The Pliable Genome: Epigenomics of Norway Spruce

Recent discoveries have highlighted multiple mitotically and meiotically inherited alterations in gene expression that could not be explained solely by changes in the DNA sequence but were acknowledged as epigenetic. The modern view on epigenetics considers it as an integral part of genetics. Epigenetic mechanisms are encoded by genes in the genome and contribute to an essential part of genomic diversity, significantly extending its regulatory abilities. Epigenetic mechanisms involve molecular chromatin alterations through DNA methylation and histone modifications, as well as, complex non-coding RNAs and related enzyme machinery leading to changes in gene expression and resulting in changing phenotypes. In plants, epigenetic mechanisms may occur over their lifetime and across multiple generations, and can contribute substantially to phenotypic plasticity, stress responses, disease resistance, acclimation and adaptation to habitat conditions. In this review, we summarize recent advances with regards to Norway spruce epigenomics. We first consider the large size of the spruce genome that is linked to epigenetic mechanisms and why epigenomics is vitally important for spruce. Then, we discuss the molecular machinery supporting epigenetic mechanisms in Norway spruce and putative gene models involved. We presume substantial extension of gene families of epigenetic regulators and non-coding RNAs, especially in reproductive tissues. Norway spruce was the first species among forest trees in which epigenetic memory and epigenetic mechanisms were studied. The induction of an epigenetic memory during sexual reproduction and somatic embryogenesis has been described in Norway spruce. We discuss the latest results of epigenomic variation and epigenetic memory studies in Norway spruce and define the future perspectives for epigenetic studies. However, there is still a long way to decipher how the epigenetic mechanisms are involved in maintaining the stability of the spruce epigenome, how the epigenome is set to produce the epigenetic memory phenomenon and how these may result in an increased rate of adaptation to a changing environment.