Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients

DNA methylation in plants affects transposon silencing, transcriptional regulation and thus phenotypic variation. One unanswered question is whether DNA methylation could be involved in local adaptation of plant populations to their environments. If methylation alters phenotypes to improve plant response to the environment, then methylation sites or the genes that affect them could be a target of natural selection. Using reduced-representation bisulphite sequencing (RRBS) data, we assessed whether climate is associated with variation in DNA methylation levels among 58 naturally occurring, and species-wide samples of valley oak (Quercus lobata) collected across climate gradients. We identified the genomic context of these variants referencing a new draft valley oak genome sequence. Methylation data were obtained for 341 107 cytosines, of which we deemed 57 488 as single-methylation variants (SMVs), found in the CG, CHG and CHH sequence contexts. Environmental association analyses reveale...

植物DNA甲基化可调控转座子沉默与基因转录，进而影响表型变异。目前尚存一个未解决的科学问题：DNA甲基化是否参与植物种群对其生存环境的本地适应过程？若甲基化可通过改变表型增强植物对环境的响应能力，那么甲基化位点或调控甲基化的基因便可能成为自然选择的作用靶点。本研究利用简化代表性亚硫酸氢盐测序（reduced-representation bisulphite sequencing, RRBS）数据，对采集自不同气候梯度的58份天然分布、覆盖该物种全分布范围的山谷栎（Quercus lobata）样本的DNA甲基化水平变异与气候的相关性进行了评估。本研究依托最新发布的山谷栎草图基因组序列，对上述变异的基因组背景进行了鉴定。本研究共获取了341107个胞嘧啶位点的甲基化数据，其中57488个被鉴定为单甲基化变异（single-methylation variants, SMVs），这些变异分布于CG、CHG与CHH三种序列背景中。环境关联分析结果显示……