INVITED REVIEWS
Recent Advances of Non-coding RNA in Plant Growth, Development and Stress Response
- 1National Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
2National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
3Key Laboratory of Bioengineering for Tree and Flower Breeding, State Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
4College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
5Natural Resources and Planning Bureau of Weishan County, Jining 277600, China
Received date: 2024-03-18
Accepted date: 2024-06-21
Online published: 2024-06-26
Abstract
Non-coding RNA (ncRNA) is a class of RNA molecules that do not have the ability of protein coding but have a variety of biological functions, and widely exist in various organisms. With the continuous improvement of high-throughput sequencing technology, a large number of ncRNAs have been identified, and their functions and mechanisms of action are gradually being elucidated. A large number of studies have shown that ncRNAs play an important role in plant growth, development and response to stress. Although there are many reviews on the regulation of plant growth, development and stress response by a certain class of ncRNAs, it still lacks systematic and comprehensive summaries for all ncRNAs. This review first briefly introduced the classification and characterization of non-coding RNAs, followed by a focus on their roles in various stages of plant growth and development, such as seed dormancy and germination, root and leaf growth and development, flower and fruit development, fruit ripening. Furthermore, we summarized the functions and mechanisms of ncRNAs in response to stress. This review provides some theoretical references for improving varieties and improving the yield and quality of agricultural and forestry production.
Key words： miRNA; circRNA; lncRNA; growth and development; stress response
Cite this article
Lu Duxian , Zhang Yanyan , Liu Yan , Li Yanjun , Zuo Xinxiu , Lin Jinxing , Cui Yaning . Recent Advances of Non-coding RNA in Plant Growth, Development and Stress Response[J]. Chinese Bulletin of Botany, 2024 , 59(5) : 709 -725 . DOI: 10.11983/CBB24043
References
| [1] | Achard P, Herr A, Baulcombe DC, Harberd NP (2004). Modulation of floral development by a gibberellin-regulated microRNA. Development 131, 3357-3365. |
| [2] | Ai G, Li TL, Zhu H, Dong XH, Fu XW, Xia CY, Pan WY, Jing MF, Shen DY, Xia A, Tyler BM, Dou DL (2023). BPL3 binds the long non-coding RNA nalncFL7 to suppress FORKED-LIKE7 and modulate HAI1-mediated MPK3/6 dephosphorylation in plant immunity. Plant Cell 35, 598- 616. |
| [3] | Bao ML, Bian HW, Zha YL, Li FY, Sun YZ, Bai B, Chen ZH, Wang JH, Zhu MY, Han N (2014). miR396a-mediated basic helix-loop-helix transcription factor bHLH74 repression acts as a regulator for root growth in Arabidopsis seedlings. Plant Cell Physiol 55, 1343-1353. |
| [4] | Bernardi Y, Ponso MA, Belén F, Vegetti AC, Dotto MC (2022). MicroRNA miR394 regulates flowering time in Arabidopsis thaliana. Plant Cell Rep 41, 1375-1388. |
| [5] | Cao DC, Xu HM, Zhao YY, Deng X, Liu YX, Soppe WJJ, Lin JX (2016). Transcriptome and degradome sequencing reveals dormancy mechanisms of Cunninghamia lanceolata seeds. Plant Physiol 172, 2347-2362. |
| [6] | Cao ZY, Zhao T, Wang LY, Han J, Chen JW, Hao YP, Guan XY (2021). The lincRNA XH123 is involved in cotton cold-stress regulation. Plant Mol Biol 106, 521-531. |
| [7] | Chen J, Liu Q, Yuan LY, Shen WZ, Shi QX, Qi GJ, Chen T, Zhang ZF (2023a). Osa-miR162a enhances the resistance to the brown planthopper via α-linolenic acid metabolism in rice (Oryza sativa). J Agric Food Chem 71, 11847-11859. |
| [8] | Chen L, Luan YS, Zhai JM (2015). Sp-miR396a-5p acts as a stress-responsive genes regulator by conferring tolerance to abiotic stresses and susceptibility to Phytophthora nicotianae infection in transgenic tobacco. Plant Cell Rep 34, 2013-2025. |
| [9] | Chen L, Zhang P, Fan Y, Lu Q, Li Q, Yan JB, Muehlbauer GJ, Schnable PS, Dai MQ, Li L (2018). Circular RNAs mediated by transposons are associated with transcriptomic and phenotypic variation in maize. New Phytol 217, 1292-1306. |
| [10] | Chen YQ, Lu J, Wang WN, Fan CG, Yuan GZ, Sun JJ, Liu JY, Wang CQ (2023b). Rose long noncoding RNA lncWD83 promotes flowering by modulating ubiquitination of the floral repressor RcMYC2L. Plant Physiol 193, 2573- 2591. |
| [11] | Cheng JP, Zhang Y, Li ZW, Wang TY, Zhang XT, Zheng BL (2018). A lariat-derived circular RNA is required for plant development in Arabidopsis. Sci China Life Sci 61, 204-213. |
| [12] | Chung PJ, Park BS, Wang H, Liu J, Jang IC, Chua NH (2016). Light-inducible MiR163 targets PXMT1 transcripts to promote seed germination and primary root elongation in Arabidopsis. Plant Physiol 170, 1772-1782. |
| [13] | Conn VM, Hugouvieux V, Nayak A, Conos SA, Capovilla G, Cildir G, Jourdain A, Tergaonkar V, Schmid M, Zubieta C, Conn SJ (2017). A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants 3, 17053. |
| [14] | Cui J, Jiang N, Meng J, Yang GL, Liu WW, Zhou XX, Ma N, Hou XX, Luan YS (2019). LncRNA33732-respiratory burst oxidase module associated with WRKY1 in tomato- Phytophthora infestans interactions. Plant J 97, 933-946. |
| [15] | Cuperus JT, Fahlgren N, Carrington JC (2011). Evolution and functional diversification of MIRNA genes. Plant Cell 23, 431-442. |
| [16] | Du QG, Wang K, Zou C, Xu C, Li WX (2018). The PILNCR1-miR399 regulatory module is important for low phosphate tolerance in maize. Plant Physiol 177, 1743-1753. |
| [17] | Fan J, Quan WL, Li GB, Hu XH, Wang Q, Wang H, Li XP, Luo XT, Feng Q, Hu ZJ, Feng H, Pu M, Zhao JQ, Huang YY, Li Y, Zhang Y, Wang WM (2020). circRNAs are involved in the rice-Magnaporthe oryzae interaction. Plant Physiol 182, 272-286. |
| [18] | Fang J, Zhang FT, Wang HR, Wang W, Zhao F, Li ZJ, Sun CH, Chen FM, Xu F, Chang SQ, Wu L, Bu QY, Wang PR, Xie JK, Chen F, Huang XH, Zhang YJ, Zhu XG, Han B, Deng XJ, Chu CC (2019). Ef-cd locus shortens rice maturity duration without yield penalty. Proc Natl Acad Sci USA 116, 18717-18722. |
| [19] | Gao Z, Li J, Luo M, Li H, Chen QJ, Wang L, Song SR, Zhao LP, Xu WP, Zhang CX, Wang SP, Ma C (2019). Characterization and cloning of grape circular RNAs identified the cold resistance-related Vv-circATS1. Plant Physiol 180, 966-985. |
| [20] | Gao ZH, Nie JT, Wang HS (2021). MicroRNA biogenesis in plant. Plant Growth Regul 93, 1-12. |
| [21] | Ghorbani A, Izadpanah K, Peters JR, Dietzgen RG, Mitter N (2018). Detection and profiling of circular RNAs in uninfected and maize Iranian mosaic virus-infected maize. Plant Sci 274, 402-409. |
| [22] | Guo GH, Liu XY, Sun FL, Cao J, Huo N, Wuda B, Xin MM, Hu ZR, Du JK, Xia R, Rossi V, Peng HR, Ni ZF, Sun QX, Yao YY (2018). Wheat miR9678 affects seed germination by generating phased siRNAs and modulating abscisic acid/gibberellin signaling. Plant Cell 30, 796-814. |
| [23] | He ZH, Lan YM, Zhou XK, Yu BJ, Zhu T, Yang F, Fu LY, Chao HY, Wang JH, Feng RX, Zuo SM, Lan WZ, Chen CL, Chen M, Zhao X, Hu KM, Chen DJ (2024). Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis. Plant Commun 5, 100717. |
| [24] | Herbst J, Nagy SH, Vercauteren I, De Veylder L, Kunze R (2023). The long non-coding RNA LINDA restrains cellular collapse following DNA damage in Arabidopsis thaliana. Plant J 116, 1370-1384. |
| [25] | Hu G, Lei Y, Liu JF, Hao MY, Zhang ZN, Tang Y, Chen AM, Wu JH (2020). The ghr-miR164 and GhNAC100 modulate cotton plant resistance against Verticillium dahlia. Plant Sci 293, 110438. |
| [26] | Huang XP, Zhang HY, Guo R, Wang Q, Liu XZ, Kuang WG, Song HY, Liao JL, Huang YJ, Wang ZH (2021). Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice. Planta 253, 26. |
| [27] | Hyun Y, Richter R, Coupland G (2017). Competence to flower: age-controlled sensitivity to environmental cues. Plant Physiol 173, 36-46. |
| [28] | Jia YQ, Zhao HM, Niu YN, Wang YC (2023). Identification of birch lncRNAs and mRNAs responding to salt stress and characterization of functions of lncRNA. Hortic Res 10, uhac277. |
| [29] | Jia YQ, Zhao HM, Niu YN, Wang YC (2024). Long noncoding RNA from Betula platyphylla, BplncSIR1, confers salt tolerance by regulating BpNAC2 to mediate reactive oxygen species scavenging and stomatal movement. Plant Biotechnol J 22, 48-65. |
| [30] | Jiang YL, Li ZW, Liu XZ, Zhu TT, Xie K, Hou QC, Yan TW, Niu CF, Zhang SW, Yang MB, Xie RR, Wang J, Li JP, An XL, Wan XY (2021). ZmFAR1 and ZmABCG26 regulated by microRNA are essential for lipid metabolism in maize anther. Int J Mol Sci 22, 7916. |
| [31] | Jiao P, Ma RQ, Wang CL, Chen NN, Liu SY, Qu J, Guan SY, Ma YY (2022). Integration of mRNA and microRNA analysis reveals the molecular mechanisms underlying drought stress tolerance in maize (Zea mays L.). Front Plant Sci 13, 932667. |
| [32] | Jing WK, Gong FF, Liu GQ, Deng YL, Liu JQ, Yang WJ, Sun XM, Li YH, Gao JP, Zhou XF, Ma N (2023). Petal size is controlled by the MYB73/TPL/HDA19-miR159- CKX6 module regulating cytokinin catabolism in Rosa hybrida. Nat Commun 14, 7106. |
| [33] | Ke LL, Zhou ZW, Xu XW, Wang X, Liu YL, Xu YT, Huang Y, Wang ST, Deng XX, Chen LL, Xu Q (2019). Evolutionary dynamics of lincRNA transcription in nine citrus species. Plant J 98, 912-927. |
| [34] | Komatsu S, Kitai H, Suzuki HI (2023). Network regulation of microRNA biogenesis and target interaction. Cells 12, 306. |
| [35] | Koyama T, Mitsuda N, Seki M, Shinozaki K, Ohme-Takagi M (2010). TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis. Plant Cell 22, 3574-3588. |
| [36] | Koyama T, Sato F, Ohme-Takagi M (2017). Roles of miR319 and TCP transcription factors in leaf development. Plant Physiol 175, 874-885. |
| [37] | Lee RC, Feinbaum RL, Ambros V (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854. |
| [38] | Li BQ, Feng C, Zhang WH, Sun SM, Yue DD, Zhang XL, Yang XY (2023). Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress. Int J Biol Macromol 253, 126558. |
| [39] | Li MZ, Si XY, Liu Y, Liu YC, Cheng X, Dai ZR, Yu XL, Ali M, Lu G (2022a). Transcriptomic analysis of ncRNA and mRNA interactions during leaf senescence in tomato. Int J Biol Macromol 222, 2556-2570. |
| [40] | Li N, Liu TT, Guo F, Yang JW, Shi YG, Wang SG, Sun DZ (2022b). Identification of long non-coding RNA-microRNA-mRNA regulatory modules and their potential roles in drought stress response in wheat (Triticum aestivum L.). Front Plant Sci 13, 1011064. |
| [41] | Li P, Yang H, Wang L, Liu HJ, Huo HQ, Zhang CJ, Liu AZ, Zhu AD, Hu JY, Lin YJ, Liu L (2019). Physiological and transcriptome analyses reveal short-term responses and formation of memory under drought stress in rice. Front Genet 10, 55. |
| [42] | Li W, Chen YD, Wang YL, Zhao J, Wang YJ (2022c). Gypsy retrotransposon-derived maize lncRNA GARR2 modulates gibberellin response. Plant J 110, 1433-1446. |
| [43] | Lin Z, Long JM, Yin Q, Wang B, Li HL, Luo JZ, Wang HC, Wu AM (2019). Identification of novel lncRNAs in Eucalyptus grandis. Ind Crop Prod 129, 309-317. |
| [44] | Liu F, Xu YR, Chang KX, Li SN, Liu ZG, Qi SD, Jia JB, Zhang M, Crawford NM, Wang Y (2019). The long noncoding RNA T5120 regulates nitrate response and assimilation in Arabidopsis. New Phytol 224, 117-131. |
| [45] | Liu H, Yuan K, Hu YY, Wang S, He QG, Feng CT, Liu JP, Wang ZH (2023a). Construction and analysis of the tapping panel dryness-related lncRNA/circRNA-miRNA-mRNA ceRNA network in latex of Hevea brasiliensis. Plant Physiol Biochem 205, 108156. |
| [46] | Liu HJ, Shen EL, Wu H, Ma WH, Chen H, Lin YJ (2022a). Trans-kingdom expression of an insect endogenous microRNA in rice enhances resistance to striped stem borer Chilo suppressalis. Pest Manag Sci 78, 770-777. |
| [47] | Liu NK, Xu YZ, Li Q, Cao YX, Yang DC, Liu SS, Wang XK, Mi YJ, Liu Y, Ding CX, Liu Y, Li Y, Yuan YW, Gao G, Chen JF, Qian WQ, Zhang XM (2022b). A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth. Cell Host Microbe 30, 1124-1138. |
| [48] | Liu X, Li DY, Zhang DL, Yin DD, Zhao Y, Ji CJ, Zhao XF, Li XB, He Q, Chen RS, Hu SN, Zhu LH (2018). A novel antisense long noncoding RNA, TWISTED LEAF, maintains leaf blade flattening by regulating its associated sense R2R3-MYB gene in rice. New Phytol 218, 774-788. |
| [49] | Liu XQ, Gao YB, Liao JK, Miao M, Chen K, Xi FH, Wei WT, Wang HH, Wang YS, Xu X, Reddy ASN, Gu LF (2021). Genome-wide profiling of circular RNAs, alternative splicing, and R-loops in stem-differentiating xylem of Populus trichocarpa. J Integr Plant Biol 63, 1294-1308. |
| [50] | Liu Y, Zhu QF, Li WY, Chen P, Xue J, Yu Y, Feng YZ (2023b). The pivotal role of noncoding RNAs in flowering time regulation. Genes 14, 2114. |
| [51] | Ma HY, Yang T, Li Y, Zhang J, Wu T, Song TT, Yao YC, Tian J (2021). The long noncoding RNA MdLNC499 bridges MdWRKY1 and MdERF109 function to regulate early- stage light-induced anthocyanin accumulation in apple fruit. Plant Cell 33, 3309-3330. |
| [52] | Mammarella MF, Lucero L, Hussain N, Muñoz-Lopez A, Huang Y, Ferrero L, Fernandez-Milmanda GL, Manavella P, Benhamed M, Crespi M, Ballare CL, Marcos JG, Cubas P, Ariel F (2023). Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controls shade avoidance syndrome in Arabidopsis. EMBO J 42, e113941. |
| [53] | Mao JY, Wei SY, Chen YN, Yang YH, Yin TM (2023). The proposed role of MSL-lncRNAs in causing sex lability of female poplars. Hortic Res 10, uhad042. |
| [54] | Martin RC, Liu PP, Goloviznina NA, Nonogaki H (2010). microRNA, seeds, and Darwin? Diverse function of miRNA in seed biology and plant responses to stress. J Exp Bot 61, 2229-2234. |
| [55] | Miao CB, Wang Z, Zhang L, Yao JJ, Hua K, Liu X, Shi HZ, Zhu JK (2019). The grain yield modulator miR156 regulates seed dormancy through the gibberellin pathway in rice. Nat Commun 10, 3822. |
| [56] | Nelson BR, Makarewich CA, Anderson DM, Winders BR, Troupes CD, Wu FF, Reese AL, McAnally JR, Chen XW, Kavalali ET, Cannon SC, Houser SR, Bassel-Duby R, Olson EN (2016). A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle. Science 351, 271-275. |
| [57] | Qi HR, Wu L, Shen TF, Liu SA, Cai H, Ran N, Wang JL, Xu M (2023). Overexpression of the long non-coding RNA lncWOX5 negatively regulates the development of adventitious roots in Populus. Ind Crop Prod 192, 116054. |
| [58] | Qin T, Zhao HY, Cui P, Albesher N, Xiong LM (2017). A nucleus-localized long non-coding RNA enhances drought and salt stress tolerance. Plant Physiol 175, 1321- 1336. |
| [59] | Quan MY, Liu X, Xiao L, Chen PF, Song FY, Lu WJ, Song YP, Zhang DQ (2021). Transcriptome analysis and association mapping reveal the genetic regulatory network response to cadmium stress in Populus tomentosa. J Exp Bot 72, 576-591. |
| [60] | Ren YJ, Li MS, Wang WZ, Lan W, Schenke D, Cai DG, Miao Y (2021). MicroRNA840 (MIR840) accelerates leaf senescence by targeting the overlapping 3'UTRs of PPR and WHIRLY3 in Arabidopsis thaliana. Plant J 109, 126- 143. |
| [61] | Rodriguez RE, Mecchia MA, Debernardi JM, Schommer C, Weigel D, Palatnik JF (2010). Control of cell proliferation in Arabidopsis thaliana by microRNA miR396. Development 137, 103-112. |
| [62] | Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK (1976). Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci USA 73, 3852- 3856. |
| [63] | Sekhar S, Das S, Panda D, Mohanty S, Mishra B, Kumar A, Navadagi DB, Sah RP, Pradhan SK, Samantaray S, Baig MJ, Behera LB, Mohapatra T (2022). Identification of microRNAs that provide a low light stress tolerance- mediated signaling pathway during vegetative growth in rice. Plants 11, 2558. |
| [64] | Shahid S, Kim G, Johnson NR, Wafula E, Wang F, Coruh C, Bernal-Galeano V, Phifer T, Depamphilis CW, Westwood JH, Axtell MJ (2018). MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Nature 553, 82-85. |
| [65] | Shamloo-Dashtpagerdi R, Sisakht JN, Tahmasebi A (2022). MicroRNA miR1118 contributes to wheat (Triticum aestivum L.) salinity tolerance by regulating the Plasma Membrane Intrinsic Proteins1;5 (PIP1;5) gene. J Plant Physiol 278, 153827. |
| [66] | Sharma D, Tiwari M, Pandey A, Bhatia C, Sharma A, Trivedi PK (2016). MicroRNA858 is a potential regulator of phenylpropanoid pathway and plant development. Plant Physiol 171, 944-959. |
| [67] | Shin WJ, Nam AH, Kim JY, Kwak JS, Song JT, Seo HS (2022). Intronic long noncoding RNA, RICE FLOWERING ASSOCIATED (RIFLA), regulates OsMADS56-mediated flowering in rice. Plant Sci 320, 111278. |
| [68] | Silva GFFE, Silva EM, Da Silva Azevedo M, Guivin MAC, Ramiro DA, Figueiredo CR, Carrer H, Peres LEP, Nogueira FTS (2014). microRNA156-targeted SPL/SBP box transcription factors regulate tomato ovary and fruit development. Plant J 78, 604-618. |
| [69] | Song RJ, Ma SQ, Xu JJ, Ren X, Guo PL, Liu HJ, Li P, Yin F, Liu M, Wang Q, Yu L, Liu JL, Duan BW, Rahman NA, Wołczyński S, Li GM, Li XD (2023). A novel polypeptide encoded by the circular RNA ZKSCAN1 suppresses HCC via degradation of mTOR. Mol Cancer 22, 16. |
| [70] | Song YP, Bu CH, Chen PF, Liu P, Zhang DQ (2021). Miniature inverted repeat transposable elements cis-regulate circular RNA expression and promote ethylene biosynthesis, reducing heat tolerance in Populus tomentosa. J Exp Bot 72, 1978-1994. |
| [71] | Sun N, Bu YF, Wu XY, Ma XC, Yang HB, Du L, Li XJ, Xiao JW, Lin JX, Jing YP (2023). Comprehensive analysis of lncRNA-mRNA regulatory network in Populus associated with xylem development. J Plant Physiol 287, 154055. |
| [72] | Tang YJ, Qu ZP, Lei JJ, He RQ, Adelson DL, Zhu YL, Yang ZB, Wang D (2021). The long noncoding RNA FRILAIR regulates strawberry fruit ripening by functioning as a noncanonical target mimic. PLoS Genet 17, e1009461. |
| [73] | Tognacca RS, Botto JF (2021). Post-transcriptional regulation of seed dormancy and germination: current understanding and future directions. Plant Commun 2, 100169. |
| [74] | Traubenik S, Charon C, Blein T (2024). From environmental responses to adaptation: the roles of plant lncRNAs. Plant Physiol 195, 232-244. |
| [75] | Wang JW, Mao YB, Qi YJ (2016). Recent progress and prospects for plant non-coding RNAs. China Basic Sci 18(2), 22-29. (in Chinese) |
| 王佳伟, 毛颖波, 戚益军 (2016). 植物非编码RNA的研究进展与展望. 中国基础科学 18(2), 22-29. | |
| [76] | Wang WW, Liu Z, An XY, Jin YZ, Hou JM, Liu T (2022). Integrated high-throughput sequencing, microarray hybridization and degradome analysis uncovers microRNA- mediated resistance responses of maize to pathogen Curvularia lunata. Int J Mol Sci 23, 14038. |
| [77] | Wang XS, Chang XC, Jing Y, Zhao JL, Fang QW, Sun MY, Zhang YZ, Li WB, Li YG (2020). Identification and functional prediction of soybean circRNAs involved in low-temperature responses. J Plant Physiol 250, 153188. |
| [78] | Wang YJ, Wang YL, Chen YD (2020). Transposon-derived long noncoding RNA in plants. Chin Bull Bot 55, 768-776. (in Chinese) |
| 王益军, 王亚丽, 陈煜东 (2020). 转座子来源的植物长链非编码RNA. 植物学报 55, 768-776. | |
| [79] | Wang YQ, Fan YY, Fan D, Zhou XL, Jiao YT, Deng XW, Zhu DM (2023). The noncoding RNA HIDDEN TREASURE 1 promotes phytochrome B-dependent seed germination by repressing abscisic acid biosynthesis. Plant Cell 35, 700-716. |
| [80] | Wang Z, Zhu TQ, Ma WJ, Wang N, Qu GZ, Zhang SG, Wang JH (2018). Genome-wide analysis of long non-coding RNAs in Catalpa bungei and their potential function in floral transition using high-throughput sequencing. BMC Genet 19, 86. |
| [81] | Wen XJ, Ding Y, Tan ZL, Wang JX, Zhang DY, Wang YC (2020). Identification and characterization of cadmium stress-related lncRNAs from Betula platyphylla. Plant Sci 299, 110601. |
| [82] | Wong-Bajracharya J, Singan VR, Monti R, Plett KL, Ng V, Grigoriev IV, Martin FM, Anderson IC, Plett JM (2022). The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis. Proc Natl Acad Sci USA 119, e2103527119. |
| [83] | Wu J, Liu CX, Liu ZG, Li S, Li DD, Liu SY, Huang XQ, Liu SK, Yukawa Y (2019). Pol III-dependent cabbage BoNR8 long ncRNA affects seed germination and growth in Arabidopsis. Plant Cell Physiol 60, 421-435. |
| [84] | Xia KF, Pan XQ, Chen HP, Xu XL, Zhang MY (2023). Rice miR168a-5p regulates seed length, nitrogen allocation and salt tolerance by targeting OsOFP3, OsNPF2.4 and OsAGO1a, respectively. J Plant Physiol 280, 153905. |
| [85] | Xiong XM, Wu Y, Wang Y (2014). Research progresses in the regulation of miRNAs biogenesis and function in plants. Bull Bot Res 34, 282-288. (in Chinese) |
| 熊雪梅, 吴莹, 王洋 (2014). 植物体内调控miRNA合成与功能的机制研究进展. 植物研究 34, 282-288. | |
| [86] | Xu SJ, Dong Q, Deng M, Lin DX, Xiao J, Cheng PL, Xing LJ, Niu YD, Gao CX, Zhang WH, Xu YY, Chong K (2021). The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat. Mol Plant 14, 1525-1538. |
| [87] | Xue LZ, Sun MT, Wu Z, Yu L, Yu QH, Tang YP, Jiang FL (2020). LncRNA regulates tomato fruit cracking by coordinating gene expression via a hormone-redox-cell wall network. BMC Plant Biol 20, 162. |
| [88] | Yang SB, Yang T, Tang YP, Aisimutuola P, Zhang GR, Wang BK, Li N, Wang J, Yu QH (2020). Transcriptomic profile analysis of non-coding RNAs involved in Capsicum chinense Jacq. fruit ripening. Sci Hortic 264, 109158. |
| [89] | Yang T, Ma HY, Zhang J, Wu T, Song TT, Tian J, Yao YC (2019). Systematic identification of long noncoding RNAs expressed during light-induced anthocyanin accumulation in apple fruit. Plant J 100, 572-590. |
| [90] | Yang XQ, Fu TT, Yu RE, Zhang LC, Yang YZ, Xiao DD, Wang YY, Wang YL, Wang YW (2023). miR159a modulates poplar resistance against different fungi and bacteria. Plant Physiol Biochem 201, 107899. |
| [91] | Ye XX, Wang S, Zhao XJ, Gao N, Wang Y, Yang YM, Wu E, Jiang C, Cheng YX, Wu WW, Liu SK (2022). Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa. Plant J 110, 978-993. |
| [92] | Yu JX, Qiu KN, Sun WJ, Yang T, Wu T, Song TT, Zhang J, Yao YC, Tian J (2022). A long noncoding RNA functions in high-light-induced anthocyanin accumulation in apple by activating ethylene synthesis. Plant Physiol 189, 66-83. |
| [93] | Yu Y, Zhou YF, Feng YZ, He H, Lian JP, Yang YW, Lei MQ, Zhang YC, Chen YQ (2020). Transcriptional landscape of pathogen-responsive lncRNAs in rice unveils the role of ALEX1 in jasmonate pathway and disease resistance. Plant Biotechnol J 18, 679-690. |
| [94] | Yuan ZD, Pan JH, Chen CP, Tang YL, Zhang HS, Guo J, Yang XR, Chen LF, Li CY, Zhao K, Wang Q, Yang B, Sun CH, Deng XJ, Wang PR (2022). DRB2 modulates leaf rolling by regulating accumulation of microRNAs related to leaf development in rice. Int J Mol Sci 23, 11147. |
| [95] | Zhang L, Liu JL, Cheng JR, Sun Q, Zhang Y, Liu JG, Li HM, Zhang Z, Wang P, Cai CW, Chu ZY, Zhang X, Yuan YL, Shi YZ, Cai YF (2022). lncRNA7 and lncRNA2 modulate cell wall defense genes to regulate cotton resistance to Verticillium wilt. Plant Physiol 189, 264-284. |
| [96] | Zhang LL, Lin T, Zhu GN, Wu B, Zhang CJ, Zhu HL (2023). LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response. Hortic Res 10, uhad234. |
| [97] | Zhang N, Liu ZG, Sun SC, Liu SY, Lin JH, Peng YF, Zhang XX, Yang H, Cen X, Wu J (2020). Response of AtR8 lncRNA to salt stress and its regulation on seed germination in Arabidopsis. Chin Bull Bot 55, 421-429. (in Chinese) |
| 张楠, 刘自广, 孙世臣, 刘圣怡, 林建辉, 彭疑芳, 张晓旭, 杨贺, 岑曦, 吴娟 (2020). 拟南芥AtR8 lncRNA对盐胁迫响应及其对种子萌发的调节作用. 植物学报 55, 421-429. | |
| [98] | Zhang P, Dai MQ (2022). CircRNA: a rising star in plant biology. J Genet Genomics 49, 1081-1092. |
| [99] | Zhang P, Fan Y, Sun XP, Chen L, Terzaghi W, Bucher E, Li L, Dai MQ (2019a). A large-scale circular RNA profiling reveals universal molecular mechanisms responsive to drought stress in maize and Arabidopsis. Plant J 98, 697-713. |
| [100] | Zhang QL, Li Y, Zhang Y, Wu CB, Wang SN, Hao L, Wang SY, Li TZ (2017). Md-miR156ab and Md-miR395 target WRKY transcription factors to influence apple resistance to leaf spot disease. Front Plant Sci 8, 526. |
| [101] | Zhang XP, Dong J, Deng FN, Wang W, Cheng YY, Song LR, Hu MJ, Shen J, Xu QJ, Shen FF (2019b). The long non-coding RNA lncRNA973 is involved in cotton response to salt stress. BMC Plant Biol 19, 459. |
| [102] | Zhang XP, Shen J, Xu QJ, Dong J, Song LR, Wang W, Shen FF (2021). Long noncoding RNA lncRNA354 functions as a competing endogenous RNA of miR160b to regulate ARF genes in response to salt stress in upland cotton. Plant Cell Environ 44, 3302-3321. |
| [103] | Zhao XY, Li JR, Lian B, Gu HQ, Li Y, Qi YJ (2018). Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nat Commun 9, 5056. |
| [104] | Zheng XM, Chen YJ, Zhou YF, Shi KK, Hu X, Li DY, Ye HZ, Zhou Y, Wang K (2021). Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton. Plant Physiol 185, 179-195. |
| [105] | Zhou BY, Luo Q, Shen YH, Wei L, Song X, Liao HQ, Ni L, Shen T, Du XL, Han JY, Jiang MY, Feng SJ, Wu G (2023a). Coordinated regulation of vegetative phase change by brassinosteroids and the age pathway in Arabidopsis. Nat Commun 14, 2608. |
| [106] | Zhou J, Yang LY, Jia CL, Shi WG, Deng SR, Luo ZB (2022). Identification and functional prediction of poplar root circRNAs involved in treatment with different forms of nitrogen. Front Plant Sci 13, 941380. |
| [107] | Zhou JP, Yuan MZ, Zhao YX, Quan Q, Yu D, Yang H, Tang X, Xin XH, Cai GZ, Qian Q, Qi YP, Zhang Y (2021a). Efficient deletion of multiple circle RNA loci by CRISPR-Cas9 reveals Os06circ02797 as a putative sponge for OsMIR408 in rice. Plant Biotechnol J 19, 1240-1252. |
| [108] | Zhou LK, Zhou Z, Jiang XM, Zheng YS, Chen X, Fu Z, Xiao GF, Zhang CY, Zhang LK, Yi YX (2020). Absorbed plant MIR2911 in honeysuckle decoction inhibits SARS- CoV-2 replication and accelerates the negative conversion of infected patients. Cell Discov 6, 54. |
| [109] | Zhou R, Dong YH, Wang CX, Liu JN, Liang Q, Meng XY, Lang XY, Xu SY, Liu WJ, Zhang SH, Wang N, Yang KQ, Fang HC (2023b). LncRNA109897-JrCCR4-JrTLP1b forms a positive feedback loop to regulate walnut resistance against anthracnose caused by Colletotrichum gloeosporioides. Hortic Res 10, uhad086. |
| [110] | Zhou R, Xu LP, Zhao LP, Wang YL, Zhao TM (2018). Genome-wide identification of circRNAs involved in tomato fruit coloration. Biochem Biophys Res Commun 499, 466- 469. |
| [111] | Zhou YF, Zhang YC, Sun YM, Yu Y, Lei MQ, Yang YW, Lian JP, Feng YZ, Zhang Z, Yang L, He RR, Huang JH, Cheng Y, Liu YW, Chen YQ (2021b). The parent-of-origin lncRNA MISSEN regulates rice endosperm development. Nat Commun 12, 6525. |
| [112] | Zhu TD, Yang CW, Xie Y, Huang S, Li L (2023). Shade- induced lncRNA PUAR promotes shade response by repressing PHYA expression. EMBO Rep 24, e56105. |
| [113] | Zhu YX, Jia JH, Yang L, Xia YC, Zhang HL, Jia JB, Zhou R, Nie PY, Yin JL, Ma DF, Liu LC (2019). Identification of cucumber circular RNAs responsive to salt stress. BMC Plant Biol 19, 164. |
| [114] | Zou XY, Ali F, Jin SX, Li FG, Wang Z (2022). RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton. BMC Plant Biol 22, 61. |