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Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents
Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological ad...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10653590/ https://www.ncbi.nlm.nih.gov/pubmed/37972291 http://dx.doi.org/10.1093/gbe/evad197 |
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author | Courcelle, Maxime Fabre, Pierre-Henri Douzery, Emmanuel J P |
author_facet | Courcelle, Maxime Fabre, Pierre-Henri Douzery, Emmanuel J P |
author_sort | Courcelle, Maxime |
collection | PubMed |
description | Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny. |
format | Online Article Text |
id | pubmed-10653590 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-106535902023-11-16 Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents Courcelle, Maxime Fabre, Pierre-Henri Douzery, Emmanuel J P Genome Biol Evol Article Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny. Oxford University Press 2023-11-16 /pmc/articles/PMC10653590/ /pubmed/37972291 http://dx.doi.org/10.1093/gbe/evad197 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Article Courcelle, Maxime Fabre, Pierre-Henri Douzery, Emmanuel J P Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents |
title | Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents |
title_full | Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents |
title_fullStr | Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents |
title_full_unstemmed | Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents |
title_short | Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents |
title_sort | phylogeny, ecology, and gene families covariation shaped the olfactory subgenome of rodents |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10653590/ https://www.ncbi.nlm.nih.gov/pubmed/37972291 http://dx.doi.org/10.1093/gbe/evad197 |
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