Nested Insertions and Accumulation of Indels in Coding-MULEs (Mutator-like Transposable Elements) are Negatively Correlated with Abundance of MULEs in Maize and Rice

Mutator-like transposable elements (MULEs) are widespread in plants. MULEs were first discovered in maize where there are a total of 12,900 MULEs in the genome consisting of 2.5 Gb. This is in comparison with rice, which harbors over 30,000 MULEs in a smaller genome (400 Mb). Since maize and rice are close relatives, the differential amplification of MULEs in the two species raised the question that what the underlying mechanism is. We hypothesize this is attributed to different copy numbers of coding MULEs, with the potential to generate transposase that is required for transposition.  To this end, we mined the two genomes and detected 530 and 476 MULEs containing transposase sequence (coding-MULEs) in maize and rice, respectively. Over 1/3 of the coding MULEs harbor nested insertions, with similar ratio in the two genomes.  Among the maize elements with nested insertions, 32% have insertions in coding regions and over half of them harbor two or more insertions. In contrast, less than 1/5 of the rice elements fall into each category, suggesting that nested insertions in maize are more disruptive. In addition, pare-wise comparison of coding MULEs indicates the presence of significantly more indels among maize elements than rice elements. Taken together, more disruptive nested insertions combined with higher frequency of indels resulted in few (6%) coding MULEs that may encode functional transposase in maize. In contrast, 38% of the coding MULEs in rice retain intact coding regions, which may explain why there are more MULEs in rice than that in maize.