Identification Of Novel LTR-Retrotransposons And Their Transcriptional Activation Analysis In Foxtail Millet

LTR-retrotransposons are a class of transposable elements?TEs?,which initate their transposition through a copy and paste mechanism via RNA intermediates and produce new copies.LTR-retrotransposons are uniquitous in most eukaryotes,and are the main driving force of the genomic expasion and species evolution.The waves of expansion and contraction in their numbers can result in dramatic differences in the overall architecture of the genomes of even closely related plant species.In addition to these gross effects on the overall architecture of genomes,LTR-retrotranposon activity can cause a broad range of changes in gene expression and function,from subtle quantitative effects to the rewiring of regulatory networks and the evolution of entirely new genes.As one of the oldest crops,foxtail millet has 8,700 years cultural history.As a diploid C4 grasses,foxtail millet is an important foodstuff and continues to be cultivated in semiarid areas.In addition to the high nutrition and stress-resistance,foxtail millet is closely related to several biofuel grasses with complex genomes,such as pearl millet,switchgrass and napier grass.The publication of foxtail millet genomic information promote the reserch on the structure and function of retrotransposons in biofuel grasses and its role in species evolution,speciation and gene regulation.In the process of annotating transposable elements?TEs?in the foxtail millet genome,we identified four LTR-retrotransposons using the software LTR-Finder,which were 5034 bp-6668 bp which have less copies and high similarity among every family?>95%?,also including the typical structure LTR,TSD,PBS,PPT.The analysis of blastn and blastx indicated no sequence similarity to any other described TEs,we named them G,J,M,P.The four LTR-retrotransposons also contain gag and pol,two genes necessary for transpositional process,so these LTR retrotransposons were newly activated and might still be actived.According to the order of INT,RT and RH in the POL ORFs,the four LTR-retrotransposons were belong to Ty1-copia elements.Analysis the copy numbers of G,J,M,P showed that each of these four LTR retrotransposons had 5,11,41 and 23 copies,distributed in the 9 chromosomes of foxtail millet genome.It was far lower relative to the thousands copies.Insertion times of all intact copies of these four LTR-retrotransposons were calculated,showed that all copies of these LTR-retrotransposons integrated into the genome 0-2 Mya,only the insertion time of M041 was 2.692 Mya.The average insertion time of these four LTR retrotransposons were 0.392 Mya,1.014 Mya,0.570 Mya,0.182 Mya,and most were focused on 0-1Mya.This indicated that these LTR-retrotransposons were newly integrated into the genome and might still be actived.The insertion time of P was the least in these LTR-retrotransposons,there were 21 copies lower 0.3 Mya.Analysis of the flanking sequence of the LTR-retrotransposons,showed that transposon can inserst into the genes or near the genes.Some of these genes are associated with growth and development,secondary metabolites and transcription factors,while others are closely related to the stress response.The expression analysis of the transposons on the stress conditions,such as salt,drought,cold and O₃,showed that the expression of the transposons was different under stress.one transposon under different stress can present entirely different expressional changes,the expression of the different transposons were also different under the same stress.Our results suggested that,in the foxtail millet genome,there were some newly inserted low-copy LTR-retrotransposons,which were surrounded by the genes associated with growth and development and stress response.Further,the expression of these LTR-retrotransposons was alterative under stress,so the results of this study could provide a theorecal basis for the study of the role of LTR-retrotransposons in genome evolution and fonctional gene expression in foxtail millet.