DNA methylation is an evolutionary ancient epigenetic modification that is phylogenetically widespread. Comparative studies of the methylome across a diverse range of non-conventional and conventional model organisms is expected to help reveal how the landscape of DNA methylation and its functions have evolved. Here, we explore the DNA methylation profile of two species of the crustacean Daphnia using whole genome bisulfite sequencing. We then compare our data with the methylomes of two insects and two mammals to achieve a better understanding of the function of DNA methylation in Daphnia. Using RNA-sequencing data for all six species, we investigate the correlation between DNA methylation and gene expression. DNA methylation in Daphnia is mainly enriched within the coding regions of genes, with the highest methylation levels observed at exons 2-4. In contrast, vertebrate genomes are globally methylated, and increase towards the highest methylation levels observed at exon 2, and maintained across the rest of the gene body. Although DNA methylation patterns differ among all species, their methylation profiles share a bimodal distribution across the genomes. Genes with low levels of CpG methylation and gene expression are mainly enriched for species specific genes. In contrast, genes associated with high methylated CpG sites are highly transcribed and evolutionary conserved across all species. Finally, the positive correlation between internal exons and gene expression potentially points to an evolutionary conserved mechanism, whereas the negative regulation of gene expression via methylation of promoters and exon 1 is potentially a secondary mechanism that has been evolved in vertebrates.

Jouni Kvist

Camila Gonçalves Athanàsio

Omid Shams Solari

James B Brown

John K Colbourne

Michael E Pfrender

Leda Mirbahai

Genome Biology and Evolution

关于期刊基因组生物学和进化 (GBE) 在进化生物学和基因组学之间发表领先的原创研究。考虑发表的论文报告了新的进化发现，这些发现涉及自然基因组多样性、群体基因组学、基因组的结构、功能、组织和表达、比较基因组学、蛋白质组学和环境基因组相互作用。还考虑了来自计算生物学、结构生物学、发育生物学和细胞生物学领域的主要进化见解，以及基因组进化领域的理论进展。 GBE 的范围包括所有分类水平和所有生命形式的全基因组进化研究——在种群内或跨领域。其目的是进一步理解基因组的进化背景，并从全基因组的角度进一步理解进化。

The journal "Genome Biology and Evolution" focuses on publishing leading original research in the fields of genome biology and evolution. The papers considered for publication report new evolutionary discoveries related to natural genomic diversity, population genomics, the structure, function, organization, and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Additionally, significant evolutionary insights from computational biology, structural biology, developmental biology, and cell biology, as well as theoretical advancements in the field of genomic evolution, are also considered. The scope of the journal encompasses whole-genome evolutionary studies across all taxonomic levels and forms of life, whether within populations or across domains. Its aim is to enhance the understanding of the evolutionary context of genomes and to further explore evolution from a whole-genome perspective.

《Genome Biology and Evolution》期刊专注于发表关于基因组生物学和进化的领先原创研究。考虑发表的论文报告新的进化发现，这些发现涉及自然基因组多样性、群体基因组学、基因组的结构、功能、组织和表达、比较基因组学、蛋白质组学以及环境基因组的相互作用。此外，来自计算生物学、结构生物学、发育生物学和细胞生物学领域的主要进化见解，以及基因组进化领域的理论进展也在考虑之列。该期刊的范围涵盖所有分类水平和生命形式的全基因组进化研究，无论是在种群内还是跨领域。其目的是进一步理解基因组的进化背景，并从全基因组的视角深入探讨进化过程。

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective

The positive correlation between internal exons and gene expression potentially points to an evolutionary conserved mechanism, whereas the negative regulation of gene expression via methylation of promoters and exon 1 is potentially a secondary mechanism that has been evolved in vertebrates.

Category	Quartile
生物学	2
生物学, 遗传学	2
生物学, 进化生物学	3

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective

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Journal Info

Category	Quartile
GENETICS & HEREDITY	2