Ariane Bize1, Cédric Midoux2,3,4, Mahendra Mariadassou3,4, Sophie Schbath3,4, Patrick Forterre5,6, Violette Da Cunha7. 1. Université Paris-Saclay, INRAE, PROSE, F-92761, Antony, France. ariane.bize@inrae.fr. 2. Université Paris-Saclay, INRAE, PROSE, F-92761, Antony, France. 3. Université Paris-Saclay, INRAE, MaIAGE, F-78350, Jouy-en-Josas, France. 4. Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, F-78350, Jouy-en-Josas, France. 5. Institut Pasteur, Unité de Virologie des Archées, Département de Microbiologie, 25 Rue du Docteur Roux, 75015, Paris, France. patrick.forterre@pasteur.fr. 6. Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France. patrick.forterre@pasteur.fr. 7. Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
Abstract
BACKGROUND: K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors. RESULTS: For cells, the 5-mer profiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-mer profiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-mer profile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikingly retain the specific imprint of their own viral or plasmid taxonomic family in their 5-mer profile. CONCLUSION: This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected only recent host transfer events, suggesting the fast evolution of short k-mer profiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.
BACKGROUND: K-mer-based methods have greatly advanced in recent years, largely driven by the realization of their biological significance and by the advent of next-generation sequencing. Their speed and their independence from the annotation process are major advantages. Their utility in the study of the mobilome has recently emerged and they seem a priori adapted to the patchy gene distribution and the lack of universal marker genes of viruses and plasmids. To provide a framework for the interpretation of results from k-mer based methods applied to archaea or their mobilome, we analyzed the 5-mer DNA profiles of close to 600 archaeal cells, viruses and plasmids. Archaea is one of the three domains of life. Archaea seem enriched in extremophiles and are associated with a high diversity of viral and plasmid families, many of which are specific to this domain. We explored the dataset structure by multivariate and statistical analyses, seeking to identify the underlying factors. r> RESULTS: For cells, the 5-merprofiles were inconsistent with the phylogeny of archaea. At a finer taxonomic level, the influence of the taxonomy and the environmental constraints on 5-merprofiles was very strong. These two factors were interdependent to a significant extent, and the respective weights of their contributions varied according to the clade. A convergent adaptation was observed for the class Halobacteria, for which a strong 5-mer signature was identified. For mobile elements, coevolution with the host had a clear influence on their 5-merprofile. This enabled us to identify one previously known and one new case of recent host transfer based on the atypical composition of the mobile elements involved. Beyond the effect of coevolution, extrachromosomal elements strikinglyretain the specific imprint of their own viral orplasmid taxonomic family in their 5-merprofile. r> CONCLUSION: This specific imprint confirms that the evolution of extrachromosomal elements is driven by multiple parameters and is not restricted to host adaptation. In addition, we detected onlyrecent host transfer events, suggesting the fast evolution of short k-merprofiles. This calls for caution when using k-mers for host prediction, metagenomic binning or phylogenetic reconstruction.
Authors: Veronika B Dubinkina; Dmitry S Ischenko; Vladimir I Ulyantsev; Alexander V Tyakht; Dmitry G Alexeev Journal: BMC Bioinformatics Date: 2016-01-16 Impact factor: 3.169
Authors: David Moi; Shunsuke Nishio; Xiaohui Li; Clari Valansi; Mauricio Langleib; Nicolas G Brukman; Kateryna Flyak; Christophe Dessimoz; Daniele de Sanctis; Kathryn Tunyasuvunakool; John Jumper; Martin Graña; Héctor Romero; Pablo S Aguilar; Luca Jovine; Benjamin Podbilewicz Journal: Nat Commun Date: 2022-07-06 Impact factor: 17.694