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The similarity between Xist exons and mobile elements was searched for using the same programs and parameters.
The statistical analysis of gene-families, resistance genes and mobile elements was performed by ShotgunFunctionalizeR 1.03 using custom-made annotations and the Poisson model for direct comparisons [24].
A lower prevalence of mobile elements was found around the fimbrial cluster flf.
The presence of mobile elements was investigated as source of intraclonal variation.
In fact, the density of mobile elements was highest on p2 and p3, where 8 and 12% respectively of the total genetic content constituted of such elements.
In some cases, e.g. NT1, NT2, and NT6 of ST344 or NT22 and NT24 of ST1153, the content of mobile elements was indeed distinct between strains, which might explain the variability found.
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Genes from these mobile elements were considered to belong to mobilized or mobilizable gene families.
In terms of mobility, the primary response of a host genome to the presence of mobile elements is repressive, as unregulated mobile element activity will lead to an unbearable mutational load.
The distributions of genes and mobile elements are represented as stacked areas.
Mobile elements were identified using a number of homology and de novo structural pattern finding algorithms and manual curation.
But in many species mobile elements are efficiently restricted by defense mechanisms, which have evolved to suppress and regulate parasitic elements.
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