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Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification
Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Univ Sao Paulo, Brazil.
Wageningen Univ and Res, Netherlands; Netherlands Inst Ecol NIOO KNAW, Netherlands; Swedish Univ Agr Sci, Sweden.
Swedish Univ Agr Sci, Sweden.
Linköping University, Department of Physics, Chemistry and Biology, Theoretical Biology. Linköping University, Faculty of Science & Engineering.ORCID iD: 0000-0001-7856-2925
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2019 (English)In: Epigenetics, ISSN 1559-2294, E-ISSN 1559-2308Article in journal (Refereed) Epub ahead of print
Abstract [en]

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.

Place, publisher, year, edition, pages
TAYLOR & FRANCIS INC , 2019.
Keywords [en]
genetic variation; DNA methylation; CpG; single nucleotide polymorphisms; copy number variations; germ line; Gallus gallus
National Category
Genetics
Identifiers
URN: urn:nbn:se:liu:diva-158571DOI: 10.1080/15592294.2019.1609868ISI: 000469727100001PubMedID: 31070073OAI: oai:DiVA.org:liu-158571DiVA, id: diva2:1334797
Note

Funding Agencies|Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior [99999.008097/2014-03]; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo [2018/13600-0, 2014/08704-0, 2016/20440-3]; H2020 European Research Council [322206]

Available from: 2019-07-03 Created: 2019-07-03 Last updated: 2019-07-03

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