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The utility of ISMapper was further demonstrated by profiling genome-wide IS 6110 insertions in 138 publicly available Mycobacterium tuberculosis genomes, revealing lineage-specific insertions and multiple insertion hotspots.
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This observation suggests that there may be significant bias due to P-element insertion hotspots.
Flexible genomic elements are often large and integrate into the genome at select insertion hotspots (Touchon et al., 2009).
Relying on defined insertion "hotspots" in the P. aeruginosa genomes suffers from the limitation that novel insertion sites may only become apparent as more sequences are examined [ 76].
Superimposed on the generally random pattern of insertion site locations, there appear to be insertion hotspots and coldspots, the most evident example being the hotspot for local reinsertion near the donor site on linkage group 3. 305 insertions were localized in the genome sequence.
Elsewhere in the TuMV genome, an average insertion rate of 0.001% per nucleotide was seen with both samples and no other insertion "hotspots" were detected of similar magnitude to the pipo slip site (Appendix Fig S1).
There was no physical clustering of recombination in distinct regions of the chromosome, which may be suggestive of hotspots or multiple insertions via a single recombination event in any of the 62 strains.
Only 25% of the genes that are hotspots for piggyBac insertion were identified in our screens, but all but one of hotspot genes that were hit had multiple insertions.
One problem is Tn916's tendency towards multiple insertions, with several studies detecting multiple Tn916 insertions in 65 75% of all isolated C. perfringens mutants [12], [13].
For multiple insertions at positions 315 (C-insertions), 455 (T-insertions), 524 (AC-insertions), and 573 (C-insertions) only the first insertion was weighted.
This points to the existence of an insertion hotspot for this particular prophage in the P. putida core genome (Manna et al., 2004).
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