animal genomes as the main component.Transposons integrate into other loci thereby impacting target gene expression or generating new genomic segments to produce variation.The research on the feature and function of TEs contributed to a deeper understanding about the genome and the evolutionary process.Chinese Spring is an allohexaploid species with a large genome and mainly composed of transposons.The assembly of bread wheat genome accelerates the study of TEs,so that we can learn more about conservation and diversity of the wheat genome.Chinese Spring is the staple grain crop currently which has been widely cultivated because of strong adaptability.Study on TE is sincere to increase production and improve quality.In our study,through comparing available computational methods,we conducted comprehensive analyses of transposons in wheat genome.Based on homology,sequences in the library were aligned to reference genome to identify transposons.It was found that transposons accounted for about 80% of the wheat genome,mainly composed of Gypsy,Copia and CACTA.Their proportions and classes are comparable across the three subgenomes,among which A subgenome has the highest proportion but D subgenome has the lowest proportion.Almost all of the transposons are located in the intergenic region thereby minimizing the impairment on gene expression.There are also a small proportion of transposons distributed in the gene and gene upstream regions,which may have an impact on gene activity.Besides,thousands of miniature transposable elements are detected which tend to be enriched around genes.Ages of Gypsy and Copia were calculated based on structure and sequence.The result indicates that Gypsy is older than Copia.In addition,young TEs preferentially integrate in the end of chromosomes.Transposons in the genome of wheat progenitors were identified using the approach mentioned above.It indicated that there was no significant difference in the content and type of transposon between the subgenomes of hexaploid and the progenitors.The study explored the functions of transposons from the aspects of impacting genome structure and regulating gene expression.Gypsy and Copia have similar 3 'transduction capabilities,enabling downstream sequence replication and transposition,thus promoting genome evolution and diversification.According to epigenetic features,wheat genome marked by regulatory epigenetic markers could be divided into 15 classes.TEs are enriched for H3 lysine 9 di-methylation and H3 lysine 27 tri-methylation,and with high DNA methylation level.We further revealed that TEs marked with H3 lysine 27 tri-methylation were preferentially localized to the proximal region of genes.Through the above analysis,this study identified transposons in the genome of Chinese Spring and the candidate progenitors.The content and type of transposons in each genome are relatively consistent.Different TE families have different structural characteristics and target genes.Transposons have mainly experienced sequence mutations and fragment loss during evolution,but the overall transposon of the genome has not changed significantly during polyploidization.Most transposons in hexaploid wheat are inhibited by various histone modifications and DNA methylation,which are closely related to their functions.As an important research method,the development of bioinformatics has achieved large-scale analysis of the whole genome and integrated analysis of multi-omics data.Understanding the characteristics of transposons are essential for research to study their biological processes and functions.