Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Arnaud Belcour; Jeanne Got; Méziane Aite; Ludovic Delage; Jonas Collén; Clémence Frioux; Catherine Leblanc; Simon M. Dittami; Samuel Blanquart; Gabriel V. Markov; Anne Siegel

doi:10.1101/gr.277056.122

Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

¹Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France;
²Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France;
³Inria, INRAE, Université de Bordeaux, 33400 Talence, France

↵4 These authors contributed equally to this work.
↵5 These authors contributed equally to this work.

Corresponding authors: arnaud.belcour{at}inria.fr, anne.siegel{at}irisa.fr

Abstract

Comparative analysis of genome-scale metabolic networks (GSMNs) may yield important information on the biology, evolution, and adaptation of species. However, it is impeded by the high heterogeneity of the quality and completeness of structural and functional genome annotations, which may bias the results of such comparisons. To address this issue, we developed AuCoMe, a pipeline to automatically reconstruct homogeneous GSMNs from a heterogeneous set of annotated genomes without discarding available manual annotations. We tested AuCoMe with three data sets, one bacterial, one fungal, and one algal, and showed that it successfully reduces technical biases while capturing the metabolic specificities of each organism. Our results also point out shared and divergent metabolic traits among evolutionarily distant algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life.

Footnotes

[Supplemental material is available for this article.]
Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277056.122.

Received June 22, 2022.
Accepted May 23, 2023.

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.