At a single gene level, TE insertions can result in loss of gene function, reprogramming of gene expression, gene deletions, rearrangements or transposition, coding-sequence exaptation and epigenetic effects, all of which have been well documented in a number of plant species (reviewed in [ 28]).
ISP is also observed between the complementary oligonucleotides in chromosomes, which has been attributed to genome-wide large-scale inversion, inversion transposition and coding sequence compositional symmetry between the strands.
This later can be a challenging problem since more or less extensive edits may have been performed on the original copy: insertion or removal of useless chunks of code, rewriting of expressions, transposition of code, inlining and outlining of functions, etc.
Only 2 of the 13 insertions interrupted coding sequences, indicative of selection against transposition events that interrupt expression of the capsular biosynthesis genes (as other IS insertions within CDSs presumably occur but are deleterious in competition with encapsulated strains).
These fragments are interspersed with DNA repeats, pseudogenes and genes coding for products involved in DNA replication, integration and transposition.
These elements harbor a transposase coding region flanked by TIRs, which are needed for the transposition reaction.
Considering that ≈ 91% of M. tuberculosis genome is composed by coding regions [ 66], it highlights the deleterious effects of transposition into certain genes essential to viability or to the successful completion of the pathogen's infectious cycle.
MFA genes coding for the a-factor mating pheromone in budding yeasts are known to be difficult to identify due to their short size 32-388 residues), high sequence divergence and an apparently high rate of gene duplication or transposition [ 25].
This process, called transposition, is catalyzed by transposases, coded for by TEs themselves.
In general, genome scans reveal at least three functional categories: active copies (canonical elements), relic copies (equivalent to pseudogenes), and nonautonomous copies (unable to code for the transposition machinery, but mobile when trans-mobilized).
