Plant Systematics and Evolution

, Volume 287, Issue 1–2, pp 19–28 | Cite as

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

  • Ling Xu
  • Yue Zhang
  • Yuan Su
  • Lin Liu
  • Jing Yang
  • Youyong Zhu
  • Chengyun Li
Original Article


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.


Rice genome LTR retrotransposons LTR-FINDER Element structure Insertion time 

Supplementary material

606_2010_285_MOESM1_ESM.doc (494 kb)
Supple file (DOC 494 kb)


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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Ling Xu
    • 1
    • 2
  • Yue Zhang
    • 1
  • Yuan Su
    • 1
  • Lin Liu
    • 1
  • Jing Yang
    • 1
  • Youyong Zhu
    • 1
  • Chengyun Li
    • 1
  1. 1.Key Laboratory of Agro-biodiversity and Pest Management of the Ministry of Education of ChinaYunnan Agricultural UniversityKunmingChina
  2. 2.Baoshan CollegeBaoshanChina

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