Table_5_The Seagrass Methylome Is Associated With Variation in Photosynthetic Performance Among Clonal Shoots.xlsx

Evolutionary theory predicts that clonal organisms are more susceptible to extinction than sexually reproducing organisms, due to low genetic variation and slow rates of evolution. In agreement, conservation management considers genetic variation as the ultimate measure of a population’s ability to survive over time. However, clonal plants are among the oldest living organisms on our planet. Here, we test the hypothesis that clonal seagrass meadows display epigenetic variation that complements genetic variation as a source of phenotypic variation. In a clonal meadow of the seagrass Zostera marina, we characterized DNA methylation among 42 shoots. We also sequenced the whole genome of 10 shoots to correlate methylation patterns with photosynthetic performance under exposure to and recovery from 27°C, while controlling for somatic mutations. Here, we show for the first time that clonal seagrass shoots display DNA methylation variation that is independent from underlying genetic variation, and associated with variation in photosynthetic performance under experimental conditions. It remains unknown to what degree this association could be influenced by epigenetic responses to transplantation-related stress, given that the methylomes showed a strong shift under acclimation to laboratory conditions. The lack of untreated control samples in the heat stress experiment did not allow us to distinguish methylome shifts induced by acclimation from such induced by heat stress. Notwithstanding, the co-variation in DNA methylation and photosynthetic performance may be linked via gene expression because methylation patterns varied in functionally relevant genes involved in photosynthesis, and in the repair and prevention of heat-induced protein damage. While genotypic diversity has been shown to enhance stress resilience in seagrass meadows, we suggest that epigenetic variation plays a similar role in meadows dominated by a single genotype. Consequently, conservation management of clonal plants should consider epigenetic variation as indicator of resilience and stability.进化论预测，相较于有性繁殖生物，克隆生物（clonal organisms）因遗传变异（genetic variation）水平较低且进化速率缓慢，更易走向灭绝。这一结论与保护管理领域的共识相符：遗传变异是衡量种群长期生存能力的终极指标。然而，克隆植物却是地球上现存最古老的生物类群之一。本研究旨在验证如下假说：克隆海草床所呈现的表观遗传变异（epigenetic variation）可作为遗传变异的补充，共同构成表型变异（phenotypic variation）的来源。我们以一片大叶藻（Zostera marina）克隆海草床为研究对象，对42株植株的DNA甲基化（DNA methylation）水平进行了表征分析；同时还对其中10株植株的全基因组进行了测序，以在控制体细胞突变（somatic mutations）混杂效应的前提下，探究27℃热胁迫暴露及后续恢复过程中，甲基化模式与光合性能之间的关联。本研究首次证实，在实验条件下，克隆海草植株所呈现的DNA甲基化变异独立于其潜在的遗传变异，且与光合性能的差异显著相关。但由于甲基化组（methylomes）在适应实验室环境的过程中发生了显著改变，目前尚不清楚这种关联在多大程度上会受到移植相关胁迫的表观遗传应答的影响。由于本次热胁迫实验未设置未处理的对照样本，我们无法区分由实验室环境适应引发的甲基化组改变与热胁迫诱导的甲基化组变化。尽管如此，DNA甲基化与光合性能的共变异或许可通过基因表达建立关联：甲基化模式在与光合功能、热诱导蛋白质损伤修复及预防相关的功能基因中存在显著差异。尽管已有研究证实，基因型多样性可提升海草床的胁迫抗性，本研究认为表观遗传变异在单基因型主导的海草床中也能发挥类似的作用。因此，克隆植物的保护管理工作应将表观遗传变异作为衡量其抗性与稳定性的重要指标。