Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes.
Eutheria
GC content
Landscapes
Metatheria
Molecular clock
Neutral evolution
Protein evolution
Substitution rate
Journal
BMC ecology and evolution
ISSN: 2730-7182
Titre abrégé: BMC Ecol Evol
Pays: England
ID NLM: 101775613
Informations de publication
Date de publication:
04 08 2021
04 08 2021
Historique:
received:
08
11
2019
accepted:
22
07
2021
entrez:
5
8
2021
pubmed:
6
8
2021
medline:
10
8
2021
Statut:
epublish
Résumé
Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.
Sections du résumé
BACKGROUND
Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence.
RESULTS
We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins.
CONCLUSIONS
A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.
Identifiants
pubmed: 34348656
doi: 10.1186/s12862-021-01882-x
pii: 10.1186/s12862-021-01882-x
pmc: PMC8336415
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
153Subventions
Organisme : Fonds Wetenschappelijk Onderzoek
ID : G078814N
Organisme : Fonds Wetenschappelijk Onderzoek
ID : SBO151086
Organisme : onderzoeksraad, ku leuven
ID : C14/18/094
Organisme : fonds wetenschappelijk onderzoek
ID : G0E1420N, G098321N
Informations de copyright
© 2021. The Author(s).
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