1. Aguirre, G. and Pilon, M. (2016). Copper delivery to chloroplast proteins and its regulation. Frontiers in Plant Science, 6: 174909. [DOI:10.3389/fpls.2015.01250]

2. Ahmad, W. (2016). Ethnopharmacology of Quercus infectoria Olivier galls: A review. Hippocratic Journal of Unani Medicine, 11: 105-18.

3. Ahmadi, E., Kowsari, M., Azadfar, D. and Jouzani, G.S. (2018). Rapid and economical protocols for genomic and metagenomic DNA extraction from oak (Quercus brantii Lindl.). Annals of Forest Science, 75: 1-14. [DOI:10.1007/s13595-018-0705-y]

4. Askari, F., Azadi, A., Namavar-Jahromi, B., Tansaz, M., Mirzapour Nasiri, A. and Mohagheghzadeh, A. (2020). A Comprehensive review about Quercus infectoria G. Olivier Gall. Research Journal of Pharmacognosy, 7: 69-77.

5. Aung, B., Gruber, M.Y. and Hannoufa, A. (2015). The microRNA156 system: a tool in plant biotechnology. Biocatalysis and Agricultural Biotechnology, 4: 432-442. [DOI:10.1016/j.bcab.2015.08.002]

6. Banc, R., Rusu, M.E., Filip, L. and Popa, D.-S. (2023). Phytochemical profiling and biological activities of quercus sp. galls (Oak galls): a systematic review of studies published in the last 5 years. Plants, 12: 3873. [DOI:10.3390/plants12223873]

7. Barczak-Brzyżek, A., Brzyżek, G., Koter, M., Siedlecka, E., Gawroński, P. and Filipecki, M. (2022). Plastid retrograde regulation of miRNAs expression in response to light stress. BMC Plant Biology, 22: 150. [DOI:10.1186/s12870-022-03525-9]

8. Chaves, I., Lin, Y.C., Pinto-Ricardo, C., Van de Peer, Y. and Miguel, C. (2014). miRNAs profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns. Tree genetics & Genomes, 10: 721-737. [DOI:10.1007/s11295-014-0717-1]

9. Clément, M., Leonhardt, N., Droillard, M.J., Reiter, I., Montillet, J.L., Genty, B., Lauriere, C., Nussaume, L. and Noël, L.D. (2011). The cytosolic/nuclear HSC70 and HSP90 molecular chaperones are important for stomatal closure and modulate abscisic acid-dependent physiological responses in Arabidopsis. Plant Physiology, 156: 1481-1492. [DOI:10.1104/pp.111.174425]

10. Devis, D., Firth, S.M., Liang, Z. and Byrne, M.E. (2015). Dosage sensitivity of RPL9 and concerted evolution of ribosomal protein genes in plants. Frontiers in Plant Science, 6: 168975. [DOI:10.3389/fpls.2015.01102]

11. Deng, Y. and Lu, S. (2017). Biosynthesis and regulation of phenylpropanoids in plants. Critical Reviews in Plant Sciences, 36: 257-290. [DOI:10.1080/07352689.2017.1402852]

12. Djami-Tchatchou, A.T. and Straker, C.J. (2012). The isolation of high quality RNA from the fruit of avocado (Persea americana Mill.). South African Journal of Botany, 78: 44-46. [DOI:10.1016/j.sajb.2011.04.009]

13. Elham, A., Arken, M., Kalimanjan, G., Arkin, A. and Iminjan, M. (2020). A review of the phytochemical, pharmacological, pharmacokinetic, and toxicological evaluation of Quercus infectoria galls. Journal of Ethnopharmacology, 237: 113592. [DOI:10.1016/j.jep.2020.113592]

14. Garg, R. and Jain, M. (2013) RNA-Seq for transcriptome analysis in non-model plants. In: Jain, M. and Garg, R., Eds., Legume Genomics: Methods and Protocol, pp. 43-58, Springer, New York, USA. [DOI:10.1007/978-1-62703-613-9_4]

15. Giron, D., Huguet, E., Stone, G.N. and Body, M. (2016). Insect-induced effects on plants and possible effectors used by galling and leaf-mining insects to manipulate their host-plant. Journal of Insect Physiology, 84: 70-89. [DOI:10.1016/j.jinsphys.2015.12.009]

16. Griffiths-Jones, S. (2006). miRBase: the microRNA sequence database. In: Ying, S.Y. ed., MicroRNA Protocols, pp. 129-138, Totowa, Humana Press, New Jersey, USA. [DOI:10.1385/1-59745-123-1:129]

17. Gutiérrez-García, C., Ahmed, S.S., Ramalingam, S., Selvaraj, D., Srivastava, A., Paul, S. and Sharma, A. (2021). Identification of microRNAs from medicinal plant Murraya koenigii by high-throughput sequencing and their functional implications in secondary metabolite biosynthesis. Plants, 11: 46. [DOI:10.3390/plants11010046]

18. Hao, K., Wang, Y., Zhu, Z., Wu, Y., Chen, R. and Zhang, L. (2022). miR160: An indispensable regulator in plant. Frontiers in Plant Science, 13: 833322. [DOI:10.3389/fpls.2022.833322]

19. He, F., Pan, Q.H., Shi, Y. and Duan, C.Q. (2008). Biosynthesis and genetic regulation of proanthocyanidins in plants. Molecules, 13: 2674-2703. [DOI:10.3390/molecules13102674]

20. Hossain, R., Quispe, C., Saikat, A.S.M., Jain, D., Habib, A., Janmeda, P., Islam, M.T., Daştan, S.D., Kumar, M. and Butnariu, M. (2022). Biosynthesis of secondary metabolites based on the regulation of microRNAs. BioMed Research International, 2022: 9349897. [DOI:10.1155/2022/9349897]

21. Jeena, G.S., Singh, N. and Shukla, R.K. (2022). An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism. Plant Cell Reports, 41(8): 1-21. [DOI:10.1007/s00299-022-02877-8]

22. Karami, S., Shiran, B., Ravash, R. and Fallahi, H. (2023). A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress. PLoS One, 18: e0287761. [DOI:10.1371/journal.pone.0287761]

23. Kaur, G., Hamid, H., Ali, A., Alam, M.S. and Athar, M. (2004). Antiinflammatory evaluation of alcoholic extract of galls of Quercus infectoria. Journal of Ethnopharmacology, 90: 285-292. [DOI:10.1016/j.jep.2003.10.009]

24. Khare, S., Singh, N., Singh, A., Hussain, I., Niharika, K., Yadav, V., Bano, C., Yadav, R.K. and Amist, N. (2020). Plant secondary metabolites synthesis and their regulations under biotic and abiotic constraints. Journal of Plant Biology, 63: 203-216. [DOI:10.1007/s12374-020-09245-7]

25. Kumar, M., Prakash, S., Kumari, N., Pundir, A., Punia, S., Saurabh, V., Choudhary, P., Changan, S., Dhumal, S. and Pradhan, P.C. (2021). Beneficial role of antioxidant secondary metabolites from medicinal plants in maintaining oral health. Antioxidants, 10: 1061. [DOI:10.3390/antiox10071061]

26. Li, H., Lin, Q., Yan, M., Wang, M., Wang, P., Zhao, H., Wang, Y., Ni, D. and Guo, F. (2021). Relationship between secondary metabolism and miRNAs for important flavor compounds in different tissues of tea plant (Camellia sinensis) as revealed by genome-wide miRNAs analysis. Journal of Agricultural and Food Chemistry, 69: 2001-2012. [DOI:10.1021/acs.jafc.0c07440]

27. Li, W., He, Z., Yang, S., Ye, Y., Jiang, H. and Wang, L. (2019). Construction and analysis of a library of miRNAs in gold-coloured mutant leaves of L. Folia Horticulturae, 31: 81-92. [DOI:10.2478/fhort-2019-0005]

28. Liu, M.-H., Yang, B.R., Cheung, W.F., Yang, K.Y., Zhou, H.F., Kwok, J.S.L., Liu, G.C., Li, X.F., Zhong, S. and Lee, S.M.Y. (2015). Transcriptome analysis of leaves, roots and flowers of Panax notoginseng identifies genes involved in ginsenoside and alkaloid biosynthesis. BMC Genomics, 16: 1-12. [DOI:10.1186/s12864-015-1477-5]

29. Loke, K.K., Rahnamaie-Tajadod, R., Yeoh, C.C., Goh, H.H., Mohamed-Hussein, Z.A., Zainal, Z., Ismail, I. and Noor, N.M. (2017). Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids. PeerJournal, 5: e2938. [DOI:10.7717/peerj.2938]

30. López de Heredia, U. and Vázquez-Poletti, J. (2016). RNA-seq analysis in forest tree species: bioinformatic problems and solutions. Tree Genet. Genomes, 12: 30. [DOI:10.1007/s11295-016-0995-x]

31. Luo, Y., Zhang, X., Luo, Z., Zhang, Q. and Liu, J. (2015). Identification and characterization of microRNAs from Chinese pollination constant non-astringent persimmon using high-throughput sequencing. BMC Plant Biology, 15: 1-18. [DOI:10.1186/s12870-014-0400-6]

32. Marcela, V.-H., Gerardo, V.M., Agustín, A.R.C., Antonio, G.M.M., Oscar, R., Diego, C.P. and Cruz-Hernández, A. (2019). MicroRNAs associated with secondary metabolites production. In: Soto-Hernández, M., García-Mateos, R. and Palma-Tenango, M. Eds., Plant Physiological Aspects of Phenolic Compounds, pp. 51-64, BoD-Books on Demand, Norderstedt, GER. [DOI:10.5772/intechopen.83804]

33. Martin, J.A. and Wang, Z. (2011). Next-generation transcriptome assembly. Nature Reviews Genetics, 12: 671-682. [DOI:10.1038/nrg3068]

34. Mehrnia, Mohamad, Nejadsatari, taher, Asadi, Mostafa, Mehregan and Iraj (2013). The introduction of Quercus infectoria as a medicinal plant In the Zagros mountains and determination its DNA Barcoding. 15: 111-120.

35. Mehta, A., Gupta, H., Rawal, R., Mankad, A., Tiwari, T., Patel, M. and Ghosh, A. (2016). In silico microRNA identification from stevia rebaudiana transcriptome assembly. European Journal of Medicinal Plants, 15: 1-14. [DOI:10.9734/EJMP/2016/25221]

36. Mir Drikvand, R. and Samiei, K. (2020). Evaluation and Comparison of the efficiency of different molecular markers in estimating genetic distance of different persian oak (Quercus brantii Lindi.) populations in Lorestan province, Iran. Plant Genetic Researches, 7: 33-46 (In Persian). [DOI:10.52547/pgr.7.1.3]

37. Mir Drikvand, R., Sohrabi, S.S., ُSohrabi, S.M. and Samiei, K. (2019). Identification and characterization of conserved miRNAs of Coriandrum sativum L. using next-generation sequencing data. Crop Biotechnology, 9(25):.59-74 (In Persian).

38. Moin, M., Bakshi, A., Madhav, M. and Kirti, P. (2017). Expression profiling of ribosomal protein gene family in dehydration stress responses and characterization of transgenic rice plants overexpressing RPL23A for water-use efficiency and tolerance to drought and salt stresses. Frontiers in Chemistry, 5: 97. [DOI:10.3389/fchem.2017.00097]

39. Negi, A., Shukla, A., Jaiswar, A., Shrinet, J. and Jasrotia, R.S. (2022). Applications and challenges of microarray and RNA-sequencing. In: Singh, D.B. and, Rajesh Kumar Pathak, R.K., Ed., Bioinformatics Methods and Applications, pp. 91-103, Academic Press address, Cambridge, UK. [DOI:10.1016/B978-0-323-89775-4.00016-X]

40. Numnark, S., Mhuantong, W., Ingsriswang, S. and Wichadakul, D. (2012). C-mii: a tool for plant miRNAs and target identification. Paper presented at the BMC Genomics, 13: 1-10. [DOI:10.1186/1471-2164-13-S7-S16]

41. Owusu Adjei, M., Zhou, X., Mao, M., Rafique, F. and Ma, J. (2021). MicroRNAs roles in plants secondary metabolism. Plant Signaling & Behavior, 16: 1915590. [DOI:10.1080/15592324.2021.1915590]

42. Pagano, L., Rossi, R., Paesano, L., Marmiroli, N. and Marmiroli, M. (2021). miRNAs regulation and stress adaptation in plants. Environmental and Experimental Botany, 184: 104369. [DOI:10.1016/j.envexpbot.2020.104369]

43. Pasandideh Arjmand, M., Samizadeh Lahiji, H., Biglouei, M.H. and Mohsenzadeh Golfazani, M. (2021). In silico identification of drought responsive miRNAs target genes in Canola (Brassica napus). Journal of Plant Research (Iranian Journal of Biology), 36(2): 110-126 (In Persian).

44. Pirbaluti, F.G., Saravi, A.T. and Arani, A.M. (2017). Karyotypic analysis of Quercus infectoria G.Olive Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research, 25(2): 324-336 (In Persian).

45. Ramezani, M., Nazarian-Firouzabadi, F., Ismaili, A. and Sohrabi, S.S. (2022). De novo transcriptome assembly and conserved microRNAs identification of medicinal plant, Kelussia odoratissima Mozaff. Crop Biotechnology, 11(37): 55-76 (In Persian).

46. Ramsøe, A., Clark, M.S. and Sleight, V.A. (2020). Gene network analyses support subfunctionalization hypothesis for duplicated hsp70 genes in the Antarctic clam. Cell Stress and Chaperones, 25: 1111-1116. [DOI:10.1007/s12192-020-01118-9]

47. Singh, N., Srivastava, S., Shasany, A.K. and Sharma, A. (2016). Identification of miRNAs and their targets involved in the secondary metabolic pathways of Mentha spp. Computational Biology and Chemistry, 64: 154-162. [DOI:10.1016/j.compbiolchem.2016.06.004]

48. Sobral, R., Silva, H.G., Laranjeira, S., Magalhães, J., Andrade, L., Alhinho, A.T. and Costa, M.M.R. (2020). Unisexual flower initiation in the monoecious Quercus suber L.: a molecular approach. Tree Physiology, 40: 1260-1276. [DOI:10.1093/treephys/tpaa061]

49. Sohrabi, S.S., Ismaili, A., Nazarian, F. and Hossein, F. (2020). Identification and characterization of conserved miRNAs in lentil. Cellular and Molecular Research (Iranian Journal of Biology), 32(4): 432-444 (In Persian).

50. Song, Y., Feng, L., Alyafei, M.A.M., Jaleel, A. and Ren, M. (2021). Function of chloroplasts in plant stress responses. International Journal of Molecular Sciences, 22(24): 13464. [DOI:10.3390/ijms222413464]

51. Tayel, A.A., El-Sedfy, M.A., Ibrahim, A.I. and Moussa, S.H. (2018). Application of Quercus infectoria extract as a natural antimicrobial agent for chicken egg decontamination. Revista Argentina de Microbiologia, 50: 391-397. [DOI:10.1016/j.ram.2017.12.003]

52. Vashisht, I., Mishra, P., Pal, T., Chanumolu, S., Singh, T.R. and Chauhan, R.S. (2015). Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa. Planta, 241: 1255-1268. [DOI:10.1007/s00425-015-2255-y]

53. Vivek, A. and Kumar, S. (2021). Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq. Briefings in Bioinformatics, 22: bbaa322. [DOI:10.1093/bib/bbaa322]

54. Wu, F., Du, Z., Hu, Z., Gan, L., Khaldun, A.B.M., Amombo, E., Huang, X. and Fan, J. (2023). Metabolomic analysis of arabidopsis ost1-4 mutant revealed the cold response regulation mechanisms by OPEN STOMATA 1 (OST1) at metabolic level. Agronomy, 13: 2567. [DOI:10.3390/agronomy13102567]

55. Ye, G., Zhang, H., Chen, B., Nie, S., Liu, H., Gao, W., Wang, H., Gao, Y. and Gu, L. (2019). De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth. The Plant Journal, 97: 779-794. [DOI:10.1111/tpj.14159]

56. Yusof, W.N.S.W. and Abdullah, H. (2020). Phytochemicals and cytotoxicity of Quercus infectoria ethyl acetate extracts on human cancer cells. Tropical Life Sciences Research, 31: 69. [DOI:10.21315/tlsr2020.31.1.5]

57. Zhang, B., Pan, X., Cox, S., Cobb, G. and Anderson, T. (2006). Evidence that miRNAs are different from other RNAs. Cellular and Molecular Life Sciences CMLS, 63: 246-254. [DOI:10.1007/s00018-005-5467-7]

58. Zhang, S., Wu, Y., Huang, X., Wu, W., Lyu, L. and Li, W. (2022). Research progress about microRNAs involved in plant secondary metabolism. International Journal of Biological Macromolecules, 216: 820-829. [DOI:10.1016/j.ijbiomac.2022.07.224]