ISCompare: a new tool for the identification of differentially located insertion sequences on bacteria

AMBROSIS N; LOZANO M; MOGRO E

Virtual

Congreso; Unity in Diversity | ISME; 2020

International Society for Microbial Ecology

Bacterial genomes are composed by a core and anaccessory genome. The first composed ofhousekeeping and essential genes, while the secondis composed in its majority by mobile geneticelements, including transposable elements (Tes).Insertion sequences (ISs) are the smallest TEsformed by imperfect terminal inverted repeats (IRs)and a transposase. ISs are relevant because theyhave an important role in genome evolution, andcontribute to bacterial genome plasticity andadaptability. ISs can spread in a genome, presentingdifferent locations in nearly related strains, andproducing phenotypic variations. We developedISCompare to profile IS mobilization events inrelated bacterial strains. ISCompare uses blastn tolook for ISs on a query genome assembly, extractsthe IS flanks and maps them to the referencegenome. After filtering and analysis steps, a list ofdifferentially located ISs is reported. ISCompare wasvalidated using artificial genomes simulatedrandom IS insertions and real sequences fromEscherichia coli, Pseudomonas aeruginosa,Bordetella pertussis and Ensifer meliloti. In the firstcase, ISCompare performed very well, achievinghigh precision 100% and sensitivity 94%. For realgenomes a precision greater than 89% in averagewas observed, false positive arising mostly fromconsecutive IS insertions and repeated sequences.Finally we compared ISCompare with ISSeeker,achieving the same or better results, with theadvantage that ISCompare can analyse multiple ISsat the same time. We think that ISCompare providesan easy and straightforward approach to look fordifferentially located ISs on bacterial genomes.