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Conception et mise en oeuvre d’une approche bioinformatique dédiée à l’identification des ICE, IME et éléments composites dans les génomes de Firmicutes

Abstract : ICEs (Integrative Conjugative Elements) and IMEs (Integrative Mobilizable Elements) are bacterial mobile elements that play a key role in horizontal transfers. They have the capacity to integrate and transfer by conjugation from one bacterium to another. These elements are widespread in bacterial genomes but are still poorly understood. Their automatic identification is a challenge and they are generally not annotated in genomes. So far, only two bioinformatic approaches allow the detection of ICEs and IMEs, but their reliability remains highly variable, particularly among Firmicutes. Moreover, neither of these approaches can accurately detect composite elements consisting of nested or accreted ICEs and IMEs, which are frequently observed in bacterial genomes. We have developed a strategy and a tool called ICEscreen to identify ICEs and IMEs in the genomes of Firmicutes, including nested or accreted elements. Our tool starts with the detection of four signature proteins (SPs) that are essential to the functioning of these elements and then carries out the detection and typing of the elements based on the colocalization of the SPs and the characterisation of their content. Our tool uses a dedicated algorithm to solve the structure of the elements whether they are composite or not. To perform these steps, we have built a bank of ICEs and IMEs signature proteins from a list of genes known to be involved in the dynamics of these elements in streptococci and also public HMM profiles and HMM profiles constructed especially for this study. To validate the ICEscreen results, we built a dataset, FirmiData, consisting of 40 genomes of Firmicutes for which the ICEs and IMEs were annotated semi-manually and curated. We then compared the results of ICEscreen with those of two reference tools: CONJscan and ICEfinder. ICEscreen detects almost all the elements of the reference (96%) making it a more powerful tool than CONJscan (58%) and especially ICEfinder (53%) on our dataset. ICEscreen is thus a tool for the annotation and discovery of ICE and IME in the genomes of Firmicutes, which can help to better characterize their contribution to horizontal gene transfers, particularly during the transmission of antibiotic resistance, with which they are frequently associated.
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Submitted on : Wednesday, June 30, 2021 - 11:41:19 AM
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Julie Lao. Conception et mise en oeuvre d’une approche bioinformatique dédiée à l’identification des ICE, IME et éléments composites dans les génomes de Firmicutes. Ecotoxicologie. Université de Lorraine, 2021. Français. ⟨NNT : 2021LORR0063⟩. ⟨tel-03274589⟩



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