The Formation of DNA Transposon-Induced Tandem Direct Duplications and Their Occurrence Across 21 Plant Species

Recent whole genome sequencing has begun to reveal significant levels of Tandem Direct Duplication (TDD) in eukaryotic genomes. The formation of TDDs is commonly explained by Non-Allelic Homologous Recombination (NAHR), for example by unequal crossover between two Transposable Element (TE) copies.  However, a recent study in maize shows that Reversed-Ends Transposition (RET) of Ac/Ds elements is also capable of inducing small to large (10 kb to > 5Mb) TDD at a frequency of 0.5% to 1%, when the two Ac/Ds elements are ~800 bp apart ( Zhang, J., Zuo, T., and Peterson, T. 2013. PLoS Genet 9, e1003691).  Still unclear is the overall extent and relative impact of DNA transposon-induced TDD in plant genomes. To address this question, we are developing and implementing a bioinformatics pipeline to identify transposon-induced TDDs in any sequenced genome.  Initial tests show that 14 out of 21 plant genomes contain one or more TDDs that were initiated by DNA TEs. The frequency of TDDs generated by RET and NAHR varies among plant species; however, the RET-induced TDDs are generally found at similar or greater frequency than those induced by NAHR.  Our results indicate that RET could have played an important role in generating TDDs and other genomic rearrangements during plant genome evolution.