Genome-Wide Comparative Analysis of Transposable Elements by Matrix-TE Method Revealed Indica and Japonica Rice Evolution

Transposons (TEs) are known to change the gene expression and function, and subsequently cause plant speciation and evolution. Nevertheless, efficient and new approaches are required to investigate the role of TEs in the plant genome structural variations. Here, we reported the method named matrix-TE to investigate the differentiation of intact and truncated LTR/TEs comprehensively in Indica and Japonica rice throughout whole genomes with a special eye on centromeric regions. Six LTR/TE super-families were identified in both Indica and Japonica rice genomes, and the TE ORF references were extracted by phylogenetic analysis. Indica rice specific TE peak P-Gypsy and Japonica rice specific TE peak P-Copia were observed, and were further analyzed by Gaussian probability density function (GPDF) fit. The individual TE peak P-Gypsy was observed in centromeric regions of the Indica genome. By the matrix-TE method, the divergence of Indica and Japonica genomes, especially their centromeric regions, mainly resulted from the Ty3/Gypsy insertion events at 0.77 Mya. Our data indicate that the optimized matrix-TE approach may be used to specifically analyze the TE content, family evolution, and time of the TE insertions.

Automated summary

In this study, a method called matrix-TE was used to comprehensively investigate the differentiation of LTR/TEs in plant genomes. The results showed that there were six LTR/TE superfamilies in Indica and Japonica rice genomes, and the divergence between the two genomes was mainly caused by Ty3/Gypsy insertion events.