MudrA-like sequences from rice and sugarcane cluster as two bona fide transposon clades and two domesticated transposases

The Mutator system of maize has been described as the most active and mutagenic plant transposon. The autonomous element MuDR contains two genes: mudrA encoding the transposase and mudrB whose product function remains undetermined. MudrA-like coding domain showed to be the most abundantly expressed transposon-related sequence in sugarcane transcriptome. A previous report identified the existence of at least four clades of mudrA-like sequences in sugarcane, rice and arabidopsis, which already existed prior to the Monocot–Eudicot split. To gain understanding about the abundance, distribution, copy number and diversity of mudrA-like sequences, a comparative study between sugarcane and rice was performed. As a result, it was possible to identify that copy number greatly differs and, at least in grasses, there was a class-specific amplification with a burst of Class II elements. Structural analyses performed on rice genomic sequences revealed that while Class I and Class II clades comprise elements with transposon features, Class III and Class IV no longer possess TIRs and correspond to domesticated transposases.