Identification And Characterization Of New Transposon Of Genome Heavy Marked Crops

Transposable elements (TEs) are DNA sequences that move from one location in the genome to another, and they are a major component of the flowering plants genome. Depending on the different type of transposition, we usually divided them into DNA transposons and retro transposons. Although transposons are non-coding DNA, but some studies suggest that they play an important role in genome evolution. The next generation sequence let us have cheaper and faster way to locate the non-reference transposable elements base on the reference genome. Here, we used the resequencing data with the paired-end mapping methods to discover the non-reference TEs in rice, maize and sorghum, whole genome characteristics analysis of non-ref TEs shows the difference between species, groups and accessions. The main findings of the study are as follows:1 Transposon shows differences in reference genome of rice, maize and sorghum. Approximately 37% of the rice genome,76% of the maize genome and 58% of the sorghum genome are composed of TEs. And the sequence divergence rate of DNA transposon in rice is greater than others. There is difference between the three types of crops on the same transposon.2 Identify the non-ref transposons in the crops with the resequencing data. We predicted the non-ref TEs in 125 materials with the resequcing data in rice, maize and sorghum, which the reads depth coverage of 6X-45X. The average numbers of non-ref TEs were obtained 261,796 and 793, and there’s no significant correlation between the numbers of non-ref TEs with the data depth.3 There are differences in the category of non-ref TEs in rice, maize and sorghum. In class of non-ref TEs, rice has more DNA than LTR, but there are more LTR in the non-ref TEs, maize and sorghum genome have more LTR, and there is more DNA in the non-ref TEs. In addition, the subclass of transposon sees the differences between the groups of crop. RPKM values of non-ref TEs are shown a strong correlation between the sorghum accessions.4 The non-ref TEs has some impact on the genes. We analyzed the non-ref TEs insertion site and found the maize and sorghum transposon insertion site closer to the gene. Rice non-ref TEs has the higher proportion of insertion into the coding region of the gene. Also in the distribution of non-ref TEs in chromosomes, there is a strong correlation (p=0.88) between non-ref TEs numbers with the genes numbers in sorghum; and the correlation coefficient was 0.67 in maize.5 Annotations of non-ref TE affected genes. Interptro results show that most of the genes related protein kinases. GO enrichment analysis results are shown in rice, maize and sorghum enriched genes affected in both the ATP binding site of the protein amino acid phosphorylation, protein kinase activity, and apoptosis, and the affected gene function in rice and maize were enriched to defense reaction.We completed the first predicted the non-ref TEs in the rice, maize and sorghum base on the resequencing data, and analyzed the whole genome character of non-ref TEs. We revealed the features and differences of the non-ref TEs between in the three crops and also analyzed the differences between in the three groups of these crops. This will help us to understand the evolution of the transposon in these crops. Results suggest that non-ref TEs tend to be inserted into a gene region in crops, and non-ref TEs play a key role in the adaptive evolution.