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Section: Genomics
Topic: Genetics/Genomics, Microbiology

A rapid and simple method for assessing and representing genome sequence relatedness

Briand, M1 ; Bouzid, M1; Hunault, G2; Legeay, M3; Fischer-Le Saux, M1; Barret, M1
1 Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France
2 Université d’Angers, Laboratoire d’Hémodynamique, Interaction Fibrose et Invasivité tumorale hépatique, UPRES 3859, IFR 132, F-49045 Angers, France
3 Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark

10.24072/pcjournal.37 - Peer Community Journal, Volume 1 (2021), article no. e24.

Get full text PDF Peer reviewed and recommended by PCI

Coherent genomic groups are frequently used as a proxy for bacterial species delineation through computation of overall genome relatedness indices (OGRI). Average nucleotide identity (ANI) is a widely employed method for estimating relatedness between genomic sequences. However, pairwise comparisons of genome sequences based on ANI is relatively computationally intensive and therefore precludes analyses of large datasets composed of thousands of genome sequences.In this work we proposed a workflow to compute and visualize relationships between genomic sequences. A dataset containing more than 3,500 Pseudomonas genome sequences was successfully classified with an alternative OGRI based on k-mer counts in few hours with the same precision as ANI. A new visualization method based on zoomable circle packing was employed for assessing relationships among the 350 groups generated. Amendment of databases with these Pseudomonas groups greatly improved the classification of metagenomic read sets with k-mer-based classifier. The developed workflow was integrated in the user-friendly KI-S tool that is available at the following address: https://iris.angers.inra.fr/galaxypub-cfbp

Published online:
DOI: 10.24072/pcjournal.37
Type: Software tool
Briand, M 1; Bouzid, M 1; Hunault, G 2; Legeay, M 3; Fischer-Le Saux, M 1; Barret, M 1

1 Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France
2 Université d’Angers, Laboratoire d’Hémodynamique, Interaction Fibrose et Invasivité tumorale hépatique, UPRES 3859, IFR 132, F-49045 Angers, France
3 Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Denmark
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Briand, M; Bouzid, M; Hunault, G; Legeay, M; Fischer-Le Saux, M; Barret, M. A rapid and simple method for assessing and representing genome sequence relatedness. Peer Community Journal, Volume 1 (2021), article  no. e24. doi : 10.24072/pcjournal.37. https://peercommunityjournal.org/articles/10.24072/pcjournal.37/

Peer reviewed and recommended by PCI : 10.24072/pci.genomics.100001

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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