LTR retrotransposons and tandem repeats in Musa genomes and their contribution to Musa diversity and genome evolution

Musa is a large genus that includes many important staple crops particular in Asia and Africa. Pseudoviridae, LARD-like and three different groups of Metaviridae elements were identified based on their RT sequence heterogeneity. Additionally, full length elements were identified in published BAC sequences. Most of the LTR-retrotransposons were degenerated and disrupted at different positions, by other types of repetitive DNAs (retrotransposons and tandem repeats). Metaviridae elements are generally present in higher copy numbers than Pseudoviridae elements, and the A genome contains more retrotransposons than the B genome, possibly explaining the larger genome size of the A genome. However, genome specific LTR-retrotransposons were not detected. Retrotransposons were clustered in the centromeric regions, Pseudoviridae elements showing a more dispersed pattern while LARD-like and some of the Metaviridae elements were also found at the Nucleolar Organizing Region (NOR). Two genome-specific repeats, organised in long arrays are located at the NOR loci of seven Musa taxa and additionally at some to all centromeres of selected taxa. Different degrees of methylation of LTR retrotransposons and tandem repeat DNA, the latter generally being under-methylated were observed. The transcribed copies of the 45SrDNA sequences at the NOR are interspersed by MuTR repeats and weakly methylated, while the distal part of the NOR region and the chromosomal satellite beyond contains MuTR, Metavirdae and LARD-like sequences that are heavily methylated. The close chromosomal proximity and insertion within each other postulates a possible link in the evolution of LTR-retrotransposons, tandem repeats and 5S rRNA genes, but also a role of retrotransposon sequences in gene regulation RNA transcripts of both metaviridae and MuTR repeats indicates their activity, but also that they might be involved in siRNA silencing mechanisms.