Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway.
Sci Data. 2023 Mar 1;10(1):114. doi: 10.1038/s41597-023-01996-5.
The mechanisms underlying the fast genome evolution that occurs during animal domestication are poorly understood. Here, we present a genome-wide epigenetic dataset that quantifies DNA hydroxymethylation at single nucleotide resolution among full-sib Nile tilapia (Oreochromis niloticus) with distinct growth performance. In total, we obtained 355 million, 75 bp reads from 5 large- and 5 small-sized fish on an Illumina NextSeq500 platform. We identified several growth-related genes to be differentially hydroxymethylated, especially within gene bodies and promoters. Previously, we proposed that DNA hydroxymethylation greatly affects the earliest responses to adaptation and potentially drives genome evolution through its targeted enrichment and elevated nucleotide transversion rates. This dataset can be analysed in various contexts (e.g., epigenetics, evolution and growth) and compared to other epigenomic datasets in the future, namely DNA methylation and histone modifications. With forthcoming advancements in genome research, this hydroxymethylation dataset will also contribute to better understand the epigenetic regulation of key genomic features, such as cis-regulatory and transposable elements.
动物驯化过程中发生的快速基因组进化的机制尚不清楚。在这里，我们提供了一个全基因组表观遗传数据集，该数据集以单核苷酸分辨率量化了具有不同生长性能的全同胞尼罗罗非鱼（Oreochromis niloticus）中的 DNA 羟甲基化。我们总共从 5 条大型鱼和 5 条小型鱼在 Illumina NextSeq500 平台上获得了 3.55 亿个 75bp 的读取。我们鉴定了一些与生长相关的基因存在差异羟甲基化，特别是在基因体和启动子内。之前，我们提出 DNA 羟甲基化极大地影响了对适应的最早反应，并通过其靶向富集和提高核苷酸转换率潜在地推动了基因组进化。该数据集可以在各种情况下进行分析（例如，表观遗传学、进化和生长），并在未来与其他表观基因组数据集（如 DNA 甲基化和组蛋白修饰）进行比较。随着基因组研究的未来进展，该羟甲基化数据集也将有助于更好地理解关键基因组特征的表观遗传调控，例如顺式调控元件和转座元件。
