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/.
Highlights
Essential genes, such as housekeeping genes or genes involved in interaction networks, remain stable during evolution due to their central biological role and tend to evolve under purifying selection [1,2,3]
Our analysis is more complete, as Gene Loss Analyzer DAGOBAH eXtension (GLADX) makes it possible to show what happened in all lineages and species of the dataset
We created the GLADX module implemented in the DAGOBAH framework as an attempt to totally automate the analysis of lineage-specific gene losses
Summary
Essential genes, such as housekeeping genes or genes involved in interaction networks, remain stable during evolution due to their central biological role and tend to evolve under purifying selection [1,2,3]. The more the gene is important, the more it tends to be universally conserved. The counterintuitive concept that gene losses may be an important driver of evolutionary change via adaptive changes was named the ‘‘less is more’’ hypothesis [8]. The lineage-specific gene losses of well-established genes can be due to deletion events or to pseudogenizations. This kind of pseudogenes is called unitary pseudogenes [9]. Once that a gene was deactivated by a deleterious mutation it becomes a pseudogene which evolves free from selective constraints and undergoes a progressive erosion of the signal by accumulation of numerous further mutations until the footprint of the original sequence becomes unrecognizable in the genome among the non-coding signal. When pseudogenization is not too old, mutations of this kind are still observable
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