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Cited by 9Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenome Rearrangement Algorithms

GLADX: an automated approach to analyze the lineage-specific loss and pseudogenization of genes

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Dainat, Jacques, Paganini, Julien, Pontarotti, Pierre, Gouret, Philippe·2012·PLoS ONE
DOI 10.1371/journal.pone.0038792PMC PMC3377690
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Abstract

A well-established ancestral gene can usually be found, in one or multiple copies, in different descendant species. Sometimes during the course of evolution, all the representatives of a well-established ancestral gene disappear in specific lineages; such gene losses may occur in the genome by deletion of a DNA fragment or by pseudogenization. The loss of an entire gene family in a given lineage may reflect an important phenomenon, and could be due either to adaptation, or to a relaxation of selection that leads to neutral evolution. Therefore, the lineage-specific gene loss analyses are important to improve the understanding of the evolutionary history of genes and genomes. In order to perform this kind of study from the increasing number of complete genome sequences available, we developed a unique new software module called GLADX in the DAGOBAH framework, based on a comparative genomic approach. The software is able to automatically detect, for all the species of a phylum, the presence/absence of a representative of a well-established ancestral gene, and by systematic steps of re-annotation, confirm losses, detect and analyze pseudogenes and find novel genes. The approach is based on the use of highly reliable gene phylogenies, of protein predictions and on the analysis of genomic mutations. All the evidence associated to evolutionary approach provides accurate information for building an overall view of the evolution of a given gene in a selected phylum. The reliability of GLADX has been successfully tested on a benchmark analysis of 14 reported cases. It is the first tool that is able to fully automatically study the lineage-specific losses and pseudogenizations. GLADX is available at http://ioda.univ-provence.fr/IodaSite/gladx/.

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  • The most obvious approach to look for evidence of relaxed selection has been to identify loss of trait or pseudogenization.

    “The most obvious approach has been to identify loss of trait or pseudogenization (e.g., Dainat et al. [2012]).”

    From RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015) · cites this paper as Dainat et al. [2012]

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Cited by

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Authors
Dainat, J., Paganini, J., Pontarotti, P., & Gouret, P.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Dainat, Jacques
ORCID
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2012-06-18
Volume
7
Issue
6
Pages
e38792
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0038792
PMC
PMC3377690
OpenAlex
W2008417320
Cited by
9
References
1
Citations by year
2022: 1 · 2021: 1 · 2018: 2 · 2016: 2 · 2014: 2 · 2013: 1
FWCI
0.36
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Funders
Agence Nationale de la Recherche (ANR-07-BLAN-0054)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
pseudogenization, pseudogenes, gene family evolution, comparative genomics, gene presence/absence, genome annotation, gene phylogeny, genome evolution
MeSH terms
Acyltransferases, Animals, Humans, Genetic Linkage, Phylogeny, Pseudogenes, Software, Sulfotransferases, Gene Deletion, Internet, Genomics

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