TY - JOUR

T1 - Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

AU - Vernaz, Grégoire

AU - Malinsky, Milan

AU - Svardal, Hannes

AU - Du, Mingliu

AU - Tyers, Alexandra M.

AU - Santos, M. Emília

AU - Durbin, Richard

AU - Genner, Martin J.

AU - Turner, George F.

AU - Miska, Eric A.

N1 - © 2021. Crown.

PY - 2021/10/7

Y1 - 2021/10/7

N2 - Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

AB - Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

KW - Animals

KW - Chromosome Mapping

KW - Cichlids/genetics

KW - DNA Transposable Elements

KW - Epigenesis, Genetic

KW - Epigenome

KW - Evolution, Molecular

KW - Gene Expression

KW - Genomics

KW - Lakes

KW - Liver

KW - Malawi

KW - Sequence Analysis, DNA

KW - Species Specificity

U2 - 10.1038/s41467-021-26166-2

DO - 10.1038/s41467-021-26166-2

M3 - Article

C2 - 34620871

VL - 12

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 5870

ER -