References
- Ahuja MR, Neale DB (2005) Evolution of Genome Size in Conifers. Silvae Genetica 54(3):126–137. https://doi.org/10.1515/sg-2005-0020
- Alakärppä E, Salo HM, Valledor L, et al (2018) Natural variation of DNA methylation and gene expression may determine local adaptations of Scots pine populations. Journal of Experimental Botany 69(21):5293–5305. https://doi.org/10.1093/jxb/ery292
- Altschul SF, Gish W, Miller W, et al (1990) Basic local alignment search tool. Journal of Molecular Biology 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
- Ashikawa I (2001) Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. The Plant Journal 26(6):617–25. https://doi.org/10.1046/j.1365-313x.2001.01062.x
- Ausin I, Feng S, Yu C, et al (2016) DNA methylome of the 20-gigabase Norway spruce genome. Proceedings of the National Academy of Science of the USA 113(50):E8106–E8113. https://doi.org/10.1073/pnas.1618019113
- Bartels A, Han Q, Nair P, et al (2018) Dynamic DNA Methylation in Plant Growth and Development. International Journal of Molecular Sciences 19(7):2144. https://doi.org/10.3390/ijms19072144
- Beck D, Ben Maamar M, Skinner MK (2022) Genome-wide CpG density and DNA methylation analysis method (MeDIP, RRBS, and WGBS) comparisons. Epigenetics 17(5):518–530. https://doi.org/10.1080/15592294.2021.1924970
- Boulias K, Greer EL (2021) Detection of DNA Methylation in Genomic DNA by UHPLC-MS/MS. Methods in Molecular Biology 2198:79–90. https://doi.org/10.1007/978-1-0716-0876-0_7
- Dar FA, Mushtaq NU, Saleem S, et al (2022) Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. International Journal of Genomics 2022:1092894. https://doi.org/10.1155/2022/1092894
- Dobbertin M (2005) Tree growth as indicator of tree vitality and of tree reaction to environmental stress: A review. European Journal of Forest Research 124:319–333. https://doi.org/10.1007/s10342-005-0085-3
- García-García I, Méndez-Cea B, Gallego FJ, et al (2024) Genomic insights into climate change-induced forest dieback in Abies alba hotspots of decline. European Journal of Forest Research. https://doi.org/10.1007/s10342-024-01737-2
- García-García I, Méndez-Cea B, González de Andrés E, et al (2023) Climate and Soil Microsite Conditions Determine Local Adaptation in Declining Silver Fir Forests. Plants 12(14):2607. https://doi.org/10.3390/plants12142607
- García-García I, Méndez-Cea B, Martín-Gálvez D, et al (2022) Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline. Frontiers in Plant Science 12:797958. https://doi.org/10.3389/fpls.2021.797958
- González de Andrés E, Gazol A, Querejeta JI, et al (2022) The role of nutritional impairment in carbon-water balance of silver fir drought-induced dieback. Global Change Biology 28(14):4439–4458. https://doi.org/10.1111/gcb.16170
- Huang XY, Chao DY, Koprivova A, et al (2016) Nuclear Localised MORE SULPHUR ACCUMULATION1 Epigenetically Regulates Sulphur Homeostasis in Arabidopsis thaliana. PLoS Genetics 12(9):e1006298. https://doi.org/10.1371/journal.pgen.1006298
- Kenchanmane Raju SK, Ritter EJ, Niederhuth CE (2019) Establishment, maintenance, and biological roles of non-CG methylation in plants. Essays in Biochemistry 63(6):743–755. https://doi.org/10.1042/EBC20190032
- Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27(11):1571–2. https://doi.org/10.1093/bioinformatics/btr167
- Kumar S, Mohapatra T (2021) Dynamics of DNA Methylation and Its Functions in Plant Growth and Development. Frontiers in Plant Science 12:596236. https://doi.org/10.3389/fpls.2021.596236
- Kurdyukov S, Bullock M (2016) DNA Methylation Analysis: Choosing the Right Method. Biology 5(1):3. https://doi.org/10.3390/biology5010003
- Li J, Han F, Yuan T, et al (2023) The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine. Nature Communications 14(1):1947. https://doi.org/10.1038/s41467-023-37684-6
- Linares JC, Camarero JJ (2012) Silver Fir Defoliation Likelihood Is Related to Negative Growth Trends and High Warming Sensitivity at Their Southernmost Distribution Limit. ISRN Forestry 2012:437690. https://doi.org/10.5402/2012/437690
- Martin GT, Seymour DK, Gaut BS (2021) CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation. Genome Biology and Evolution 13(8):evab144. https://doi.org/10.1093/gbe/evab144
- Mosca E, Cruz F, Gómez-Garrido J, et al (2019) A Reference Genome Sequence for the European Silver Fir (Abies alba Mill.): A Community-Generated Genomic Resource. Genes Genome Genetics (G3) 9(7):2039–2049. https://doi.org/10.1534/g3.119.400083
- Nicotra AB, Atkin OK, Bonser SP, et al (2010) Plant phenotypic plasticity in a changing climate. Trends in Plant Science 15(12):684–92. https://doi.org/10.1016/j.tplants.2010.09.008
- Niu S, Li J, Bo W, et al (2022) The Chinese pine genome and methylome unveil key features of conifer evolution. Cell 185(1):204–217.e14. https://doi.org/10.1016/j.cell.2021.12.006
- Pigliucci M, Murren CJ, Schlichting CD (2006) Phenotypic plasticity and evolution by genetic assimilation. Journal of Experimental Biology 209:2362–7. https://doi.org/10.1242/jeb.02070
- Puizina J, Sviben T, Krajacić-Sokol I, et al (2008) Cytogenetic and molecular characterization of the Abies alba genome and its relationship with other members of the Pinaceae. Plant Biology 10(2):256–67. https://doi.org/10.1111/j.1438-8677.2007.00018.x
- Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26(1):139–140. https://doi.org/10.1093/bioinformatics/btp616
- Sáez-Laguna E, Guevara MÁ, Díaz LM, et al (2014) Epigenetic variability in the genetically uniform forest tree species Pinus pinea L. PLoS One 9(8):e103145. https://doi.org/10.1371/journal.pone.0103145
- Stotz GC, Salgado-Luarte C, Escobedo VM, et al (2021) Global trends in phenotypic plasticity of plants. Ecology Letters 24(10):2267–2281. https://doi.org/10.1111/ele.13827
- Suzuki M, Liao W, Wos F, et al (2018) Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Research 28(9):1364–1371. https://doi.org/10.1101/gr.232587.117
- Takuno S, Ran JH, Gaut B (2016) Evolutionary patterns of genic DNA methylation vary across land plants. Nature Plants 2:15222. https://doi.org/10.1038/nplants.2015.222
- Vu GTH, Cao HX, Hofmann M, et al (2023) Uncovering epigenetic and transcriptional regulation of growth in Douglas-fir: identification of differential methylation regions in mega-sized introns. Plant Biotechnology Journal 22(4):863–875. https://doi.org/10.1111/pbi.14229
- Zhang H, Lang Z, Zhu JK (2018) Dynamics and function of DNA methylation in plants. Nature Reviews Molecular Cell Biology 19(8):489–506. https://doi.org/10.1038/s41580-018-0016-z
- Zuo J, Wang Y, Zhu B, et al (2018) Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit. Genes 9(5):266. https://doi.org/10.3390/genes9050266