CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution

Juan F. Guerra Maldonado,Antony T. Vincent,Martin Chenal,Frederic J. Veyrier

doi:10.1186/s12864-020-07232-3

Juan F. Guerra Maldonado, Antony T. Vincent + Show 2 more

Open Access

https://doi.org/10.1186/s12864-020-07232-3

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Journal: BMC Genomics	Publication Date: Nov 26, 2020
Citations: 3	License type: open-access

Affiliation: Institut National de la Recherche Scientifique

Abstract

BackgroundThe evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a result of natural selection. Using phylogeny and genome comparisons, evolutionary paths can be somehow retraced, with recent events being much easier to detect than older ones. For this reason, multiple tools are available to study the evolutionary events within genomes of single species, such as gene composition alterations, or subtler mutations such as SNPs. However, these tools are generally designed to compare similar genomes and require advanced skills in bioinformatics. We present CAPRIB, a unique tool developed in Java that allows to determine the amino acid changes, at the genus level, that correlate with phenotypic differences between two groups of organisms.ResultsCAPRIB has a user-friendly graphical interface and uses databases in SQL, making it easy to compare several genomes without the need for programming or thorough knowledge in bioinformatics. This intuitive software narrows down a list of amino acid changes that are concomitant with a given phenotypic divergence at the genus scale. Each permutation found by our software is associated with two already described statistical values that indicate its potential impact on the protein’s function, helping the user decide which promising candidates to further investigate. We show that CAPRIB is able to detect already known mutations and uncovers many more, and that this tool can be used to question molecular phylogeny. Finally, we exemplify the utility of CAPRIB by pinpointing amino acid changes that coincided with the emergence of slow-growing mycobacteria from their fast-growing counterparts. The software is freely available at https://github.com/BactSymEvol/Caprib.ConclusionsCAPRIB is a new bioinformatics software aiming to make genus-scale comparisons accessible to all. With its intuitive graphical interface, this tool identifies key amino acid changes concomitant with a phenotypic divergence. By comparing fast and slow-growing mycobacteria, we shed light on evolutionary hotspots, such as the cytokinin pathway, that are interesting candidates for further experimentations.

Highlights

The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others
Description of Comparative Analyses of Proteins In Bacteria (CAPRIB) main functions In order to investigate the amino acid changes that may have been involved in the evolution of a group of organisms and in the emergence of a new phenotype, we have created CAPRIB, a tool with an easy-touse graphical interface (Fig. 1b)
To guide users through all of the amino acid (AA) changes found by CAPRIB, the latter integrates an interface allowing to check if the permutations are in conserved domains according to the NCBI Conserved Domain Database (CDD) database

Summary

Introduction

The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a result of natural selection. Using phylogeny and genome comparisons, evolutionary paths can be somehow retraced, with recent events being much easier to detect than older ones. Gene deletions and insertions are two major genetic events that have been linked with bacterial evolution. A recent study suggests that the unique cell envelope of bacteria members of the order Corynebacteriales, such as Mycobacterium tuberculosis, might be the result of a stepwise acquisition of multiple genes [11], supporting the importance of these events in bacterial evolution. Given the increase of genomic studies, a considerable number of tools have been developed in recent years to investigate the evolution of the gene repertoire, such as MycoHIT [8], SaturnV [12], GET_HOMOLOGUES [13], and Roary [14]

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