[1]

Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, et al. 2008. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453:1239−43

doi: 10.1038/nature07002
[2]

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
[3]

Zhang P, Wu W, Chen Q, Chen M. 2019. Non-Coding RNAs and their Integrated Networks. Journal of Integrative Bioinformatics 16:20190027

doi: 10.1515/jib-2019-0027
[4]

Mercer TR, Dinger ME, Mattick JS. 2009. Long non-coding RNAs: insights into functions. Nature Reviews Genetics 10:155−59

doi: 10.1038/nrg2521
[5]

Jha UC, Nayyar H, Jha R, Khurshid M, Zhou M, et al. 2020. Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation. BMC Plant Biology 20:466

doi: 10.1186/s12870-020-02595-x
[6]

Wierzbicki AT, Haag JR, Pikaard CS. 2008. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135:635−48

doi: 10.1016/j.cell.2008.09.035
[7]

Gil N, Ulitsky I. 2020. Regulation of gene expression by cis-acting long non-coding RNAs. Nature Reviews Genetics 21:102−17

doi: 10.1038/s41576-019-0184-5
[8]

Ponting CP, Oliver PL, Reik W. 2009. Evolution and functions of long noncoding RNAs. Cell 136:629−41

doi: 10.1016/j.cell.2009.02.006
[9]

Guil S, Esteller M. 2012. Cis-acting noncoding RNAs: friends and foes. Nature Structural & Molecular Biology 19:1068−75

doi: 10.1038/nsmb.2428
[10]

Fatica A, Bozzoni I. 2014. Long non-coding RNAs: new players in cell differentiation and development. Nature Reviews Genetics 15:7−21

doi: 10.1038/nrg3606
[11]

Zhang H, Guo H, Hu W, Ji W. 2020. The emerging role of long non-coding RNAs in plant defense against fungal stress. International Journal of Molecular Sciences 21:2659

doi: 10.3390/ijms21082659
[12]

Zhao X, Li J, Lian B, Gu H, Li Y, et al. 2018. Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nature Communications 9:5056

doi: 10.1038/s41467-018-07500-7
[13]

Wang Y, Luo X, Sun F, Hu J, Zha X, et al. 2018. Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice. Nature Communications 9:3516

doi: 10.1038/s41467-018-05829-7
[14]

Zhou Y, Zhang Y, Sun Y, Yu Y, Lei M, et al. 2021. The parent-of-origin lncRNA MISSEN regulates rice endosperm development. Nature Communications 12:6525

doi: 10.1038/s41467-021-26795-7
[15]

Song X, Hu J, Wu T, Yang Q, Feng X, et al. 2021. Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage. Horticulture Research 8:48

doi: 10.1038/s41438-021-00484-4
[16]

Ulitsky I, Bartel DP. 2013. lincRNAs: genomics, evolution, and mechanisms. Cell 154:26−46

doi: 10.1016/j.cell.2013.06.020
[17]

Liu X, Hao L, Li D, Zhu L, Hu S. 2015. Long non-coding RNAs and their biological roles in plants. Genomics, Proteomics & Bioinformatics 13:137−47

doi: 10.1016/j.gpb.2015.02.003
[18]

Fabbri M, Girnita L, Varani G, Calin GA. 2019. Decrypting noncoding RNA interactions, structures, and functional networks. Genome Research 29:1377−88

doi: 10.1101/gr.247239.118
[19]

Carlevaro-Fita J, Johnson R. 2019. Global Positioning System: Understanding long noncoding RNAs through subcellular localization. Molecular Cell 73:869−83

doi: 10.1016/j.molcel.2019.02.008
[20]

Kopp F, Mendell JT. 2018. Functional classification and experimental dissection of long noncoding RNAs. Cell 172:393−407

doi: 10.1016/j.cell.2018.01.011
[21]

Wu J, Liu C, Liu Z, Li S, Li D, et al. 2019. Pol III-dependent cabbage BoNR8 long ncRNA affects seed germination and growth in Arabidopsis. Plant & Cell Physiology 60:421−35

doi: 10.1093/pcp/pcy220
[22]

Wang M, Zhao W, Gao L, Zhao L. 2018. Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening. BMC Plant Biology 18:75

doi: 10.1186/s12870-018-1300-y
[23]

Chen L, Zhu QH, Kaufmann K. 2020. Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses. Planta 252:92

doi: 10.1007/s00425-020-03480-5
[24]

Mehraj H, Shea DJ, Takahashi S, Miyaji N, Akter A, et al. 2021. Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa. PLoS One 16:e0242530

doi: 10.1371/journal.pone.0242530
[25]

Deng P, Liu S, Nie X, Song W, Wu L. 2018. Conservation analysis of long non-coding RNAs in plants. Science China Life Sciences 61:190−98

doi: 10.1007/s11427-017-9174-9
[26]

van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. 2014. Ten years of next-generation sequencing technology. Trends in Genetics 30:418−26

doi: 10.1016/j.tig.2014.07.001
[27]

Ilott NE, Ponting CP. 2013. Predicting long non-coding RNAs using RNA sequencing. Methods 63:50−59

doi: 10.1016/j.ymeth.2013.03.019
[28]

Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, et al. 2013. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods 10:1177−84

doi: 10.1038/nmeth.2714
[29]

Roberts RJ, Carneiro MO, Schatz MC. 2013. The advantages of SMRT sequencing. Genome Biology 14:405

doi: 10.1186/gb-2013-14-6-405
[30]

van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. 2018. The third revolution in sequencing technology. Trends in Genetics 34:666−81

doi: 10.1016/j.tig.2018.05.008
[31]

Wang B, Tseng E, Regulski M, Clark TA, Hon T, et al. 2016. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nature Communications 7:11708

doi: 10.1038/ncomms11708
[32]

Dong L, Liu H, Zhang J, Yang S, Kong G, et al. 2015. Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research. BMC Genomics 16:1039

doi: 10.1186/s12864-015-2257-y
[33]

Zhu FY, Chen MX, Ye NH, Shi L, Ma KL, et al. 2017. Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. The Plant Journal 91:518−33

doi: 10.1111/tpj.13571
[34]

Tan C, Liu H, Ren J, Ye X, Feng H, et al. 2019. Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC Plant Biol 19:517

doi: 10.1186/s12870-019-2133-z
[35]

Clavijo BJ, Venturini L, Schudoma C, Accinelli GG, Kaithakottil G, et al. 2017. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Research 27:885−96

doi: 10.1101/gr.217117.116
[36]

Zhang L, Hu J, Han X, Li J, Gao Y, et al. 2019. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nature Communications 10:1494

doi: 10.1038/s41467-019-09518-x
[37]

Li N, Meng Z, Tao M, Wang Y, Zhang Y, et al. 2020. Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L. BMC Genomics 21:850

doi: 10.1186/s12864-020-07277-4
[38]

Yu T, Tzeng DTW, Li R, Chen J, Zhong S, et al. 2019. Genome-wide identification of long non-coding RNA targets of the tomato MADS box transcription factor RIN and function analysis. Annals of Botany 123:469−82

doi: 10.1093/aob/mcy178
[39]

Song J, Cao J, Yu X, Xiang X. 2007. BcMF11, a putative pollen-specific non-coding RNA from Brassica campestris ssp chinensis. Journal of Plant Physiology 164:1097−100

doi: 10.1016/j.jplph.2006.10.002
[40]

Song JH, Cao JS, Wang CG. 2013. BcMF11, a novel non-coding RNA gene from Brassica campestris, is required for pollen development and male fertility. Plant Cell Reports 32:21−30

doi: 10.1007/s00299-012-1337-6
[41]

Zuo J, Grierson D, Courtney LT, Wang Y, Gao L, et al. 2020. Relationships between genome methylation, levels of non-coding RNAs, mRNAs and metabolites in ripening tomato fruit. The Plant Journal 103:980−94

doi: 10.1111/tpj.14778
[42]

Liu T, Wu P, Wang Q, Wang W, Zhang C, et al. 2018. Comparative transcriptome discovery and elucidation of the mechanism of long noncoding RNAs during vernalization in Brassica rapa. Plant Growth Regulation 85:27−39

doi: 10.1007/s10725-018-0371-y
[43]

Huang L, Dong H, Zhou D, Li M, Liu Y, et al. 2018. Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. The Plant Journal 96:203−22

doi: 10.1111/tpj.14016
[44]

Zhou Y, Mumtaz MA, Zhang Y, Yang Z, Hao Y, et al. 2022. Response of anthocyanin biosynthesis to light by strand-specific transcriptome and miRNA analysis in Capsicum annuum. BMC Plant Biology 22:79

doi: 10.1186/s12870-021-03423-6
[45]

Eom SH, Lee HJ, Lee JH, Wi SH, Kim SK, et al. 2019. Identification and functional prediction of drought-responsive long non-coding RNA in tomato. Agronomy 9:629

doi: 10.3390/agronomy9100629
[46]

Wang A, Hu J, Gao C, Chen G, Wang B, et al. 2019. Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp. chinensis). Scientific Reports 9:5002

doi: 10.1038/s41598-019-41428-2
[47]

Wang Y, Gao L, Zhu B, Zhu H, Luo Y, et al. 2018. Integrative analysis of long non-coding RNA acting as ceRNAs involved in chilling injury in tomato fruit. Gene 667:25−33

doi: 10.1016/j.gene.2018.05.030
[48]

Li N, Wang Z, Wang B, Wang J, Xu R, et al. 2022. Identification and characterization of long non-coding RNA in tomato roots under salt stress. Frontiers in Plant Science 13:834027

doi: 10.3389/fpls.2022.834027
[49]

Cao W, Gan L, Wang C, Zhao X, Zhang M, et al. 2021. Genome-wide identification and characterization of potato long non-coding RNAs associated with Phytophthora infestans resistance. Frontiers in Plant Science 12:619062

doi: 10.3389/fpls.2021.619062
[50]

Wang J, Yu W, Yang Y, Li X, Chen T, et al. 2015. Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection. Scientific Reports 5:16946

doi: 10.1038/srep16946
[51]

Zhou C, Zhu J, Qian N, Guo J, Yan C. 2020. Bacillus subtilis SL18r Induces Tomato Resistance Against Botrytis cinerea, Involving Activation of Long Non-coding RNA, MSTRG18363, to Decoy miR1918. Frontiers in Plant Science 11:634819

doi: 10.3389/fpls.2020.634819
[52]

Rosli HG, Sirvent E, Bekier FN, Ramos RN, Pombo MA. 2021. Genome-wide analysis uncovers tomato leaf lncRNAs transcriptionally active upon Pseudomonas syringae pv. tomato challenge. Scientific Reports 11:24523

doi: 10.1038/s41598-021-04005-0
[53]

Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP. 2011. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language. Cell 146:353−58

doi: 10.1016/j.cell.2011.07.014
[54]

Meng X, Li A, Yu B, Li S. 2021. Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation. Computational and Structural Biotechnology Journal 19:2567−74

doi: 10.1016/j.csbj.2021.04.062
[55]

Ameres SL, Horwich MD, Hung JH, Xu J, Ghildiyal M, et al. 2010. Target RNA-directed trimming and tailing of small silencing RNAs. Science 328:1534−39

doi: 10.1126/science.1187058
[56]

Baccarini A, Chauhan H, Gardner TJ, Jayaprakash AD, Sachidanandam R, Brown BD. 2011. Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells. Current Biology 21:369−76

doi: 10.1016/j.cub.2011.01.067
[57]

Xie J, Ameres SL, Friedline R, Hung JH, Zhang Y, et al. 2012. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nature Methods 9:403−9

doi: 10.1038/nmeth.1903
[58]

Yan J, Gu Y, Jia X, Kang W, Pan S, et al. 2012. Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis. The Plant Cell 24:415−27

doi: 10.1105/tpc.111.094144
[59]

Mei J, Jiang N, Ren G. 2019. The F-box protein HAWAIIAN SKIRT is required for mimicry target-induced microRNA degradation in Arabidopsis. Journal of Integrative Plant Biology 61:1121−27

doi: 10.1111/jipb.12761
[60]

Wang J, Feng Y, Ding X, Huo J, Nie W. 2021. Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing. Horticulturae 7:522

doi: 10.3390/horticulturae7120522
[61]

Zhu B, Yang Y, Li R, Fu D, Wen L, et al. 2015. RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening. Journal of Experimental Botany 66:4483−95

doi: 10.1093/jxb/erv203
[62]

Li R, Fu D, Zhu B, Luo Y, Zhu H. 2018. CRISPR/Cas9-mediated mutagenesis of lncRNA1459 alters tomato fruit ripening. The Plant Journal 94:513−24

doi: 10.1111/tpj.13872
[63]

Xiao Y, Kang B, Li M, Xiao L, Xiao H, et al. 2020. Transcription of lncRNA ACoS-AS1 is essential to trans-splicing between SlPsy1 and ACoS-AS1 that causes yellow fruit in tomato. RNA Biology 17:596−607

doi: 10.1080/15476286.2020.1721095
[64]

Yang S, Yang T, Tang Y, Aisimutuola P, Zhang G, et al. 2020. Transcriptomic profile analysis of non-coding RNAs involved in Capsicum chinense Jacq. fruit ripening. Scientia Horticulturae 264:109158

doi: 10.1016/j.scienta.2019.109158
[65]

Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, et al. 2019. Network analysis of noncoding RNAs in pepper provides insights into fruit ripening control. Scientific Reports 9:8734

doi: 10.1038/s41598-019-45427-1
[66]

Ou L, Liu Z, Zhang Z, Wei G, Zhang Y, et al. 2017. Noncoding and coding transcriptome analysis reveals the regulation roles of long noncoding RNAs in fruit development of hot pepper (Capsicum annuum L.). Plant Growth Regulation 83:141−56

doi: 10.1007/s10725-017-0290-3
[67]

Bouché F, Woods DP, Amasino RM. 2017. Winter memory throughout the plant kingdom: different paths to flowering. Plant Physiology 173:27−35

doi: 10.1104/pp.16.01322
[68]

Shea DJ, Nishida N, Takada S, Itabashi E, Takahashi S, et al. 2019. Long noncoding RNAs in Brassica rapa L. following vernalization. Scientific Reports 9:9302

doi: 10.1038/s41598-019-45650-w
[69]

Shi F, Xu H, Liu C, Tan C, Ren J, et al. 2021. Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis). BMC Genomics 22:819

doi: 10.1186/s12864-021-08110-2
[70]

Mayr E. 1986. Joseph Gottlieb Kolreuter's contributions to biology. Osiris 2:135−76

doi: 10.1086/368655
[71]

Chen L, Liu YG. 2014. Male sterility and fertility restoration in crops. Annual Review of Plant Biology 65:579−606

doi: 10.1146/annurev-arplant-050213-040119
[72]

Shi F, Pang Z, Liu C, Zhou L, Tan C, et al. 2022. Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis). Scientific Reports 12:2667

doi: 10.1038/s41598-022-06556-2
[73]

Zhou D, Chen C, Jin Z, Chen J, Lin S, et al. 2022. Transcript profiling analysis and ncRNAs' identification of male-sterile systems of Brassica campestris reveal new insights into the mechanism underlying anther and pollen development. Frontiers in Plant Science 13:806865

doi: 10.3389/fpls.2022.806865
[74]

Li P, Zhang D, Su T, Wang W, Yu Y, et al. 2020. Genome-wide analysis of mRNA and lncRNA expression and mitochondrial genome sequencing provide insights into the mechanisms underlying a novel cytoplasmic male sterility system, BVRC-CMS96, in Brassicarapa. Theoretical and Applied Genetics 133:2157−70

doi: 10.1007/s00122-020-03587-z
[75]

Lv J, Liu Z, Yang B, Deng M, Wang J, et al. 2020. Systematic identification and characterization of long non-coding RNAs involved in cytoplasmic male sterility in pepper (Capsicum annuum L.). Plant Growth Regulation 91:277−88

doi: 10.1007/s10725-020-00605-4
[76]

Liu L, Lu Y, Wei L, Yu H, Cao Y, et al. 2018. Transcriptomics analyses reveal the molecular roadmap and long non-coding RNA landscape of sperm cell lineage development. The Plant Journal 96:421−37

doi: 10.1111/tpj.14041
[77]

He J, Giusti MM. 2010. Anthocyanins: natural colorants with health-promoting properties. Annual Review of Food Science and Technology 1:163−87

doi: 10.1146/annurev.food.080708.100754
[78]

Mattioli R, Francioso A, Mosca L, Silva P. 2020. Anthocyanins: A comprehensive review of their chemical properties and health effects on cardiovascular and neurodegenerative diseases. Molecules 25:3809

doi: 10.3390/molecules25173809
[79]

Jaakola L. 2013. New insights into the regulation of anthocyanin biosynthesis in fruits. Trends in Plant Science 18:477−83

doi: 10.1016/j.tplants.2013.06.003
[80]

Tang R, Dong H, Wu W, Zhao C, Jia X, et al. 2021. A comparative transcriptome analysis of purple and yellow fleshed potato tubers reveals long non-coding RNAs and their targets functioned in anthocyanin biosynthesis. Preprint

doi: 10.21203/rs.3.rs-515121/v1
[81]

Bao Y, Nie T, Wang D, Chen Q. 2022. Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression. BMC Plant Biology 22:1

doi: 10.1186/s12870-021-03391-x
[82]

Chialva C, Blein T, Crespi M, Lijavetzky D. 2021. Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation. Scientific Reports 11:4093

doi: 10.1038/s41598-021-83514-4
[83]

Liao X, Wang J, Zhu S, Xie Q, Wang L, et al. 2020. Transcriptomic and functional analyses uncover the regulatory role of lncRNA000170 in tomato multicellular trichome formation. The Plant Journal 104:18−29

doi: 10.1111/tpj.14902
[84]

Sonnewald S, Sonnewald U. 2014. Regulation of potato tuber sprouting. Planta 239:27−38

doi: 10.1007/s00425-013-1968-z
[85]

Kolachevskaya OO, Lomin SN, Arkhipov DV, Romanov GA. 2019. Auxins in potato: molecular aspects and emerging roles in tuber formation and stress resistance. Plant Cell Reports 38:681−98

doi: 10.1007/s00299-019-02395-0
[86]

Li L, Deng M, Lyu C, Zhang J, Peng J, et al. 2020. Quantitative phosphoproteomics analysis reveals that protein modification and sugar metabolism contribute to sprouting in potato after BR treatment. Food Chemistry 325:126875

doi: 10.1016/j.foodchem.2020.126875
[87]

Hou X, Du Y, Liu X, Zhang H, Liu Y, et al. 2017. Genome-wide analysis of long non-coding RNAs in potato and their potential role in tuber sprouting process. International Journal of Molecular Sciences 19:101

doi: 10.3390/ijms19010101
[88]

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
[89]

Ghorbani F, Abolghasemi R, Haghighi M, Etemadi N, Wang S, et al. 2021. Global identification of long non-coding RNAs involved in the induction of spinach flowering. BMC Genomics 22:704

doi: 10.1186/s12864-021-07989-1
[90]

Shen E, Zhu X, Hua S, Chen H, Ye C, et al. 2018. Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus. BMC Genomics 19:745

doi: 10.1186/s12864-018-5117-8
[91]

Zhu X, Tai X, Ren Y, Chen J, Bo T. 2019. Genome-wide analysis of coding and long non-coding RNAs involved in cuticular wax biosynthesis in cabbage (Brassica oleracea L. var. capitata). International Journal of Molecular Sciences 20:2820

doi: 10.3390/ijms20112820
[92]

Zhu J. 2016. Abiotic Stress Signaling and Responses in Plants. Cell 167:313−24

doi: 10.1016/j.cell.2016.08.029
[93]

Zandalinas SI, Mittler R. 2022. Plant responses to multifactorial stress combination. New Phytologist 234:1161−67

doi: 10.1111/nph.18087
[94]

Markham KK, Greenham K. 2021. Abiotic stress through time. New Phytologist 231:40−46

doi: 10.1111/nph.17367
[95]

Waititu JK, Zhang C, Liu J, Wang H. 2020. Plant non-coding RNAs: origin, biogenesis, mode of action and their roles in abiotic stress. International Journal of Molecular Sciences 21:8401

doi: 10.3390/ijms21218401
[96]

Li Y, Li X, Yang J, He Y. 2020. Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance. Nature Communications 11:5351

doi: 10.1038/s41467-020-19186-x
[97]

Di C, Yuan J, Wu Y, Li J, Lin H, et al. 2014. Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. The Plant Journal 80:848−61

doi: 10.1111/tpj.12679
[98]

Kindgren P, Ard R, Ivanov M, Marquardt S. 2018. Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation. Nature Communications 9:4561

doi: 10.1038/s41467-018-07010-6
[99]

Qin T, Zhao H, Cui P, Albesher N, Xiong L. 2017. A nucleus-localized long non-coding RNA enhances drought and salt stress tolerance. Plant Physiology 175:1321−36

doi: 10.1104/pp.17.00574
[100]

Ullah A, Sun H, Yang X, Zhang X. 2017. Drought coping strategies in cotton: increased crop per drop. Plant Biotechnology Journal 15:271−84

doi: 10.1111/pbi.12688
[101]

Yang SJ, Vanderbeld B, Wan JX, Huang YF. 2010. Narrowing Down the Targets: Towards Successful Genetic Engineering of Drought-Tolerant Crops. Molecular Plant 3:469−90

doi: 10.1093/mp/ssq016
[102]

McDowell N, Pockman WT, Allen CD, Breshears DD, Cobb N, et al. 2008. Mechanisms of plant survival and mortality during drought: why do some plants survive while others succumb to drought. New Phytologist 178:719−39

doi: 10.1111/j.1469-8137.2008.02436.x
[103]

Lamin-Samu AT, Zhuo S, Ali M, Lu G. 2022. Long non-coding RNA transcriptome landscape of anthers at different developmental stages in response to drought stress in tomato. Genomics 114:110383

doi: 10.1016/j.ygeno.2022.110383
[104]

Tan X, Li S, Hu L, Zhang C. 2020. Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering. BMC Plant Biol 20:81

doi: 10.1186/s12870-020-2286-9
[105]

Jian H, Sun H, Liu R, Zhang W, Shang L, et al. 2022. Construction of drought stress regulation networks in potato based on SMRT and RNA sequencing data. Preprint

doi: 10.21203/rs.3.rs-1456188/v1
[106]

Eom SH, Lee HJ, Wi SH, Kim SK, Hyun TK. 2021. Identification and functional prediction of long non-coding RNAs responsive to heat stress in heading type Chinese cabbage. Zemdirbyste-Agriculture 108:371−76

doi: 10.13080/z-a.2021.108.047
[107]

Bhatia G, Singh A, Verma D, Sharma S, Singh K. 2020. Genome-wide investigation of regulatory roles of lncRNAs in response to heat and drought stress in Brassica juncea (Indian mustard). Environmental and Experimental Botany 171:103922

doi: 10.1016/j.envexpbot.2019.103922
[108]

Song X, Liu G, Huang Z, Duan W, Tan H, et al. 2016. Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage. BMC Genomics 17:297

doi: 10.1186/s12864-016-2625-2
[109]

He X, Guo S, Wang Y, Wang L, Shu S, et al. 2020. Systematic identification and analysis of heat-stress-responsive lncRNAs, circRNAs and miRNAs with associated co-expression and ceRNA networks in cucumber (Cucumis sativus L.). Physiologia Plantarum 168:736−54

doi: 10.1111/ppl.12997
[110]

Yang Z, Li W, Su X, Ge P, Zhou Y, et al. 2019. Early Response of Radish to Heat Stress by Strand-Specific Transcriptome and miRNA Analysis. Int J Mol Sci 20:3321

doi: 10.3390/ijms20133321
[111]

Zuo J, Wang Y, Zhu B, Luo Y, Wang Q, et al. 2018. Analysis of the coding and non-coding RNA transcriptomes in response to bell pepper chilling. International Journal of Molecular Sciences 19:2001

doi: 10.3390/ijms19072001
[112]

Xue L, Sun M, Wu Z, Yu L, Yu Q, et al. 2020. LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network. BMC Plant Biology 20:162

doi: 10.1186/s12870-020-02373-9
[113]

Crawford RMM. 1992. Oxygen availability as an ecological limit to plant distribution. Advances in Ecological Research 23:93−185

doi: 10.1016/S0065-2504(08)60147-6
[114]

Sairam RK, Kumutha D, Ezhilmathi K, Deshmukh PS, Srivastava GC. 2008. Physiology and biochemistry of waterlogging tolerance in plants. Biologia Plantarum 52:401−12

doi: 10.1007/s10535-008-0084-6
[115]

Kęska K, Szcześniak MW, Adamus A, Czernicka M. 2021. Waterlogging-stress-responsive LncRNAs, their regulatory relationships with miRNAs and target genes in cucumber (Cucumis sativus L.). International Journal of Molecular Sciences 22:8197

doi: 10.3390/ijms22158197
[116]

Meharg A. 2012. Marschner's Mineral Nutrition of Higher Plants. Ed. Marschner P. Third Edition. Amsterdam, Netherlands: Academic Press, Elsevier. 684 pp

[117]

Schroeder JI, Delhaize E, Frommer WB, Guerinot ML, Harrison MJ, et al. 2013. Using membrane transporters to improve crops for sustainable food production. Nature 497:60−66

doi: 10.1038/nature11909
[118]

Zhang Z, Liao H, Lucas WJ. 2014. Molecular mechanisms underlying phosphate sensing, signaling, and adaptation in plants. Journal of Integrative Plant Biology 56:192−220

doi: 10.1111/jipb.12163
[119]

Puga MI, Rojas-Triana M, de Lorenzo L, Leyva A, Rubio V, et al. 2017. Novel signals in the regulation of Pi starvation responses in plants: facts and promises. Current Opinion in Biotechnology 39:40−49

doi: 10.1016/j.pbi.2017.05.007
[120]

Ham BK, Chen J, Yan Y, Lucas WJ. 2018. Insights into plant phosphate sensing and signaling. Current Opinion in Plant Biology 49:1−9

doi: 10.1016/j.copbio.2017.07.005
[121]

Zhang Z, Zheng Y, Ham BK, Zhang S, Fei Z, et al. 2019. Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency. Journal of Integrative Plant Biology 61:492−508

doi: 10.1111/jipb.12715
[122]

Genchi G, Sinicropi MS, Lauria G, Carocci A, Catalano A. 2020. The effects of cadmium toxicity. International Journal of Environmental Research and Public Health 17:3782

doi: 10.3390/ijerph17113782
[123]

Tchounwou PB, Yedjou CG, Patlolla AK, Sutton DJ. 2012. Heavy metal toxicity and the environment. In: Molecular, Clinical and Environmental Toxicology. Experientia Supplementum, ed. Luch, A. Vol 101. Basel: Springer. pp 133–64. https://doi.org/10.1007/978-3-7643-8340-4_6

[124]

Sanità di Toppi L, Gabbrielli R. 1999. Response to cadmium in higher plants. Environmental and Experimental Botany 41:105−30

doi: 10.1016/S0098-8472(98)00058-6
[125]

Huybrechts M, Cuypers A, Deckers J, Iven V, Vandionant S, et al. 2019. Cadmium and plant development: An agony from seed to seed. International Journal of Molecular Sciences 20:3971

doi: 10.3390/ijms20163971
[126]

Feng S, Zhang X, Liu X, Tan S, Chu S, et al. 2016. Characterization of long non-coding RNAs involved in cadmium toxic response in Brassica napus. RSC Advances 6:82157−73

doi: 10.1039/C6RA05459E
[127]

Chen L, Wang Q, Zhou L, Ren F, Li D, et al. 2013. Arabidopsis CBL-interacting protein kinase (CIPK6) is involved in plant response to salt/osmotic stress and ABA. Molecular Biology Reports 40:4759−67

doi: 10.1007/s11033-013-2572-9
[128]

Takemoto D, Shibata Y, Ojika M, Mizuno Y, Imano S, et al. 2018. Resistance to Phytophthora infestans: exploring genes required for disease resistance in Solanaceae plants. Journal of General Plant Pathology 84:312−20

doi: 10.1007/s10327-018-0801-8
[129]

Ivanov AA, Ukladov EO, Golubeva TS. 2021. Phytophthora infestans: An overview of methods and attempts to combat late blight. Journal of Fungi 7:1071

doi: 10.3390/jof7121071
[130]

Cui J, Luan Y, Jiang N, Bao H, Meng J. 2017. Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co-expressing glutaredoxin. The Plant Journal 89:577−89

doi: 10.1111/tpj.13408
[131]

Cui J, Jiang N, Hou X, Wu S, Zhang Q, et al. 2020. Genome-wide identification of lncRNAs and analysis of ceRNA networks during tomato resistance to Phytophthora infestans. Phytopathology 110:456−64

doi: 10.1094/phyto-04-19-0137-r
[132]

Cui J, Jiang N, Meng J, Yang G, Liu W, et al. 2019. LncRNA33732-respiratory burst oxidase module associated with WRKY1 in tomato-Phytophthora infestans interactions. The Plant Journal 97:933−46

doi: 10.1111/tpj.14173
[133]

Jiang N, Cui J, Hou X, Yang G, Xiao Y, et al. 2020. Sl-lncRNA15492 interacts with Sl-miR482a and affects Solanum lycopersicum immunity against Phytophthora infestans. The Plant Journal 103:1561−74

doi: 10.1111/tpj.14847
[134]

Liu W, Cui J, Luan Y. 2022. Overexpression of lncRNA08489 enhances tomato immunity against Phytophthora infestans by decoying miR482e-3p. Biochemical and Biophysical Research Communications 587:36−41

doi: 10.1016/j.bbrc.2021.11.079
[135]

Jiang N, Cui J, Shi Y, Yang G, Zhou X, et al. 2019. Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction. Horticulture Research 6:28

doi: 10.1038/s41438-018-0096-0
[136]

Hou X, Cui J, Liu W, Jiang N, Zhou X, et al. 2020. LncRNA39026 enhances tomato resistance to Phytophthora infestans by decoying miR168a and inducing PR gene expression. Phytopathology 110:873−80

doi: 10.1094/PHYTO-12-19-0445-R
[137]

Zhang Y, Hong Y, Liu Y, Cui J, Luan Y. 2021. Function identification of miR394 in tomato resistance to Phytophthora infestans. Plant Cell Reports 40:1831−44

doi: 10.1007/s00299-021-02746-w
[138]

Wang J, Yang Y, Jin L, Ling X, Liu T, et al. 2018. Re-analysis of long non-coding RNAs and prediction of circRNAs reveal their novel roles in susceptible tomato following TYLCV infection. BMC Plant Biology 18:104

doi: 10.1186/s12870-018-1332-3
[139]

Yang Y, Liu T, Shen D, Wang J, Ling X, et al. 2019. Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms. PLoS Pathogens 15:e1007534

doi: 10.1371/journal.ppat.1007534
[140]

Yang F, Zhao D, Fan H, Zhu X, Wang Y, et al. 2020. Functional analysis of long non-coding RNAs reveal their novel roles in biocontrol of bacteria-induced tomato resistance to Meloidogyne incognita. International Journal of Molecular Sciences 21:911

doi: 10.3390/ijms21030911
[141]

Zheng Y, Wang Y, Ding B, Fei Z. 2017. Comprehensive transcriptome analyses reveal that potato spindle tuber viroid triggers genome-wide changes in alternative splicing, inducible trans-acting activity of phased secondary small interfering RNAs, and immune responses. Journal of Virology 91:e00247-17

doi: 10.1128/jvi.00247-17
[142]

Joshi RK, Megha S, Basu U, Rahman MH, Kav NN. 2016. Genome wide identification and functional prediction of long non-coding RNAs responsive to Sclerotinia sclerotiorum infection in Brassica napus. PLoS One 11:e0158784

doi: 10.1371/journal.pone.0158784
[143]

Zhu H, Li X, Xi D, Zhai W, Zhang Z, et al. 2019. Integrating long noncoding RNAs and mRNAs expression profiles of response to Plasmodiophora brassicae infection in Pakchoi (Brassica campestris ssp. chinensis Makino). PLoS One 14:e0224927

doi: 10.1371/journal.pone.0224927
[144]

Summanwar A, Basu U, Rahman H, Kav N. 2019. Identification of lncRNAs responsive to infection by Plasmodiophora brassicae in clubroot-susceptible and -resistant Brassica napus lines carrying resistance introgressed from rutabaga. Molecular Plant-Microbe Interactions 32:1360−77

doi: 10.1094/MPMI-12-18-0341-R
[145]

Zhang B, Su T, Li P, Xin X, Cao Y, et al. 2021. Identification of long noncoding RNAs involved in resistance to downy mildew in Chinese cabbage. Horticulture Research 8:44

doi: 10.1038/s41438-021-00479-1
[146]

Akter MA, Mehraj H, Miyaji N, Takahashi S, Takasaki-Yasuda T, et al. 2022. Transcriptional association between mRNAs and their paired natural antisense transcripts following Fusarium oxysporum inoculation in Brassica rapa L. Horticulturae 8:17

doi: 10.3390/horticulturae8010017
[147]

Yin J, Yan J, Hou L, Jiang L, Xian W, et al. 2021. Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici. BMC Genomics 22:868

doi: 10.1186/s12864-021-08183-z
[148]

Kwenda S, Birch PRJ, Moleleki LN. 2016. Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection. BMC Genomics 17:614

doi: 10.1186/s12864-016-2967-9
[149]

Glushkevich A, Spechenkova N, Fesenko I, Knyazev A, Samarskaya V, et al. 2022. Transcriptomic reprogramming, alternative splicing and RNA methylation in potato (Solanum tuberosum L.) plants in response to potato virus Y infection. Plants 11:635

doi: 10.3390/plants11050635
[150]

Nie J, Wang H, Zhang W, Teng X, Yu C, et al. 2021. Characterization of lncRNAs and mRNAs involved in powdery mildew resistance in cucumber. Phytopathology 111:1613−24

doi: 10.1094/PHYTO-11-20-0521-R
[151]

Wang Y, Gao L, Li J, Zhu B, Zhu H, et al. 2018. Analysis of long-non-coding RNAs associated with ethylene in tomato. Gene 674:151−60

doi: 10.1016/j.gene.2018.06.089
[152]

Wang X, Ai G, Zhang C, Cui L, Wang J, et al. 2016. Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato. New Phytologist 209:1442−55

doi: 10.1111/nph.13718
[153]

Zhang J, Wei L, Jiang J, Mason AS, Li H, et al. 2018. Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species. Scientific Reports 8:4960

doi: 10.1038/s41598-018-23334-1
[154]

Shu HY, Zhou H, Mu HL, Wu SH, Jiang YL, et al. 2021. Integrated analysis of mRNA and non-coding RNA transcriptome in pepper (Capsicum chinense) hybrid at seedling and flowering stages. Frontiers in Genetics 12:685788

doi: 10.3389/fgene.2021.685788
[155]

Wang P, Yu X, Zhu Z, Zhai Y, Zhao Q, et al. 2020. Global profiling of lncRNAs expression responsive to allopolyploidization in Cucumis. Genes 11:1500

doi: 10.3390/genes11121500
[156]

Wang R, Zou J, Meng J, Wang J. 2018. Integrative analysis of genome-wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids. Ecology and Evolution 8:6034−52

doi: 10.1002/ece3.4152
[157]

Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10:57−63

doi: 10.1038/nrg2484
[158]

Jiang Q, Ma R, Wang J, Wu X, Jin S, et al. 2015. LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC Genomics 16:S2

doi: 10.1186/1471-2164-16-s3-s2
[159]

Liu J, Wang H, Chua NH. 2015. Long noncoding RNA transcriptome of plants. Plant Biotechnology Journal 13:319−28

doi: 10.1111/pbi.12336
[160]

Bai Y, Dai X, Harrison AP, Chen M. 2015. RNA regulatory networks in animals and plants: a long noncoding RNA perspective. Briefings in Functional Genomics 14:91−101

doi: 10.1093/bfgp/elu017
[161]

Waseem M, Liu Y, Xia R. 2020. Long non-coding RNAs, the dark matter: An emerging regulatory component in plants. International Journal of Molecular Sciences 22:86

doi: 10.3390/ijms22010086
[162]

Rosenlund IA, Calin GA, Dragomir MP, Knutsen E. 2021. CRISPR/Cas9 to Silence Long Non-Coding RNAs. In Long Non-Coding RNAs in Cancer. Methods in Molecular Biology, ed. Navarro A. New York: Humana. pp. 175−87 https://doi.org/10.1007/978-1-0716-1581-2_12

[163]

Zhu S, Li W, Liu J, Chen CH, Liao Q, et al. 2016. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nature Biotechnology 34:1279−86

doi: 10.1038/nbt.3715
[164]

Huang W, Li H, Yu Q, Xiao W, Wang DO. 2022. LncRNA-mediated DNA methylation: an emerging mechanism in cancer and beyond. Journal of Experimental & Clinical Cancer Research 41:100

doi: 10.1186/s13046-022-02319-z
[165]

Qian X, Zhao J, Yeung PY, Zhang QC, Kwok CK. 2019. Revealing lncRNA structures and interactions by sequencing-based approaches. Trends in Biochemical Sciences 44:33−52

doi: 10.1016/j.tibs.2018.09.012
[166]

Ferrè F, Colantoni A, Helmer-Citterich M. 2016. Revealing protein–lncRNA interaction. Briefings in Bioinformatics 17:106−16

doi: 10.1093/bib/bbv031
[167]

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
[168]

Liu Y, Ke L, Wu G, Xu Y, Wu X, et al. 2017. miR3954 is a trigger of phasiRNAs that affects flowering time in citrus. The Plant Journal 92:263−75

doi: 10.1111/tpj.13650
[169]

Sun Y, Hao P, Lv X, Tian J, Wang Y, et al. 2020. A long non-coding apple RNA, MSTRG. 85814.11, acts as a transcriptional enhancer of SAUR32 and contributes to the Fe-deficiency response. The Plant Journal 103:53−67

doi: 10.1111/tpj.14706
[170]

Hu R, Sun X. 2016. lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics. Journal of Bioinformatics and Computational Biology 14:1650016

doi: 10.1142/s0219720016500165
[171]

Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A. 2016. spongeScan: A web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Research 44:W176−W180

doi: 10.1093/nar/gkw443
[172]

Jiang Q, Wang J, Wang Y, Ma R, Wu X, Li Y. 2014. TF2LncRNA: identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data. Biomed Research International 2014:317642

doi: 10.1155/2014/317642
[173]

Huang HY, Chien CH, Jen KH, Huang HD. 2006. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Research 34:W429−W434

doi: 10.1093/nar/gkl333
[174]

Graf J, Kretz M. 2020. From structure to function: Route to understanding lncRNA mechanism. BioEssays 42:2000027

doi: 10.1002/bies.202000027
[175]

Diederichs S. 2014. The four dimensions of noncoding RNA conservation. Trends in Genetics 30:121−23

doi: 10.1016/j.tig.2014.01.004