vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-25-136vavilov-4926Research ArticleБИОИНФОРМАТИКА И СИСТЕМНАЯ БИОЛОГИЯBIOINFORMATICS AND SYSTEMS BIOLOGYКомпьютерное предсказание сети взаимодействий длинных некодирующих РНК и микроРНК кукурузы на основе транскриптома мутантной линии fuzzy tasselComputational prediction of the interaction network between long non-coding RNAs and microRNAs in maize based on the transcriptome of the fuzzy tassel mutant lineЯньЦ.YanJ.

Новосибирск

Novosibirsk

t.yan5@g.nsu.ruhttps://orcid.org/0000-0002-3011-6288ПронозинА. Ю.PronozinA. Yu.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-9738-1409АфонниковД. А.AfonnikovD. A.

Новосибирск

Novosibirsk

Новосибирский национальный исследовательский государственный университетРоссияNovosibirsk State University;Russian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Курчатовский геномный центр ИЦиГ СО РАНРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationНовосибирский национальный исследовательский государственный университет; Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Курчатовский геномный центр ИЦиГ СО РАНРоссияNovosibirsk State University; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RASRussian Federation20251101202629812951303Copyright © Янь Ц., Пронозин А.Ю., Афонников Д.А., 20262026Янь Ц., Пронозин А.Ю., Афонников Д.А.Yan J., Pronozin A.Y., Afonnikov D.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4926

Длинные некодирующие РНК (днРНК) играют важную роль в регуляции экспрессии генов, включая взаимодействия с микроРНК (миРНК), выполняя функцию молекулярных «губок». Для предсказания таких взаимодействий, как правило, применяются методы биоинформатики. Для уточнения предсказаний компьютерных программ можно использовать дополнительные данные на основе коэкспрессии миРНК и днРНК. В настоящей работе исследуются потенциальные взаимодействия между днРНК и миРНК у мутантной линии кукурузы fuzzy tassel (fzt), характеризующейся сниженной экспрессией некоторых миРНК вследствие мутации в гене Dicer-like1 (DCL1) в тканях побега и соцветия. Проведена сборка транскриптомов на основе данных RNA-seq побега и соцветия кукурузы контрольной и мутантной линий. Данные были взяты из архива SRA NCBI. Для побега было идентифицировано десять днРНК, достоверно изменяющих свой уровень экспрессии между контрольной и мутантной группами, девять из них повышают экспрессию у мутантных рас тений. Для соцветия идентифицировано 34 дифференциально экспрессирующихся днРНК (20 с повышенным уровнем экспрессии у мутантных линий). Для днРНК с повышенным уровнем собственной экспрессии и миРНК с пониженным уровнем экспрессии в мутантных линиях были предсказаны потенциальные взаимодействия с помощью алгоритма машинного обу чения PmliPred. С использованием программы IntaRNA подтверждена возможность комплементарного связывания для выявленных пар миРНК–днРНК, что позволило построить конкурирующие эндогенные РНК-сети. Анализ структуры этих сетей показал, что отдельные днРНК способны связывать несколько миРНК одновременно, подтверждая их регуляторную функцию в качестве «губок» для миРНК. Полученные результаты углуб ляют понимание посттранскрипционной регуляции у кукурузы и открывают перспективы для селекционных разработок, направленных на повышение стрессоустойчивости и продуктивности растений.

Long non-coding RNAs (lncRNAs) play an important role in the regulation of gene expression, including interactions with microRNAs (miRNAs), acting as molecular “sponges”. Bioinformatics methods are generally used to predict such interactions. To refine computational predictions, additional evidence based on the co-expression of miRNAs and lncRNAs can be incorporated. In the present study, we investigated potential interactions between lncRNAs and miRNAs in the maize mutant line fuzzy tassel (fzt), which is characterized by reduced expression of certain miRNAs due to a mutation in the Dicer-like1 (DCL1) gene in shoot and tassel tissues. Transcriptome assembly was performed based on RNA-seq data from maize shoot and tassel tissues of control and mutant lines, with data obtained from the NCBI SRA archive. In the shoot, 10 lncRNAs with significantly altered expression levels between control and mutant groups were identified, 9 of which were upregulated in the mutant plants. In the tassel, 34 differentially expressed lncRNAs were identified, with 20 showing increased expression in the mutant line. For lncRNAs with increased expression and miRNAs with decreased expression in the mutant line, potential interactions were predicted using the machine learning algorithm PmliPred. The IntaRNA program was used to confirm possible complementary binding for the identified miRNA–lncRNA pairs, which enabled the construction of competing endogenous RNA (ceRNA) networks. Structural analysis of these networks revealed that certain lncRNAs are capable of binding multiple miRNAs simultaneously, supporting their regulatory role as “sponges” for miRNAs. The results obtained deepen our understanding of post-transcriptional regulation in maize and open new perspectives for breeding strategies aimed at improving stress tolerance and crop productivity.

днРНКмиРНКрегуляция геновкукурузамутация fztDCL1биоинформатикавзаимодей ствие РНКконкурирующие эндогенные РНКlncRNAmiRNAgene regulationmaizefuzzy tassel (fzt)DCL1bioinformaticsRNA interactioncompeting endogenous RNA (ceRNA)This work was supported by the budgetary project No. FWNR-2022-0020. Data processing was carried out using the computational resources of the “Bioinformatics” Center for Collective Use at the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences.This work was supported by the budgetary project No. FWNR-2022-0020. Data processing was carried out using the computational resources of the “Bioinformatics” Center for Collective Use at the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesReferencesBarrera-Rojas C.H., Otoni W.C., Nogueira F.T.S. Shaping the root system: the interplay between miRNA regulatory hubs and phy tohormones. J Exp Bot. 2021;72(20):6822-6835. doi 10.1093/jxb/erab299Barrera-Rojas C.H., Otoni W.C., Nogueira F.T.S. Shaping the root system: the interplay between miRNA regulatory hubs and phy tohormones. J Exp Bot. 2021;72(20):6822-6835. doi 10.1093/jxb/erab299Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-2120. doi 10.1093/bioinformatics/btu170Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-2120. doi 10.1093/bioinformatics/btu170Bolser D.M., Staines D.M., Perry E., Kersey P.J. Ensembl Plants: inte grating tools for visualizing, mining, and analyzing plant genomic data. In: van Dijk A. (Ed.) Plant Genomics Databases. Methods in Molecular Biology. Vol. 1533. New York: Humana Press, 2017; 1-31. doi 10.1007/978-1-4939-6658-5_1Bolser D.M., Staines D.M., Perry E., Kersey P.J. Ensembl Plants: inte grating tools for visualizing, mining, and analyzing plant genomic data. In: van Dijk A. (Ed.) Plant Genomics Databases. Methods in Molecular Biology. Vol. 1533. New York: Humana Press, 2017; 1-31. doi 10.1007/978-1-4939-6658-5_1Bray N., Pimentel H., Melsted P., Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34(5):525-527. doi 10.1038/nbt.3519Bray N., Pimentel H., Melsted P., Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34(5):525-527. doi 10.1038/nbt.3519Canto-Pastor A., Santos B., Valli A., Summers W., Schornack S., Baul combe D. Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato. Proc Natl Acad Sci USA. 2019;116(7):2755-2760. doi 10.1073/pnas.181438011Canto-Pastor A., Santos B., Valli A., Summers W., Schornack S., Baul combe D. Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato. Proc Natl Acad Sci USA. 2019;116(7):2755-2760. doi 10.1073/pnas.181438011Caruana J.C., Dhar N., Raina R. Overexpression of Arabidopsis microRNA167 induces salicylic acid-dependent defense against Pseu domonas syringae through the regulation of its targets ARF6 and ARF8. Plant Direct. 2020;4(9):e00270. doi 10.1002/pld3.270Caruana J.C., Dhar N., Raina R. Overexpression of Arabidopsis microRNA167 induces salicylic acid-dependent defense against Pseu domonas syringae through the regulation of its targets ARF6 and ARF8. Plant Direct. 2020;4(9):e00270. doi 10.1002/pld3.270Dobin A., Davis C.A., Schlesinger F., Drenkow J., Zaleski C., Jha S., Batut P., Chaisson M., Gingeras T.R. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi 10.1093/bioinformatics/bts635Dobin A., Davis C.A., Schlesinger F., Drenkow J., Zaleski C., Jha S., Batut P., Chaisson M., Gingeras T.R. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi 10.1093/bioinformatics/bts635Gao Y., Feng B., Gao C., Zhang M., Zhang X., Han X., Liu P., Wang B., Li Z. The evolution and functional roles of miR408 and its targets in plants. Int J Mol Sci. 2022;23(1):530. doi 10.3390/ijms23010530Gao Y., Feng B., Gao C., Zhang M., Zhang X., Han X., Liu P., Wang B., Li Z. The evolution and functional roles of miR408 and its targets in plants. Int J Mol Sci. 2022;23(1):530. doi 10.3390/ijms23010530He X., Guo S., Wang Y., Wang L., Shu S., Sun J. Systematic identifica tion and analysis of heat-stress-responsive lncRNAs, circRNAs and miRNAs with associated co-expression and ceRNA networks in cu cumber (Cucumis sativus L.). Physiol Plant. 2020;168(3):736-754. doi 10.1111/ppl.12997He X., Guo S., Wang Y., Wang L., Shu S., Sun J. Systematic identifica tion and analysis of heat-stress-responsive lncRNAs, circRNAs and miRNAs with associated co-expression and ceRNA networks in cu cumber (Cucumis sativus L.). Physiol Plant. 2020;168(3):736-754. doi 10.1111/ppl.12997Jiang A., Guo Z., Pan J., Yu B., Chen D., Li Y. The PIF1-miR408 PLANTACYANIN repression cascade regulates light-dependent seed germination. Plant Cell. 2021;33(5):1506-1529. doi 10.1093/plcell/koab060Jiang A., Guo Z., Pan J., Yu B., Chen D., Li Y. The PIF1-miR408 PLANTACYANIN repression cascade regulates light-dependent seed germination. Plant Cell. 2021;33(5):1506-1529. doi 10.1093/plcell/koab060Jiang P., Lian B., Liu C., Fu Z., Shen Y., Cheng Z., Ding Y. 21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells. Nat Commun. 2020;11(1):5191. doi 10.1038/s41467-020-19034-yJiang P., Lian B., Liu C., Fu Z., Shen Y., Cheng Z., Ding Y. 21-nt phasiRNAs direct target mRNA cleavage in rice male germ cells. Nat Commun. 2020;11(1):5191. doi 10.1038/s41467-020-19034-yJones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAs and their regulatory roles in plants. Annual Rev Plant Biol. 2006;57:19-53. doi 10.1146/annurev.arplant.57.032905.105218Jones-Rhoades M.W., Bartel D.P., Bartel B. MicroRNAs and their regulatory roles in plants. Annual Rev Plant Biol. 2006;57:19-53. doi 10.1146/annurev.arplant.57.032905.105218Kang Q., Jun M., Jun C., Zhang Y., Wang W. PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA–lncRNA in teraction prediction. Bioinformatics. 2020;36(10):2986-2992. doi 10.1093/bioinformatics/btaa074Kang Q., Jun M., Jun C., Zhang Y., Wang W. PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA–lncRNA in teraction prediction. Bioinformatics. 2020;36(10):2986-2992. doi 10.1093/bioinformatics/btaa074Li R., Yang Y.F., Li R., Zhu H.L., Luo Y.B. Functions of long non-cod ing RNA and its interacting mechanisms. Chin Bull Life Sci. 2016; 28(6):703-711. doi 10.13376/j.cbls/2016090Li R., Yang Y.F., Li R., Zhu H.L., Luo Y.B. Functions of long non-cod ing RNA and its interacting mechanisms. Chin Bull Life Sci. 2016; 28(6):703-711. doi 10.13376/j.cbls/2016090Li W., Cui X., Meng Z., Huang X., Xie Q., Wu H., Jin H., Zhang D., Liang W. Transcriptional regulation of Arabidopsis MIR168a and ARGONAUTE1 homeostasis in abscisic acid and abiotic stress re sponses. Plant Physiol. 2012;158(3):1279-1292. doi 10.1104/pp.111.188789Li W., Cui X., Meng Z., Huang X., Xie Q., Wu H., Jin H., Zhang D., Liang W. Transcriptional regulation of Arabidopsis MIR168a and ARGONAUTE1 homeostasis in abscisic acid and abiotic stress re sponses. Plant Physiol. 2012;158(3):1279-1292. doi 10.1104/pp.111.188789Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi 10.1186/s13059-014-0550-8Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. doi 10.1186/s13059-014-0550-8Mann M., Wright P.R., Backofen R. IntaRNA 2.0: enhanced and cus tomizable prediction of RNA–RNA interactions. Nucleic Acids Res. 2017;45(W1):W435-W439. doi 10.1093/nar/gkx279Mann M., Wright P.R., Backofen R. IntaRNA 2.0: enhanced and cus tomizable prediction of RNA–RNA interactions. Nucleic Acids Res. 2017;45(W1):W435-W439. doi 10.1093/nar/gkx279Martínez de Alba A.E., Jauvion V., Mallory A.C., Bouteiller N., Vaucheret H. The miRNA pathway limits AGO1 availability during siRNA-mediated PTGS defense against exogenous RNA. Nucleic Acids Res. 2011;39(21):9339-9344. doi 10.1093/nar/gkr590Martínez de Alba A.E., Jauvion V., Mallory A.C., Bouteiller N., Vaucheret H. The miRNA pathway limits AGO1 availability during siRNA-mediated PTGS defense against exogenous RNA. Nucleic Acids Res. 2011;39(21):9339-9344. doi 10.1093/nar/gkr590Pertea M., Pertea G.M., Antonescu C.M., Chang T.C., Mendell J.T., Salzberg S.L. StringTie enables improved reconstruction of a tran scriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290 295. doi 10.1038/nbt.3122Pertea M., Pertea G.M., Antonescu C.M., Chang T.C., Mendell J.T., Salzberg S.L. StringTie enables improved reconstruction of a tran scriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290 295. doi 10.1038/nbt.3122Preston J.C., Hileman L.C. Functional evolution in the plant SQUA MOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family. Front Plant Sci. 2013;4:80. doi 10.3389/fpls.2013.00080Preston J.C., Hileman L.C. Functional evolution in the plant SQUA MOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family. Front Plant Sci. 2013;4:80. doi 10.3389/fpls.2013.00080Pronozin A.Y., Afonnikov D.A. ICAnnoLncRNA: a snakemake pipeline for a long noncoding RNA search and annotation in transcriptomic sequences. Genes. 2023;14(7):1331. doi 10.3390/genes14071331Pronozin A.Y., Afonnikov D.A. ICAnnoLncRNA: a snakemake pipeline for a long noncoding RNA search and annotation in transcriptomic sequences. Genes. 2023;14(7):1331. doi 10.3390/genes14071331Pronozin A.Y., Afonnikov D.A. The role of long noncoding RNAs in plants. Russ J Genet. 2025;61:1-18. doi 10.1134/S1022795424701345Pronozin A.Y., Afonnikov D.A. The role of long noncoding RNAs in plants. Russ J Genet. 2025;61:1-18. doi 10.1134/S1022795424701345Ripoll J.J., Bailey L.J., Mai Q.A., Wu S.L., Hon C.T., Chapman E.J., Ditta G.S., Estelle M., Yanofsky M.F. microRNA regulation of fruit growth. Nat Plants. 2015;1(4):15036. doi 10.1038/nplants.2015.36Ripoll J.J., Bailey L.J., Mai Q.A., Wu S.L., Hon C.T., Chapman E.J., Ditta G.S., Estelle M., Yanofsky M.F. microRNA regulation of fruit growth. Nat Plants. 2015;1(4):15036. doi 10.1038/nplants.2015.36Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expres sion data. Bioinformatics. 2010;26(1):139-140. doi 10.1093/bioinformatics/btp616Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a Bioconductor package for differential expression analysis of digital gene expres sion data. Bioinformatics. 2010;26(1):139-140. doi 10.1093/bioinformatics/btp616Sheng N., Huang L., Gao L., Zhao W., Zhang Y., Wang X. A survey of computational methods and databases for lncRNA-miRNA inter action prediction. IEEE/ACM Trans Comput Biol Bioinform. 2023; 20(5):2810-2826. doi 10.1109/TCBB.2023.3264254Sheng N., Huang L., Gao L., Zhao W., Zhang Y., Wang X. A survey of computational methods and databases for lncRNA-miRNA inter action prediction. IEEE/ACM Trans Comput Biol Bioinform. 2023; 20(5):2810-2826. doi 10.1109/TCBB.2023.3264254Simão F.A., Waterhouse R.M., Ioannidis P., Kriventseva E.V., Zdob nov E.M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-3212. doi 10.1093/bioinformatics/btv351Simão F.A., Waterhouse R.M., Ioannidis P., Kriventseva E.V., Zdob nov E.M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-3212. doi 10.1093/bioinformatics/btv351Song J.B., Shu X.X., Shen Q., Guo C.Y., Jiang J., Xie L.H., Liu Y.F., Yang Z.M. Altered fruit and seed development of transgenic rape seed (Brassica napus) over-expressing microRNA394. PLoS One. 2015;10(5):e0125427. doi 10.1371/journal.pone.0125427Song J.B., Shu X.X., Shen Q., Guo C.Y., Jiang J., Xie L.H., Liu Y.F., Yang Z.M. Altered fruit and seed development of transgenic rape seed (Brassica napus) over-expressing microRNA394. PLoS One. 2015;10(5):e0125427. doi 10.1371/journal.pone.0125427Sun P., Cheng C., Lin Y., Zhu Q., Lin J., Jin Y., Yuan H., Lin Y. Com bined small RNA and degradome sequencing reveals complex microRNA regulation of catechin biosynthesis in tea (Camellia sinensis). PLoS One. 2017;12(2):e0171173. doi 10.1371/journal.pone.0171173Sun P., Cheng C., Lin Y., Zhu Q., Lin J., Jin Y., Yuan H., Lin Y. Com bined small RNA and degradome sequencing reveals complex microRNA regulation of catechin biosynthesis in tea (Camellia sinensis). PLoS One. 2017;12(2):e0171173. doi 10.1371/journal.pone.0171173Sun Q., Csorba T., Skourti-Stathaki K., Proudfoot N.J., Dean C. R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science. 2013;340(6132):619-621. doi 10.1126/science.1234848Sun Q., Csorba T., Skourti-Stathaki K., Proudfoot N.J., Dean C. R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science. 2013;340(6132):619-621. doi 10.1126/science.1234848Sun Q., Liu X., Yang J., Wang Y., Zhang Y., Li J., Wang N., Li H., Wang J. MicroRNA528 affects lodging resistance of maize by regu lating lignin biosynthesis under nitrogen-luxury conditions. Mol Plant. 2018;11(6):806-814. doi 10.1016/j.molp.2018.03.013Sun Q., Liu X., Yang J., Wang Y., Zhang Y., Li J., Wang N., Li H., Wang J. MicroRNA528 affects lodging resistance of maize by regu lating lignin biosynthesis under nitrogen-luxury conditions. Mol Plant. 2018;11(6):806-814. doi 10.1016/j.molp.2018.03.013Sunkar R., Li Y.F., Jagadeeswaran G. Functions of microRNAs in plant stress responses. Trends Plant Sci. 2012;17(4):196-203. doi 10.1016/j.tplants.2012.01.010Sunkar R., Li Y.F., Jagadeeswaran G. Functions of microRNAs in plant stress responses. Trends Plant Sci. 2012;17(4):196-203. doi 10.1016/j.tplants.2012.01.010Thompson B.E., Basham C., Hammond R., Sidorenko L., Becker M.G., Neuffer M.G., Meeley R.B., Timmermans M.C.P., Chandler V.L., Hake S. The dicer-like1 homolog fuzzy tassel is required for the regu- lation of meristem determinacy in the inflorescence and vegetative growth in maize. Plant Cell. 2014;26(12):4702-4717. doi 10.1105/tpc.114.132670Thompson B.E., Basham C., Hammond R., Sidorenko L., Becker M.G., Neuffer M.G., Meeley R.B., Timmermans M.C.P., Chandler V.L., Hake S. The dicer-like1 homolog fuzzy tassel is required for the regu- lation of meristem determinacy in the inflorescence and vegetative growth in maize. Plant Cell. 2014;26(12):4702-4717. doi 10.1105/tpc.114.132670Wang H., Wang H. The miR156/SPL module, a regulatory hub and ver satile toolbox, gears up crops for enhanced agronomic traits. Mol Plant. 2015;8(5):677-688. doi 10.1016/j.molp.2015.01.008Wang H., Wang H. The miR156/SPL module, a regulatory hub and ver satile toolbox, gears up crops for enhanced agronomic traits. Mol Plant. 2015;8(5):677-688. doi 10.1016/j.molp.2015.01.008Wang L., Wang J.W. Coding function for non-coding RNA in plants insights from miRNA encoded peptide (miPEP). Sci China Life Sci. 2015;58(5):503-505. doi 10.1007/s11427-015-4854-zWang L., Wang J.W. Coding function for non-coding RNA in plants insights from miRNA encoded peptide (miPEP). Sci China Life Sci. 2015;58(5):503-505. doi 10.1007/s11427-015-4854-zWang Y., Liu W., Wang X., Yang R., Wu Z., Wang H., Wang L., Hu Z., Guo S., Zhang H., Lin J., Fu C. MiR156 regulates anthocyanin bio synthesis through SPL targets and other microRNAs in poplar. Hor tic Res. 2020;7:118. doi 10.1038/s41438-020-00341-wWang Y., Liu W., Wang X., Yang R., Wu Z., Wang H., Wang L., Hu Z., Guo S., Zhang H., Lin J., Fu C. MiR156 regulates anthocyanin bio synthesis through SPL targets and other microRNAs in poplar. Hor tic Res. 2020;7:118. doi 10.1038/s41438-020-00341-wWu J., Yang R., Yang Z., Yao S., Zhao S., Wang Y., Li P., … Zhou X., Chu C., Qi Y., Cao X., Li Y. ROS accumulation and antiviral de fence control by microRNA528 in rice. Nat Plants. 2017;3:16203. doi 10.1038/nplants.2016.203Wu J., Yang R., Yang Z., Yao S., Zhao S., Wang Y., Li P., … Zhou X., Chu C., Qi Y., Cao X., Li Y. ROS accumulation and antiviral de fence control by microRNA528 in rice. Nat Plants. 2017;3:16203. doi 10.1038/nplants.2016.203Zhang B., Wang L., Zeng L., Zhang C., Ma H. Arabidopsis TOE pro teins convey a photoperiodic signal to antagonize CONSTANS and regulate flowering time. Genes Dev. 2015;29(9):975-987. doi 10.1101/gad.251520.114Zhang B., Wang L., Zeng L., Zhang C., Ma H. Arabidopsis TOE pro teins convey a photoperiodic signal to antagonize CONSTANS and regulate flowering time. Genes Dev. 2015;29(9):975-987. doi 10.1101/gad.251520.114Zhang L., Chia J.M., Kumari S., Stein J.C., Liu Z., Narechania A., Maher C.A., Guill K., McMullen M.D., Ware D. A genome-wide characterization of microRNA genes in maize. PLoS Genet. 2009; 5(11):e1000716. doi 10.1371/journal.pgen.1000716Zhang L., Chia J.M., Kumari S., Stein J.C., Liu Z., Narechania A., Maher C.A., Guill K., McMullen M.D., Ware D. A genome-wide characterization of microRNA genes in maize. PLoS Genet. 2009; 5(11):e1000716. doi 10.1371/journal.pgen.1000716Zou H., Guo X., Yang R., Wang D., Liu K., Gan L., Yuan Y., Qi J., Wang Y. MiR408-SmLAC3 module participates in salvianolic acid B synthesis in Salvia miltiorrhiza. Int J Mol Sci. 2021;22(14):7541. doi 10.3390/ijms22147541Zou H., Guo X., Yang R., Wang D., Liu K., Gan L., Yuan Y., Qi J., Wang Y. MiR408-SmLAC3 module participates in salvianolic acid B synthesis in Salvia miltiorrhiza. Int J Mol Sci. 2021;22(14):7541. doi 10.3390/ijms22147541

The authors declare that there are no conflicts of interest present.