Structure and evolution of full-length LTR retrotransposons in rice genome

The long terminal repeat (LTR) retrotransposons are the most abundant class of transposable elements in plant genomes and play important roles in genome divergence and evolution. Their accumulation is the main factor influencing genome size increase in plants. Rice (Oryza sativa L.) is a model monocot and is the focus of much biological research due to its economic importance. We conducted a comprehensive survey of full-length LTR retrotransposons based on the completed genome of japonica rice variety Nipponbare (TIGR Release 5), with the newly published tool LTR-FINDER. The elements could be categorized into 29 structural domain categories (SDCs), and their total copy number identified was estimated at >6,000. Most of them were relatively young: more than 90% were less than 10 My. There existed a high level of activity among them as a whole at 0–1 Mya, but different categories possessed distinct amplification patterns. Most recently inserted elements were specific to the rice genome, while a few were conserved across species. This study provides new insights into the structure and evolutionary history of the full-length retroelements in the rice genome.