Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK.
Department of Genetics, University of Cambridge, Cambridge, UK.
Nat Commun. 2021 Oct 7;12(1):5870. doi: 10.1038/s41467-021-26166-2.
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.
表观遗传变异调节基因表达，并且可以遗传。然而，关于表观遗传分歧对自然适应性多样化的贡献的知识仍然有限。马拉维湖慈鲷鱼类的大规模进化辐射，尽管序列分歧极小，但表现出广泛的表型多样性，是研究表观基因组对适应性贡献的绝佳系统。在这里，我们进行了一项比较全基因组甲基组和转录组研究，重点关注表型差异的慈鲷物种的肝脏和肌肉组织。在这两种组织中，我们发现物种之间存在大量的甲基组差异。差异甲基化区域（DMR）在进化年轻的转座子中富集，与与能量消耗和脂质代谢相关的生态相关基因的转录变化相关，表明饮食生态与甲基组差异之间存在联系。出乎意料的是，所有物种特异性 DMR 的一半在组织间共享，并且在发育基因中富集，可能反映了不同的表观遗传发育程序。我们的研究揭示了密切相关的慈鲷鱼类中大量的甲基组差异，并且代表了研究表观遗传学在物种多样化中的作用的资源。
