Spip and Squiq, two novel rice non-autonomous LTR retro-element families related to RIRE3 and RIRE8.

摘要

Transposable elements are the main components of complex genomes. Their impact on the genomes in terms of structural changes during evolution is thus one of the main focuses of today's structural genomics. Although non-autonomous transposable elements have been known for a long time, their contribution to genome evolution is poorly understood. Our present study describes two new non-autonomous LTR retrotransposons in the rice (Oryza sativa L) genome, Spip and Squiq, the LTR of which are closely related to those of the gypsy-like RIRE3 and RIRE8 LTR retrotransposon families, respectively, but the internal region of which is completely different and harbours none of the characteristic coding domains of LTR retrotransposons. Spip and Squiq thus belong to the class of LArge Retrotransposon Derivatives (LARDs). A phylogenetic study based on the sequence alignment of the LTRs of Spip/RIRE3, and of Squiq/RIRE8 show that both Spip and Squiq elements are of monophyletic origin. In addition, the estimation of the date of insertion of the copies suggests that Spip and Squiq families are of recent origin (that is, they amplified mainly within the last 2 My). Spip and Squiq are the fourth and fifth LARD families to be described in the rice genome, suggesting that this type of sequences is not rare. Moreover, these two families appear to be as numerous as their autonomous counterparts, suggesting that they have played an equivalent role in the recent history of rice..