Palidis: fast discovery of novel insertion sequences

Victoria R. Carr; Solon P. Pissis; Peter Mullany; Saeed Shoaie; David Gomez-Cabrero; David L. Moyes

doi:10.1099/mgen.0.000917

Palidis: fast discovery of novel insertion sequences

Victoria R. Carr^1,2, Solon P. Pissis^3,4, Peter Mullany⁵, Saeed Shoaie^2,6, David Gomez-Cabrero^2,7,8 and David L. Moyes²
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¹ Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK ² Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, SE1 9RT, UK ³ Centrum Wiskunde en Informatica, Amsterdam, Netherlands ⁴ Vrije Universiteit, Amsterdam, Netherlands ⁵ Department of Microbial Diseases, Eastman Dental Institute, University College London, 256 Gray’s Inn Road, London, WC1X 8LD, UK ⁶ Science for Life Laboratory, KTH – Royal Institute of Technology, Stockholm, SE-171 21, Sweden ⁷ Bioscience Program, Bioengineering Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia ⁸ Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
*Correspondence: Victoria R. Carr, [email protected]
Published: 10 March 2023 https://doi.org/10.1099/mgen.0.000917

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 bioinformatics 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.

Received: 24/10/2022
Accepted: 27/10/2022
Published Online: 10/03/2023

Keyword(s): antimicrobial resistance , horizontal gene transfer , insertion sequences , metagenome , mobile genetic element and transposon

This is an open-access article distributed under the terms of the Creative Commons Attribution License.

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/content/journal/mgen/10.1099/mgen.0.000917

Palidis: fast discovery of novel insertion sequences

M Gen 9, 000917 (2023); https://doi.org/10.1099/mgen.0.000917

/content/journal/mgen/10.1099/mgen.0.000917

Microbial Genomics

Volume 9, Issue 3

Method

Open Access

Palidis: fast discovery of novel insertion sequences

Abstract

Supplementary material 1

Supplementary material 2

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