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Palidis: fast discovery of novel insertion sequences

Carr, VR; Pissis, SP; Mullany, P; Shoaie, S; Gomez-Cabrero, D; Moyes, DL; (2023) Palidis: fast discovery of novel insertion sequences. Microbial Genomics , 9 (3) 10.1099/mgen.0.000917. Green open access

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Abstract

The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinfor-matics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.

Type: Article
Title: Palidis: fast discovery of novel insertion sequences
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1099/mgen.0.000917
Publisher version: https://doi.org/10.1099/mgen.0.000917
Language: English
Additional information: © 2023 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).
Keywords: antimicrobial resistance, horizontal gene transfer, insertion sequences, metagenome, mobile genetic element, transposon
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Eastman Dental Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Eastman Dental Institute > Microbial Diseases
URI: https://discovery.ucl.ac.uk/id/eprint/10167442
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