Do long-lived conifers react to environmental stress by somatic epigenetic priming? Genomic methylation analysis at single-base resolution by means of exome capture and bisulfite sequencing in Norway spruce

树木作为一种寿命长、世代长的固着生物，对环境变化的反应是一个重大挑战。甚至比其他生物的表观遗传机制可能代表了一个快速的，因此，树木的中央缓解策略。然而，由于针叶树的基因组庞大且重复，对针叶树的表观遗传过程和机制的探索一直很困难。随着欧洲云杉（Picea abies）第一个针叶树参考基因组的完成和高效基因组技术的全面提供，新的研究机会出现了。在这项研究中，我们的目的是调查云杉的甲基化谱，以找出是否在DNA甲基化状态的连贯变化发生依赖于环境条件（表观遗传启动）。作为原理验证，我们的目标是进行靶向亚硫酸氢盐测序，以确定云杉完整外显子组的甲基化状态。通过使用在不同环境条件下生长的成对的小巢和分株，我们将确定这些对之间的甲基化谱是否普遍不同。此外，我们将使用最近发表和注释的欧洲云杉参考基因组来事后检查在其他遗传上相同的个体之间特定基因（例如与昼夜节律、芽物候和压力相关的基因）的甲基化状态是否存在差异。显著的变化意味着基因甲基化允许生物体在生命周期内发生表型变化。

For trees as long-lived sessile organisms with long generation times, the response to environmental changes is a major challenge. Even more than for other organisms epigenetic mechanisms may represent a fast and therefore central mitigation strategy for trees. However, the exploration of epigenetic processes and mechanisms especially in conifers has been difficult due to their large and repetitive genomes. Following the completion of the first conifer reference genome of Picea abies recently, and the overall provisioning of efficient genomic techniques new research opportunities arise. In this study we aim to investigate the methylation profile of Picea abies to find out whether coherent changes in DNA methylation status occur dependent on environmental conditions (epigenetic priming). As a proof-of-principle, we aim to conduct targeted bisulfite sequencing in order to identify the methylation status of Picea abies for the complete exome. By using pairs of ortets and ramets that have been growing under different environmental conditions, we will determine whether methylation profiles differ in general between these pairs. Furthermore, we will use the recently published and annotated Picea abies reference genome to check á posteriori whether there are differences in methylation status in specific genes (e.g. related to circadian rhythms, bud phenology and stress) between otherwise genetically identical individuals. Significant changes would imply that gene methylation permits phenotypic changes within the life time of an organism.