Sugarcane Haplotype Transposon Variation And Its Effect On Allele Specific Expression

Sugarcane is an important sugar and energy crop,which widely planted in tropical and subtropical areas.Sugarcane accounts for about 80%of the world’s total sugar production,has great economic value.China is a major grower of sugarcane,and sugarcane is also an important crop in southern China.Modern cultivated sugarcane is bred from Saccharum spontaneum and Saccharum officinarum in nobilization breeding process,which is a high-ploidy interspecific hybrid with a large proportion of repeated sequences in the genome.Transposons are a kind of important repeat sequences,which exist widely in plant genome and are important in plant genome.More and more studies have shown that transposons play an important role in the size,structure and function of plant genome.In addition,modern cultivated sugarcane has obtained some excellent characters from its parents,showing heterosis,and transposons may affect the expression of alleles,contributing to the formation of heterosis.In recent years,with the development of genomics and molecular biology,it has become possible to study transposons in sugarcane genome and their influence on allelic specific expression by means of genomics and genetics.However,there are few studies on transposons and allele specific expression in sugarcane.In this study,we first identified and classified the transposon sequences of the dense and noble species of sugarcane ancestors,and studied the effect of transposon insertion deletion on allele expression differences,which laid a foundation for the analysis of the evolutionary history and heterosis of sugarcane genome.In this study,chromosome reduction material AP85-441(1n=4x=32)from the anther of SES208(2n=8x=64),S.spontaneum,was sequenced by Pac Bio Hi Fi and a high-quality chromosomal genome was assembled using new algorithm of ALLHi C2 developed by our team.In addition,the transposon map was constructed by genome-wide transposon identification of AP85-441 and LA-purple.Combined with RNA-seq data,allelic specific expressed genes that may be affected by transposons were identified.The main results are as follows:1.Assembly of AP85-441,S.spontaneumIn this study,the whole genome of AP85-441 was sequenced using Hi Fi and Hi-C Sequencing technology.It was assembled to the chromosomal level using new algorithm of ALLHi C2,and finally completed a high-quality genome.2.Genome-wide transposon identification of AP85-441 and LA-purpleIn this study,the software EDTA was used to identify transposons in AP85-441 and LA-purple,and 67.72% and 69.83% transposons were identified in AP85-441 and LA-Purple genomes.LTR retrotransposon accounted for 44.82% and 50.83% of the genome.We calculated the insertion times of these LTRs,and it was found that there were significant LTR burst events in AP85-441 and LA-purple.And found that in both genomes,the density of transposons was consistent with the distribution trend of genes.3.Effect of transposons on alleles in sugarcaneAllelic specific expressed genes AP85-441 and LA-purple were screened by RNA-seq data,and allelic specific expressed genes with transposon insertion were screened,which were enriched into some pathways by GO and KEGG functional enrichment analysis,and identified functional genes that play an important role in sugarcane growth and development,and we found that transposon insertion may affect the expression of sucrose phosphate synthase,which may be one of the reasons for the difference in sugar content between AP85-441 and LA-purple.The effect of transposons on allelic specific expressed in sugarcane was preliminarily explored.