Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico
Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico
复制标题
DOI：
10.1111/eva.12912
复制
发表时间：
2020-01-07
影响因子：
4.1
通讯作者：
Kelly, Morgan W.
中科院分区：
文献类型：
--
作者：
Johnson, Kevin M.;Kelly, Morgan W.
种群可能通过进化分化或表型可塑性对环境异质性做出反应。虽然进化分化是通过种群之间的DNA序列差异而发生的，但种群之间的可塑性分歧可能是由于表观基因组的变化而产生的。在这里，我们展示了墨西哥湾北部四个东方牡蛎种群(Crassostrea Virgiica)DNA甲基化模式和遗传结构的全基因组比较结果。我们使用限制酶切位点相关DNA测序(RADseq)和简化代表性亚硫酸氢盐测序(RRBS)相结合的方法来研究居住在四个盐度特征独特的河口的牡蛎的种群结构、F-ST的全基因平均值和DNA甲基化差异。这种方法确定了显著的种群结构，尽管密西西比河淡水边界的F-ST中等偏低(0.02)，这一发现可能反映了最近恢复牡蛎种群的努力。群体间CpG甲基化的差异大于F-ST的差异，可能反映了环境对DNA甲基化模式的影响。对所有人群的CpG甲基化模式的评估表明，只有26%的甲基化DNA是基因间的；所有差异甲基化区域(DMR)中只有17%在这些相同的区域内。位点间基因体内的DMRS与已知参与DNA损伤修复、离子运输和生殖时机的基因有关。最后，当评估基因组变异和这些群体之间的DNA甲基化之间的相关性时，我们观察到群体特有的DNA甲基化图谱与单核苷酸多态或更广泛的基因体平均F-ST趋势没有直接关联。我们的结果表明，维吉尼亚锥虫可能使用DNA甲基化来产生环境响应的塑料表型，并且甲基化的差异比等位基因频率的差异更大。
Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While evolutionary divergence occurs through DNA sequence differences among populations, plastic divergence among populations may be generated by changes in the epigenome. Here, we present the results of a genome-wide comparison of DNA methylation patterns and genetic structure among four populations of Eastern oyster (Crassostrea virginica) in the northern Gulf of Mexico. We used a combination of restriction site-associated DNA sequencing (RADseq) and reduced representation bisulfite sequencing (RRBS) to explore population structure, gene-wide averages of F-ST, and DNA methylation differences between oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low F-ST (0.02) across the freshwater boundary of the Mississippi river, a finding that may reflect recent efforts to restore oyster stock populations. Divergence between populations in CpG methylation was greater than for divergence in F-ST, likely reflecting environmental effects on DNA methylation patterns. Assessment of CpG methylation patterns across all populations identified that only 26% of methylated DNA was intergenic; and, only 17% of all differentially methylated regions (DMRs) were within these same regions. DMRs within gene bodies between sites were associated with genes known to be involved in DNA damage repair, ion transport, and reproductive timing. Finally, when assessing the correlation between genomic variation and DNA methylation between these populations, we observed population-specific DNA methylation profiles that were not directly associated with single nucleotide polymorphisms or broader gene-body mean F-ST trends. Our results suggest that C. virginica may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.