|Du, Jianchang -|
|Tian, Zhixi -|
|Bowen, Nathan -|
|Schmutz, Jeremy -|
|Ma, Jianxin -|
Submitted to: The Plant Cell
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 11, 2009
Publication Date: January 15, 2010
Citation: Du, J., Tian, Z., Bowen, N., Schmutz, J., Shoemaker, R.C., Ma, J. 2010. Bifurcation and Enhancement of Autonomous-Non-Autonomous Retrotransposon Partnership through LTR Swapping in Soybean. The Plant Cell. 22:48-61. Interpretive Summary: Genetic elements that transpose within plant genomes are important as a mechanism for driving increases in the size of genomes. The expansion of genetic material is important for generating new diversity. Some elements can transpose and insert into the genome on their own, while others require gene products provided by the autonomous elements. The co-evolution of these elements has not been studied. Here, the authors studied the largest family of soybean transposons amd determined that independent and non-independent elements share genetic material, probably through a unique process. This recombination creates regions of chromosomes where the elements are homogenized. These findings provide insight into how transposable elements co-evolve. This information is important to molecular evolutionary geneticists who are studying the timing, nature, dynamics and mechanisms of genome evolution.
Technical Abstract: Although non-autonomous LTR-retrotransposons lacking significant protein coding domains have been identified in eukaryotes, how they interact with their autonomous partners to maintain transpositional activity during host genome evolution is poorly understood. We performed a comprehensive analysis of the largest LTR-retrotransposon family in the soybean genome, designated as Gmr9. A total of 5,832 elements were identified and classified as Gmr9 elements based on LTR sequences. However, intact elements exhibited dramatic sequence divergences, dividing them into three distinct subfamilies, two autonomous subfamilies (dubbed Gmr9A1 and Gmr9A2) and a nonautonomous subfamily (dubbed Gmr9N). A complete Gmr9A1 or Gmr9A2 element contains gag and pol genes, an env-like gene, and a functionally unknown ORF1, while a complete Gmr9N element lacks the pol genes and shows little identity to the gag and env genes. The presence of a solo LTR from an unrelated family Gmr6 in 1,722 Gmr9N elements defines a recently amplified group, dubbed Gmr9N+. The Gmr6 insertion is positioned identically in all members of the Gmr9N+ lineage, indicating they all derive from a single founding Gmr9N element. Unexpectedly, Gmr9N+ was not distinguished from Gmr9A1 or Gmr9A2 based on LTR sequence conservation. Further analysis revealed extensive inter-element recombination between Gmr9A1 and Gmr9N and between Gmr9A2 and Gmr9N, and the recombinants were likely formed prior to their integration into the host genome, most likely by template switching. These processes, followed by selection, have led to subspecies- and region-specific homogenization between Gmr9A1 and Gmr9N and between Gmr9A2 and Gmr9N, and the divergence of Gmr9N elements into two distinct forms corresponding to their autonomous partners.