Transposable elements (TE) are an integral part of eukaryotic genomes; therefore, their identification, characterization and analysis remain critical in genetic and evolutionary studies. The Mutator superfamily (MULEs) are DNA TEs characterized by long terminal inverted repeats (TIR) and includes a special group of elements, called Pack-MULEs, that carry genes/gene fragments. This study aims to understand the role of terminal sequences in transposition of MULEs and the factors involved in sequence acquisition by Pack-MULEs. In addition, the repetitive content and diversity of an ancient eudicot genome was characterized to better understand the evolutionary role of MULEs as well as other TEs in angiosperms.Analyses of MULEs in rice show that these elements also capture GC rich intergenic sequences but at a much lower frequency than genes. The TIR-MULE type is predominantly involved in sequence acquisition and these elements are associated with long GC-rich TIRs which may be important in acquisition. Genes with known functions and genes with orthologs are overrepresented among parental genes of Pack-MULEs in rice, maize and Arabidopsis suggesting that Pack-MULE preferentially duplicate bona fide genes. Pack-MULEs selectively acquire and retain parental sequences through a combined effect of GC content and breadth of expression, with GC content playing a stronger role. Analysis of MULEs in maize, tomato, rice and Arabidopsis detected the formation of atypical MULEs and Pack-MULEs with multiple TIRs mostly located in tandem. The copy number of these atypical MULEs suggests their significant mobility while their tandem TIR sequences indicate sequence conservation. The successful amplification of the Pack-MULE, PM-ZIBP, demonstrates that MULEs with tandem TIRs are functional in transposition and duplication of gene sequences.Characterization of the repetitive sequence of sacred lotus (Nelumbo nucifera) shows that 50% of the genome is composed of recognizable transposable elements (TE). TE content and diversity show a comparable Copia and Gypsy LTR content, which is atypical among plants. Non canonical LTR types comprise 15.6% of the total LTR content suggesting the need to consider other end types in annotation of LTR elements. Sacred lotus also contains the highest coverage and copy number of hAT elements among all sequenced genomes to date. The 1447 Pack-MULEs in the genome provide the first evidence for the GC acquisition preference by Pack-MULEs outside the grasses.
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