References
-
Axtell, M. J. Classification and comparison of small RNAs from plants. Annu. Rev. Plant. Biol. 64, 137–159 (2013).
-
Matzke, M. A., Kanno, T., Matzke, A. J. M. & RNA-Directed, D. N. A. Methylation: the evolution of a complex epigenetic pathway in flowering plants. Annu. Rev. Plant. Biol. 66, 243–267 (2015).
-
Borges, F. & Martienssen, R. A. The expanding world of small RNAs in plants. Nat. Rev. Mol. Cell. Biol. 16, 727–741 (2015).
-
Yu, Y., Jia, T. & Chen, X. The ‘how’ and ‘where’ of plant MicroRNAs. New Phytol. 216, 1002–1017 (2017).
-
Rao, S. et al. A conserved HSF:miR169:NF-YA loop involved in tomato and Arabidopsis heat stress tolerance. Plant J. 112, 7–26 (2022).
-
Zhang, L. et al. Characterization and identification of grapevine heat stress-responsive MicroRNAs revealed the positive regulated function of vvi-miR167 in thermostability. Plant Sci. 329, 111623 (2023).
-
Li, B. et al. Sly-miR398 participates in heat stress tolerance in tomato by modulating ROS accumulation and HSP response. Agronomy 15, 294 (2025).
-
Zhou, R. et al. Unique MiRNAs and their targets in tomato leaf responding to combined drought and heat stress. BMC Plant. Biol. 20, 107 (2020).
-
Bansal, C., Balyan, S. & Mathur, S. Inferring the regulatory network of the miRNA-mediated response to individual and combined heat and drought stress in tomato. J. Plant. Biochem. Biotechnol. 30, 862–877 (2021).
-
Ravichandran, S., Ragupathy, R., Edwards, T., Domaratzki, M. & Cloutier, S. MicroRNA-guided regulation of heat stress response in wheat. BMC Genom. 20, 488 (2019).
-
USDA-APHIS. Treatment manual. 1–128. at (2016). https://www.aphis.usda.gov/sites/default/files/treatment.pdf.
-
Dautt-Castro, M. et al. Mesocarp RNA-Seq analysis of Mango (Mangifera indica L.) identify quarantine postharvest treatment effects on gene expression. Sci. Hortic. 227, 146–153 (2018).
-
López-Virgen, A. G. et al. Genome-wide identification of gene families related to MiRNA biogenesis in mangifera indica L. and their possible role during heat stress. PeerJ 12, e17737 (2024).
-
Dai, X., Zhuang, Z. & Zhao, P. X. PsRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 46, W49–W54 (2018).
-
Rajagopalan, R., Vaucheret, H., Trejo, J. & Bartel, D. P. A diverse and evolutionarily fluid set of MicroRNAs in Arabidopsis Thaliana. Genes Dev. 20, 3407–3425 (2006).
-
Wang, Y., Li, H., Sun, Q. & Yao, Y. Characterization of small RNAs derived from tRNAs, rRNAs and snornas and their response to heat stress in wheat seedlings. PLoS One. 11, e0150933 (2016).
-
Tang, G. Plant micrornas: an insight into their gene structures and evolution. Semin Cell. Dev. Biol. 21, 782–789 (2010).
-
Zhou, M. et al. Genome-wide analysis of clustering patterns and flanking characteristics for plant MicroRNA genes. FEBS J. 278, 929–940 (2011).
-
Li, Y., Pi, M., Gao, Q., Liu, Z. & Kang, C. Updated annotation of the wild strawberry Fragaria Vesca V4 genome. Hortic. Res. 6, 61 (2019).
-
Bai, S. et al. Genome-wide identification of MicroRNAs involved in the regulation of fruit ripening and climacteric stages in melon (Cucumis melo). Hortic. Res. 7, 106 (2020).
-
Mazurier, M. et al. Integrated sRNA-seq and RNA-seq analyses reveal a MicroRNA regulation network involved in cold response in Pisum sativum L. Genes (Basel). 13, 1119 (2022).
-
Cui, J., You, C. & Chen, X. The evolution of MicroRNAs in plants. Curr. Opin. Plant. Biol. 35, 61–67 (2017).
-
Hajieghrari, B. & Farrokhi, N. Investigation on the conserved MicroRNA genes in higher plants. Plant. Mol. Biol. Rep. 39, 10–23 (2021).
-
Mango Genome Consortium. The ‘Tommy atkins’ Mango genome reveals candidate genes for fruit quality. BMC Plant. Biol. 21, 1–18 (2021).
-
Wang, P. et al. The genome evolution and domestication of tropical fruit Mango. Genome Biol. 21, 60 (2020).
-
Qin, L., Xu, P. & Jiao, Y. Evolution of plant conserved MicroRNAs after Whole-Genome duplications. Genome Biol. Evol. 17, evaf045 (2025).
-
Zhang, W. et al. Multiple distinct small RNAs originate from the same MicroRNA precursors. Genome Biol. 11, R81 (2010).
-
Bologna, N. G. & Voinnet, O. The Diversity, Biogenesis, and activities of endogenous Silencing small RNAs in Arabidopsis. Annu. Rev. Plant. Biol. 65, 473–503 (2014).
-
Zhu, X. et al. High-Throughput Sequencing-Based identification of Arabidopsis MiRNAs induced by phytophthora capsici infection. Front. Microbiol. 11, 1094 (2020).
-
Zhou, R. et al. Identification of MiRNAs and their targets in wild tomato at moderately and acutely elevated temperatures by high-throughput sequencing and degradome analysis. Sci. Rep. 6, 33777 (2016).
-
Xu, R., Liu, C., Li, N. & Zhang, S. Global identification and expression analysis of stress-responsive genes of the argonaute family in Apple. Mol. Genet. Genomics. 291, 2015–2030 (2016).
-
Vaucheret, H., Mallory, A. C. & Bartel, D. P. AGO1 homeostasis entails coexpression of MIR168 and AGO1 and Preferential stabilization of miR168 by AGO1. Mol. Cell. 22, 129–136 (2006).
-
Mejía-Mendoza, M. A., Garcidueñas-Piña, C., Barrera-Figueroa, B. E. & Morales-Domínguez, J. F. Identification and profiling analysis of MicroRNAs in guava fruit (Psidium Guajava L.) and their role during ripening. Genes (Basel). 14, 2029 (2023).
-
Francischini, C. W. & Quaggio, R. B. Molecular characterization of Arabidopsis Thaliana PUF proteins – binding specificity and target candidates. FEBS J. 276, 5456–5470 (2009).
-
Cheng, P. et al. Genome-wide identification and analysis of TCP transcription factor genes in Rosa chinensis in response to abiotic stress and fungal diseases. Ornam. Plant. Res. 3, 1–11 (2023).
-
Shi, X. P. et al. MicroRNA319 family members play an important role in solanum habrochaites and S. lycopersicum responses to chilling and heat stresses. Biol. Plant. 63, 200–209 (2019).
-
Jia, P. et al. Cotton miR319b-Targeted TCP4-Like enhances plant defense against verticillium dahliae by activating GhICS1 transcription expression. Front. Plant. Sci. 13, 870882 (2022).
-
Lan, J. et al. Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules. Nat. Commun. 14, 5673 (2023).
-
Yin, H. et al. miR156/SPL9 regulates reactive oxygen species accumulation and immune response in Arabidopsis Thaliana. Phytopathology 109, 632–642 (2019).
-
Fortunato, S., Lasorella, C., Dipierro, N., Vita, F. & de Pinto, M. C. Redox signaling in plant heat stress response. Antioxidants 12, 605 (2023).
-
Jiao, P. et al. ZmTCP14, a TCP transcription factor, modulates drought stress response in Zea Mays L. Environ. Exp. Bot. 208, 105232 (2023).
-
Jones-Rhoades, M. W., Bartel, D. P. & Bartel, B. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant. Biol. 57, 19–53 (2006).
-
Wang, Y. et al. TamiR159 directed wheat TaGAMYB cleavage and its involvement in anther development and heat response. PLoS One. 7, e48445 (2012).
-
Jiang, N. et al. Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction. Hortic. Res. 6, 28 (2019).
-
Ma, W. et al. Coupling of micro RNA-directed phased small interfering RNA generation from long noncoding genes with alternative splicing and alternative polyadenylation in small RNA‐mediated gene Silencing. New Phytol. 217, 1535–1550 (2018).
-
Várallyay, É., Válóczi, A., Ágyi, Á., Burgyán, J. & Havelda, Z. Plant virus-mediated induction of miR168 is associated with repression of ARGONAUTE1 accumulation. EMBO J. 29, 3507–3519 (2010).
-
Shivaprasad, P. V. et al. A MicroRNA superfamily regulates nucleotide binding Site–Leucine-Rich repeats and other mRNAs. Plant. Cell. 24, 859–874 (2012).
-
López-Gómez, R. & Gómez-Lim, M. A. A method for extracting intact RNA from fruits rich in polysaccharides using ripe Mango mesocarp. HortScience 27, 440–442 (1992).
-
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
-
Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).
-
Axtell, M. J. & ShortStack Comprehensive annotation and quantification of small RNA genes. RNA 19, 740–751 (2013).
-
Kozomara, A., Birgaoanu, M. & Griffiths-Jones, S. MiRBase: from MicroRNA sequences to function. Nucleic Acids Res. 47, D155–D162 (2019).
-
Wong, T. et al. IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. Preprint at (2025). https://doi.org/10.32942/X2P62N
-
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78–W82 (2024).
-
Schwab, R. et al. Specific effects of MicroRNAs on the plant transcriptome. Dev. Cell. 8, 517–527 (2005).
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
-
Gotz, S. et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 36, 3420–3435 (2008).
-
Gruber, A. R., Lorenz, R., Bernhart, S. H., Neubock, R. & Hofacker, I. L. The Vienna RNA websuite. Nucleic Acids Res. 36, W70–W74 (2008).
-
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).
-
Chen, C. et al. Real-time quantification of MicroRNAs by stem–loop RT–PCR. Nucleic Acids Res. 33, e179–e179 (2005).
-
Kramer, M. F. Stem-Loop RT‐qPCR for MiRNAs. Curr. Protoc. Mol. Biol. 95, 1–15 (2011).
-
Schmittgen, T. D. & Livak, K. J. Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 3, 1101–1108 (2008).
-
Li, X. Infiltration of Nicotiana benthamiana protocol for transient expression via Agrobacterium. Bio-protocol 1, e95 (2011).
-
Ferdous, J., Hanafi, M. M., Rafii, M. Y. & Muhammad, K. A quick DNA extraction protocol: without liquid nitrogen in ambient temperature. Afr. J. Biotechnol. 11, 6956–6964 (2012).
