Our study suggests that tRNA genes and their promoters, often with associated GC-rich elements, are also an important source of rearrangements.
Segmental duplications are the most common source of such rearrangements, however we show that other CNVs not related to segmental duplications are also depleted of dosage sensitive genes.
The accumulation of mobile elements, representing a source of chromosomal rearrangements and gene inactivation, seems to have an important role in this first stage.
The accumulation of mobile elements, representing a source of chromosomal rearrangements and gene inactivation, seems to have an important role in the first stage of genome reduction in endosymbionts (Ogata et al. 2001; Andersson et al. 2002).
Recently, it was found that the helicase Srs2 in yeast [ 99], antirecombinase RTEL-1 in C. elegans [ 105], and human PARI [ 54] suppress inappropriate recombination, which is highly toxic to cells as a source of genomic rearrangements.
Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them.
The source of such genes rearrangements could be similar to the intense genetic exchanges revealed in Pam100G by the presence of the tra unit and the phage-related genes, i.e conjugative DNA transfer and/or transduction.
In particular, sources of TE rearrangements in the β-heterochromatin include tandem amplifications and nested insertions (Vaury et al. 1989; Kuhn and Heslop-Harrison 2011).
Three transposase genes were also present in the genome and may be an additional source of genetic exchange and rearrangement.
In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes.
