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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification

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Author(s):
Pertille, Fabio [1, 2] ; Da Silva, Vinicius H. [3, 4, 5] ; Johansson, Anna M. [3] ; Lindstrom, Tom [6] ; Wright, Dominic [1] ; Coutinho, Luiz L. [2] ; Jensen, Per [1] ; Guerrero-Bosagna, Carlos [1]
Total Authors: 8
Affiliation:
[1] Linkoping Univ, IFM Biol, Avian Behav Genom & Physiol Grp, Linkoping - Sweden
[2] Univ Sao Paulo, Luiz de Queiroz Coll Agr ESALQ, Anim Sci Dept, Anim Biotechnol Lab, Piracicaba, SP - Brazil
[3] Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala - Sweden
[4] Wageningen Univ & Res, Anim Breeding & Genom Ctr, Wageningen - Netherlands
[5] Netherlands Inst Ecol NIOO KNAW, Dept Anim Ecol AnE, Wageningen - Netherlands
[6] Linkoping Univ, Div Theoret Biol, IFM, Linkoping - Sweden
Total Affiliations: 6
Document type: Journal article
Source: Epigenetics; v. 14, n. 7 MAY 2019.
Web of Science Citations: 2
Abstract

DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic `flexibility' in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic `specificity' in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation. (AU)

FAPESP's process: 16/20440-3 - Epigenetic analysis of methylation profile of chickens submitted to different stress conditions in the livestock production environment
Grantee:Fábio Pértille
Support Opportunities: Scholarships in Brazil - Post-Doctoral
FAPESP's process: 14/08704-0 - Identification of loci of interest for poultry production
Grantee:Luiz Lehmann Coutinho
Support Opportunities: Research Projects - Thematic Grants
FAPESP's process: 18/13600-0 - Methylome and transcriptome analysis of chickens subjected to illumination stress in the livestock production environment
Grantee:Fábio Pértille
Support Opportunities: Scholarships abroad - Research Internship - Post-doctor