Mapping and analysis of the LINE and SINE type of repetitive elements in rice

Abstract

Non-LTR retrotransposons comprise significant portion of the plants genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. The long and short interspersed nucleotide repetitive elements (LINE and SINE) may be responsible for alteration in the expression mechanism of neighboring genes, the complete identification of these elements in the rice genome is essential in order studying their putative functional interactions with the plant genes and its role in genome composition. The main emphasis of this work is to assemble a comprehensive dataset of nonLTR (LINEs and SINEs) and the map of completely inserted LINEs and SINE type of retroelement by both intact ends (3' and 5' ends). The assembled information and work may help for further research in this direction.

Keywords: LINEs; Oryza sativa; Retroelement; SINEs.

Figure 1

Percentage distribution of transposable element in rice genome

Figure 2

Map of rice genome populated with all successful SINEs and LINEs

Figure 3

Frequency distribution LOGO of upstream sequences to the insertion site of LINEs in rice genome

Figure 4

Frequency distribution LOGO of upstream sequences to the insertion site of SINEs in rice genome