| [1] |
Adhikari K, Mendoza-Revilla J, Sohail A, Fuentes-Guajardo M, Lampert J, et al. 2019. A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia. Nature Communications 10:358 doi: 10.1038/s41467-018-08147-0 |
| [2] |
Fontes CG, Fine PVA, Wittmann F, Bittencourt PRL, Piedade MTF, et al. 2020. Convergent evolution of tree hydraulic traits in Amazonian habitats: implications for community assemblage and vulnerability to drought. New Phytologist 228:106−20 doi: 10.1111/nph.16675 |
| [3] |
Li B, Förster C, Robert CAM, Züst T, Hu L, et al. 2018. Convergent evolution of a metabolic switch between aphid and caterpillar resistance in cereals. Science Advances 4:eaat6797 doi: 10.1126/sciadv.aat6797 |
| [4] |
Xu Y, Lei Y, Su Z, Zhao M, Zhang J, et al. 2021. A chromosome-scale Gastrodia elata genome and large-scale comparative genomic analysis indicate convergent evolution by gene loss in mycoheterotrophic and parasitic plants. The Plant Journal 108:1609−23 doi: 10.1111/tpj.15528 |
| [5] |
Chen WK, Chen L, Zhang X, Yang N, Guo JH, et al. 2022. Convergent selection of a WD40 protein that enhances grain yield in maize and rice. Science 375:eabg7985 doi: 10.1126/science.abg7985 |
| [6] |
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114−20 doi: 10.1093/bioinformatics/btu170 |
| [7] |
Kim ED, Sung S. 2012. Long noncoding RNA: unveiling hidden layer of gene regulatory networks. Trends in Plant Science 17:16−21 doi: 10.1016/j.tplants.2011.10.008 |
| [8] |
Ariel F, Romero-Barrios N, Jégu T, Benhamed M, Crespi M. 2015. Battles and hijacks: noncoding transcription in plants. Trends in Plant Science 20:362−71 doi: 10.1016/j.tplants.2015.03.003 |
| [9] |
Wierzbicki AT, Blevins T, Swiezewski S. 2021. Long Noncoding RNAs in Plants. Annual Review of Plant Biology 72:245−71 doi: 10.1146/annurev-arplant-093020-035446 |
| [10] |
Wang Y, Fan X, Lin F, He G, Terzaghi W, et al. 2014. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. PNAS 111:10359−64 doi: 10.1073/pnas.1409457111 |
| [11] |
Yu J, Qiu K, Sun W, Yang T, Wu T, et al. 2022. A long noncoding RNA functions in high-light-induced anthocyanin accumulation in apple by activating ethylene synthesis. Plant Physiology 189:66−83 doi: 10.1093/plphys/kiac049 |
| [12] |
Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, et al. 2012. Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression. Plos Genetics 8:e1002841 doi: 10.1371/journal.pgen.1002841 |
| [13] |
Liu J, Jung C, Xu J, Wang H, Deng S, et al. 2012. Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis. The Plant Cell 24:4333−45 doi: 10.1105/tpc.112.102855 |
| [14] |
Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, et al. 2014. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505:635−40 doi: 10.1038/nature12943 |
| [15] |
Kulkarni S, Lied A, Kulkarni V, Rucevic M, Martin MP, et al. 2019. CCR5AS lncRNA variation differentially regulates CCR5, influencing HIV disease outcome. Nature Immunology 20:824−34 doi: 10.1038/s41590-019-0406-1 |
| [16] |
Xiao S, Cao S, Huang Q, Xia L, Deng M, et al. 2019. The RNA N6-methyladenosine modification landscape of human fetal tissues. Nature Cell Biology 21:651−61 doi: 10.1038/s41556-019-0315-4 |
| [17] |
Fang J, Lutz JA, Wang L, Shugart HH, Yan X. 2020. Using climate-driven leaf phenology and growth to improve predictions of gross primary productivity in North American forests. Global Change Biology 26:6974−88 doi: 10.1111/gcb.15349 |
| [18] |
Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916−19 doi: 10.1126/science.1186366 |
| [19] |
Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, et al. 2018. Contribution of epigenetic variation to adaptation in Arabidopsis. Nature Communications 9:4446 doi: 10.1038/s41467-018-06932-5 |
| [20] |
Wei X, Song X, Wei L, Tang S, Sun J, et al. 2017. An epiallele of rice AK1 affects photosynthetic capacity. Journal of Integrative Plant Biology 59:158−63 doi: 10.1111/jipb.12518 |
| [21] |
Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, et al. 2016. Methylome evolution in plants. Genome Biology 17:264 doi: 10.1186/s13059-016-1127-5 |
| [22] |
Matzke MA, Mosher RA. 2014. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nature Reviews Genetics 15:394−408 doi: 10.1038/nrg3683 |
| [23] |
Xu W, Yang T, Wang B, Han B, Zhou H, et al. 2018. Differential expression networks and inheritance patterns of long non-coding RNAs in castor bean seeds. The Plant Journal 95:324−40 doi: 10.1111/tpj.13953 |
| [24] |
Du Q, Yang X, Xie J, Quan M, Xiao L, et al. 2019. Time-specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus. Plant Biotechnology Journal 17:608−24 doi: 10.1111/pbi.13002 |
| [25] |
Ci D, Song Y, Du Q, Tian M, Han S, et al. 2016. Variation in genomic methylation in natural populations of Populus simonii is associated with leaf shape and photosynthetic traits. Journal of Experimental Botany 67:723−37 doi: 10.1093/jxb/erv485 |
| [26] |
McKown AD, Guy RD, Klápště J, Geraldes A, Friedmann M, et al. 2014. Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. New Phytologist 201:1263−76 doi: 10.1111/nph.12601 |
| [27] |
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37:907−15 doi: 10.1038/s41587-019-0201-4 |
| [28] |
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, et al. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Development 25:1915−27 doi: 10.1101/gad.17446611 |
| [29] |
Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139−40 doi: 10.1093/bioinformatics/btp616 |
| [30] |
Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, et al. 2019. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biology 20:278 doi: 10.1186/s13059-019-1910-1 |
| [31] |
Kang Y, Yang D, Kong L, Hou M, Meng Y, et al. 2017. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Research 45:W12−W16 doi: 10.1093/nar/gkx428 |
| [32] |
Sun L, Zhang Z, Bailey TL, Perkins AC, Tallack MR, et al. 2012. Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study. BMC Bioinformatics 13:331 doi: 10.1186/1471-2105-13-331 |
| [33] |
Li A, Zhang J, Zhou Z. 2014. PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme. BMC Bioinformatics 15:311 doi: 10.1186/1471-2105-15-311 |
| [34] |
Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European molecular biology open software suite. Trends Genet 16:276−77 doi: 10.1016/S0168-9525(00)02024-2 |
| [35] |
Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, et al. 2010. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 16:1478−87 doi: 10.1261/rna.1951310 |
| [36] |
Tian J, Song Y, Du Q, Yang X, Ci D, et al. 2016. Population genomic analysis of gibberellin-responsive long non-coding RNAs in Populus. Journal of Experimental Botany 67:2467−82 doi: 10.1093/jxb/erw057 |
| [37] |
Tafer H, Amman F, Eggenhofer F, Stadler PF, Hofacker IL. 2011. Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics 27:1934−40 doi: 10.1093/bioinformatics/btr281 |
| [38] |
Langfelder P, Horvath S. 2007. Eigengene networks for studying the relationships between co-expression modules. BMC Systems Biology 1:54 doi: 10.1186/1752-0509-1-54 |
| [39] |
Ye X, Wang S, Zhao X, Gao N, Wang Y, et al. 2022. Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa. Plant Journal 110:978−93 doi: 10.1111/tpj.15714 |
| [40] |
Csűös M. 2010. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26:1910−12 doi: 10.1093/bioinformatics/btq315 |
| [41] |
Krueger F, Andrews SR. 2011. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571−72 doi: 10.1093/bioinformatics/btr167 |
| [42] |
Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 14:178−92 doi: 10.1093/bib/bbs017 |
| [43] |
Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, et al. 2012. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biology 13:87 doi: 10.1186/gb-2012-13-10-r87 |
| [44] |
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357−59 doi: 10.1038/nmeth.1923 |
| [45] |
Tang S, Dong Y, Liang D, Zhang Z, Ye C, et al. 2015. Analysis of the drought stress-responsive transcriptome of black cottonwood (Populus trichocarpa) using deep RNA sequencing. Plant Molecular Biology Reporter 33:424−38 doi: 10.1007/s11105-014-0759-4 |
| [46] |
Scoffoni C, Chatelet DS, Pasquet-kok J, Rawls M, Donoghue MJ, et al. 2016. Hydraulic basis for the evolution of photosynthetic productivity. Nature Plants 2−16072 doi: 10.1038/nplants.2016.72 |
| [47] |
Lusk CH, Wright I, Reich PB. 2003. Photosynthetic differences contribute to competitive advantage of evergreen angiosperm trees over evergreen conifers in productive habitats. New Phytologist 160:329−36 doi: 10.1046/j.1469-8137.2003.00879.x |
| [48] |
Wang HV, Chekanova JA. 2017. Long Noncoding RNAs in Plants. In Long Non Coding RNA Biology. Advances in Experimental Medicine and Biology, ed. Rao M. vol 1008. Singapore: Springer. pp. 133−54. https://doi.org/10.1007/978-981-10-5203-3_5 |
| [49] |
Wang H, Niu QW, Wu HW, Liu J, Ye J, et al. 2015. Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits. The Plant Journal 84:404−16 doi: 10.1111/tpj.13018 |
| [50] |
Golicz AA, Singh MB, Bhalla PL. 2018. The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome. Plant Physiology 176:2133−47 doi: 10.1104/pp.17.01657 |
| [51] |
Ganguly DR, Crisp PA, Eichten SR, Pogson BJ. 2017. The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress. Plant Physiology 175:1893−912 doi: 10.1104/pp.17.00744 |
| [52] |
Shen Y, Zhang J, Liu Y, Liu S, Liu Z, et al. 2018. DNA methylation footprints during soybean domestication and improvement. Genome Biology 19:128 doi: 10.1186/s13059-018-1516-z |
| [53] |
Shi Y, Zhang X, Chang X, Yan M, Zhao H, et al. 2021. Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple. BMC Plant Biology 21:14 doi: 10.1186/s12870-020-02814-5 |
| [54] |
Ramírez Gonzales L, Shi L, Bergonzi SB, Oortwijn M, Franco-Zorrilla JM, et al. 2021. Potato CYCLING DOF FACTOR 1 and its lncRNA counterpart StFLORE link tuber development and drought response. The Plant Journal 105:855−69 doi: 10.1111/tpj.15093 |
| [55] |
Yuan J, Li J, Yang Y, Tan C, Zhu Y, et al. 2018. Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. The Plant Journal 93:814−27 doi: 10.1111/tpj.13804 |
| [56] |
Quan M, Liu X, Xiao L, Chen P, Song F, et al. 2021. Transcriptome analysis and association mapping reveal the genetic regulatory network response to cadmium stress in Populus tomentosa. Journal of Experimental Botany 72:576−91 doi: 10.1093/jxb/eraa434 |
| [57] |
Hezroni H, Ben-Tov Perry R, Meir Z, Housman G, Lubelsky Y, et al. 2017. A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes. Genome Biology 18:15 doi: 10.1186/s13059-017-1293-0 |
| [58] |
Deng J, Kong W, Mou X, Wang S, Zeng W. 2018. Identifying novel candidate biomarkers of RCC based on WGCNA analysis. Personalized Medicine 15:381−94 doi: 10.2217/pme-2017-0091 |
| [59] |
Ishii H, Yoshimura KI, Mori A. 2009. Convergence of leaf display and photosynthetic characteristics of understory Abies amabilis and Tsuga heterophylla in an old-growth forest in southwestern Washington State, USA. Tree Physiology 29:989−98 doi: 10.1093/treephys/tpp040 |
| [60] |
van Bezouw RFHM, Keurentjes JJB, Harbinson J, Aarts MGM. 2019. Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency. The Plant Journal 97:112−33 doi: 10.1111/tpj.14190 |
| [61] |
Yang T, Ma H, Zhang J, Wu T, Song T, et al. 2019. Systematic identification of long noncoding RNAs expressed during light-induced anthocyanin accumulation in apple fruit. The Plant Journal 100:572−90 doi: 10.1111/tpj.14470 |
| [62] |
Washietl S, Kellis M, Garber M. 2014. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Research 24:616−28 doi: 10.1101/gr.165035.113 |
| [63] |
Tao X, Li M, Zhao T, Feng S, Zhang H, et al. 2021. Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation. Plant Physiology 186:2152−68 doi: 10.1093/plphys/kiab179 |
| [64] |
Liu J, Last RL. 2017. A chloroplast thylakoid lumen protein is required for proper photosynthetic acclimation of plants under fluctuating light environments. PNAS 114:E8110−E8117 doi: 10.1073/pnas.1712206114 |
| [65] |
Klimmek F, Sjödin A, Noutsos C, Leister D, Jansson S. 2006. Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants. Plant Physiology 140:793−804 doi: 10.1104/pp.105.073304 |
| [66] |
Peterson RB, Schultes NP. 2014. Light-harvesting complex B7 shifts the irradiance response of photosynthetic light-harvesting regulation in leaves of Arabidopsis thaliana. Journal of Plant Physiology 171:311−18 doi: 10.1016/j.jplph.2013.09.007 |
| [67] |
Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, et al. 2016. Epigenomic diversity in a global collection of Arabidopsis thaliana Accessions. Cell 166:492−505 doi: 10.1016/j.cell.2016.06.044 |
| [68] |
De Kort H, Panis B, Deforce D, Van Nieuwerburgh F, Honnay O. 2020. Ecological divergence of wild strawberry DNA methylation patterns at distinct spatial scales. Molecular Ecology 29:4871−81 doi: 10.1111/mec.15689 |
| [69] |
Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, et al. 2014. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Molecular Cell 55:383−96 doi: 10.1016/j.molcel.2014.06.011 |
| [70] |
Wang M, Yuan D, Tu L, Gao W, He Y, et al. 2015. Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytologist 207:1181−97 doi: 10.1111/nph.13429 |
| [71] |
Rakyan VK, Down TA, Balding DJ, Beck S. 2011. Epigenome-wide association studies for common human diseases. Nature Reviews Genetics 12:529−41 doi: 10.1038/nrg3000 |
| [72] |
Lu W, Xiao L, Quan M, Wang Q, El-Kassaby YA, et al. 2020. Linkage-linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus. New Phytologist 225:1218−33 doi: 10.1111/nph.16220 |
| [73] |
De Kort H, Toivainen T, Van Nieuwerburgh F, Andrés J, Hytönen TP, et al. 2022. Signatures of polygenic adaptation align with genome-wide methylation patterns in wild strawberry plants. New Phytologist 235:1501−14 doi: 10.1111/nph.18225 |
| [74] |
Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, et al. 2013. Epigenetic and genetic influences on DNA methylation variation in maize populations. The Plant Cell 25:2783−97 doi: 10.1105/tpc.113.114793 |
| [75] |
Xu G, Lyu J, Li Q, Liu H, Wang D, et al. 2020. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement. Nature Communications 11:12 doi: 10.1038/s41467-019-13875-y |
| [76] |
Xiao L, Du Q, Fang Y, Quan M, Lu W, et al. 2021. Genetic architecture of the metabolic pathway of salicylic acid biosynthesis in Populus. Tree Physiology 41:2198−215 doi: 10.1093/treephys/tpab068 |
| [77] |
Yang Z, Xu F, Wang H, Teschendorff AE, Xie F, et al. 2021. Pan-cancer characterization of long non-coding RNA and DNA methylation mediated transcriptional dysregulation. EBioMedicine 68:103399 doi: 10.1016/j.ebiom.2021.103399 |
| [78] |
Yang Y, Chen L, Gu J, Zhang H, Yuan J, et al. 2017. Recurrently deregulated lncRNAs in hepatocellular carcinoma. Nature Communications 8:14421 doi: 10.1038/ncomms14421 |
| [79] |
Marney CB, Anderson ES, Adnan M, Peng KL, Hu Y, et al. 2021. p53-intact cancers escape tumor suppression through loss of long noncoding RNA Dino. Cell Reports 35:109329 doi: 10.1016/j.celrep.2021.109329 |
| [80] |
Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, et al. 2013. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 503:371−76 doi: 10.1038/nature12598 |
| [81] |
Zhou X, Jacobs TB, Xue LJ, Harding SA, Tsai CJ. 2015. Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennial Populus reveals 4-coumarate: CoA ligase specificity and redundancy. New Phytologist 208:298−301 doi: 10.1111/nph.13470 |
| [82] |
Vojta A, Dobrinic P, Tadic V, Bockor L, Korac P, et al. 2016. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Research 44:5615−28 doi: 10.1093/nar/gkw159 |