مطالعه بیوانفورماتیکی عوامل رونویسی bHLH دخیل در بیوسنتز سزکویی‌ترپن‌لاکتون‌ها در آفتابگردان

Alfieri, M., Vaccaro, M. C., Cappetta, E., Ambrosone, A., De Tommasi, N., & Leone, A. (2018). Coactivation of MEP-biosynthetic genes and accumulation of abietane diterpenes in Salvia sclarea by heterologous expression of WRKY and MYC2 transcription factors. Scientific Reports, 8(1), 11009. https://doi.org/10.1038/s41598-018-29389-4

Álvarez-Calero, J. M., Ruiz, E., López-Pérez, J. L., Jaraiz, M., Rubio, J. E., Jorge, Z. D., Suarez, M., & Massanet, G. M. (2018). 15-Hydroxygermacranolides as sources of structural diversity: synthesis of sesquiterpene lactones by cyclization and rearrangement reactions. Experimental and DFT study. The Journal of Organic Chemistry, 83(10), 5480-5495. https://doi.org/10.1021/acs.joc.8b00407

Amrehn, E., Aschenbrenner, A.-K., Heller, A., & Spring, O. (2016). Localization of sesquiterpene lactone biosynthesis in cells of capitate glandular trichomes of Helianthus annuus (Asteraceae). Protoplasma, 253(2), 447-455. https://doi.org/10.1007/s00709-015-0823-4

Badouin, H., Gouzy, J., Grassa, C. J., Murat, F., Staton, S. E., Cottret, L., Lelandais-Brière, C., Owens, G. L., Carrère, S., & Mayjonade, B. (2017). The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature, 546(7656), 148-152. https://doi.org/10.1038/nature22380

Basak, A. (2022). ER bodies and their impact in shaping root microbiota . https://doi.org/10.1038/nature22380

Bassolino, L., Buti, M., Fulvio, F., Pennesi, A., Mandolino, G., Milc, J., Francia, E., & Paris, R. (2020). In silico identification of MYB and bHLH families reveals candidate transcription factors for secondary metabolic pathways in Cannabis sativa L. Plants, 9(11), 1540. https://doi.org/10.3390/plants9111540

Burns, J. J., Shealy, B. T., Greer, M. S., Hadish, J. A., McGowan, M. T., Biggs, T., Smith, M. C., Feltus, F. A., & Ficklin, S. P. (2022). Addressing noise in co-expression network construction. Briefings in bioinformatics, 23(1). https://doi.org/10.1093/bib/bbab495

Castillon, A., Shen, H., & Huq, E. (2007). Phytochrome interacting factors: central players in phytochrome-mediated light signaling networks. Trends in plant science, 12(11), 514-521. https://doi.org/10.1016/j.tplants.2007.10.001

Chang, S., Li, Q., Huang, B., Chen, W., & Tan, H. (2023). Genome-wide identification and characterisation of bHLH transcription factors in Artemisia annua. BMC plant biology, 23(1), 63. https://doi.org/10.1186/s12870-023-04063-8

Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & Xia, R. (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular plant, 13(8), 1194-1202.

Chen, T., Li, Y., Xie, L., Hao, X., Liu, H., Qin, W., Wang, C., Yan, X., Wu-Zhang, K., & Yao, X. (2021). AaWRKY17, a positive regulator of artemisinin biosynthesis, is involved in resistance to Pseudomonas syringae in Artemisia annua. Horticulture Research, 8. https://doi.org/10.1016/j.molp.2020.06.009

Eidi, M., Abdolalizadeh, S., Nasirpour, M. H., Zahiri, J., & Garshasbi, M. (2024). 123FASTQ: an intuitive and efficient tool for preprocessing Illumina FASTQ reads. bioRxiv, 2024.2003. 2008.584032. https://doi.org/10.1101/2024.03.08.584032

Fasoli, B., Lin, J. C., Bowling, D. R., Mitchell, L., & Mendoza, D. (2018). Simulating atmospheric tracer concentrations for spatially distributed receptors: updates to the Stochastic Time-Inverted Lagrangian Transport model's R interface (STILT-R version 2). Geoscientific Model Development, 11(7), 2813-2824. https://doi.org/10.5194/gmd-11-2813-2018

Frey, M., Schmauder, K., Pateraki, I., & Spring, O. (2018). Biosynthesis of Eupatolide—A metabolic route for sesquiterpene lactone formation involving the P450 enzyme CYP71DD6. ACS Chemical Biology, 13(6), 1536-1543. https://doi.org/10.1021/acschembio.8b00126.

Galisteo, A., Pérez Rodríguez, Á., González, A., Barrero, A. F., & Quílez del Moral, J. F. (2024). Terpenoid diversity in sunflower (Helianthus annuus L.) and their potential in crop protection. Phytochemistry Reviews, 23(3), 583-623. https://doi.org/10.1007/s11101-023-09903-x

Guo, J., Sun, B., He, H., Zhang, Y., Tian, H., & Wang, B. (2021). Current understanding of bHLH transcription factors in plant abiotic stress tolerance. International Journal of Molecular Sciences, 22(9), 4921. https://doi.org/10.3390/ijms22094921

Guo, X.-J., & Wang, J.-R. (2017). Global identification, structural analysis and expression characterization of bHLH transcription factors in wheat. BMC plant biology, 17(1), 90. https://doi.org/10.1016/B978-0-12-800854-6.00003-8

Hong, J. C. (2016). General aspects of plant transcription factor families. In Plant transcription factors, 35-56. Elsevier. https://doi.org/10.1007/s11240-021-02049-8

Huang, H., Xing, S., Tang, K., & Jiang, W. (2021). AaWRKY4 upregulates artemisinin content through boosting the expressions of key enzymes in artemisinin biosynthetic pathway. Plant Cell, Tissue and Organ Culture (PCTOC), 146(1), 97-105. https://doi.org/10.1007/s11240-021-02049-8

Hurrah, I. M., Kumar, A., & Abbas, N. (2025). Synergistic interaction of AaMYC2 and AaMYC2-LIKE enhances artemisinin production in Artemisia annua L. Journal of Biotechnology, 402, 69-78. https://doi.org/10.1016/j.jbiotec.2025.03.007

Jindal, S., & Ali, A. (2025). First detection and identification of southern tomato virus infecting tomatoes in oklahoma with complete genome characterization and insights into global genetic diversity. Viruses, 17(9), 1193. https://doi.org/10.3390/v17091193

Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology, 37(8), 907-915. https://doi.org/10.1038/s41587-019-0201-4

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & Subgroup, G. P. D. P. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. https://doi.org/10.1093/bioinformatics/btp352

Li, J., Li, X., Han, P., Liu, H., Gong, J., Zhou, W., Shi, B., Liu, A., & Xu, L. (2021). Genome-wide investigation of bHLH genes and expression analysis under different biotic and abiotic stresses in Helianthus annuus L. International Journal of Biological Macromolecules, 189, 72-83. https://doi.org/10.1016/j.ijbiomac.2021.08.072

Li, J., Sima, W., Ouyang, B., Wang, T., Ziaf, K., Luo, Z., Liu, L., Li, H., Chen, M., & Huang, Y. (2012). Tomato SlDREB gene restricts leaf expansion and internode elongation by downregulating key genes for gibberellin biosynthesis. Journal of Experimental Botany, 63(18), 6407-6420. https://doi.org/10.1093/jxb/ers295

Liao, Y., Smyth, G. K., & Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930. https://doi.org/10.1093/bioinformatics/btt656

Majdi, M., Liu, Q., Karimzadeh, G., Malboobi, M. A., Beekwilder, J., Cankar, K., de Vos, R., Todorović, S., Simonović, A., & Bouwmeester, H. (2011). Biosynthesis and localization of parthenolide in glandular trichomes of feverfew (Tanacetum parthenium L. Schulz Bip.). Phytochemistry, 72(14-15), 1739-1750. https://doi.org/10.1016/j.phytochem.2011.04.021

Majid, I., Kumar, A., & Abbas, N. (2019). A basic helix loop helix transcription factor, AaMYC2-Like positively regulates artemisinin biosynthesis in Artemisia annua L. Industrial Crops and Products, 128, 115-125. https://doi.org/10.1016/j.indcrop.2018.10.083

Maqsood, H., Munir, F., Amir, R., & Gul, A. (2022). Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. Frontiers in Plant Science, 13, 1031679. https://doi.org/10.3389/fpls.2022.1031679

Matías‐Hernández, L., Jiang, W., Yang, K., Tang, K., Brodelius, P. E., & Pelaz, S. (2017). Aa MYB 1 and its orthologue At MYB 61 affect terpene metabolism and trichome development in Artemisia annua and Arabidopsis thaliana. The Plant Journal, 90(3), 520-534. https://doi.org/10.1111/tpj.13509

Mohammad, Hurrah, I. M., Kumar, A., & Abbas, N. (2023). Synergistic interaction of two bHLH transcription factors positively regulates artemisinin biosynthetic pathway in Artemisia annua L. Physiologia plantarum, 175(1), e13849. https://doi.org/10.1111/ppl.13849

Nallamilli, B. R. R., Zhang, J., Mujahid, H., Malone, B. M., Bridges, S. M., & Peng, Z. (2013). Polycomb group gene OsFIE2 regulates rice (Oryza sativa) seed development and grain filling via a mechanism distinct from Arabidopsis. PLoS genetics, 9(3), e1003322. https://doi.org/10.1371/journal.pgen.1003322

Nouri, M.-Z., Moumeni, A., & Komatsu, S. (2015). Abiotic stresses: insight into gene regulation and protein expression in photosynthetic pathways of plants. International Journal of Molecular Sciences, 16(9), 20392-20416. https://doi.org/10.3390/ijms160920392

Pires, N., & Dolan, L. (2010). Origin and diversification of basic-helix-loop-helix proteins in plants. Molecular biology and evolution, 27(4), 862-874. https://doi.org/10.1093/molbev/msp288

Schmitz, R. J., Grotewold, E., & Stam, M. (2022). Cis-regulatory sequences in plants: their importance, discovery, and future challenges. The Plant Cell, 34(2), 718-741. . https://doi.org/10.1093/plcell/koab281

Serin, E. A., Nijveen, H., Hilhorst, H. W., & Ligterink, W. (2016). Learning from co-expression networks: possibilities and challenges. Frontiers in Plant Science, 7, 444. https://doi.org/10.3389/fpls.2016.00444

Shen, Q., Lu, X., Yan, T., Fu, X., Lv, Z., Zhang, F., Pan, Q., Wang, G., Sun, X., & Tang, K. (2016). The jasmonate‐responsive Aa MYC 2 transcription factor positively regulates artemisinin biosynthesis in Artemisia annua. New Phytologist, 210(4), 1269-1281. https://doi.org/10.1111/nph.13874

Spring, O. (2021). Sesquiterpene lactones in sunflower oil. Lwt, 142, 111047. https://doi.org/10.1016/j.lwt.2021.111047

Spring, O., Schmauder, K., Lackus, N. D., Schreiner, J., Meier, C., Wellhausen, J., Smith, L. V., & Frey, M. (2020). Spatial and developmental synthesis of endogenous sesquiterpene lactones supports function in growth regulation of sunflower. Planta, 252(1), 2. https://doi.org/10.1007/s00425-020-03409-y

Sultana, M., Tayyab, M., Sunil, Parveen, S., Hussain, M., Saeed, S., Riaz, Z., & Shabbir, S. (2025). In silico molecular characterization of TGF-β gene family in Bufo bufo: genome-wide analysis. Journal of Biomolecular Structure and Dynamics, 43(12), 5834-5848. https://doi.org/10.1080/07391102.2024.2313168

Swift, J., Alvarez, J. M., Araus, V., Gutiérrez, R. A., & Coruzzi, G. M. (2020). Nutrient dose-responsive transcriptome changes driven by Michaelis–Menten kinetics underlie plant growth rates. Proceedings of the National Academy of Sciences, 117(23), 12531-12540. https://doi.org/10.1073/pnas.191861911

Tissot, N., Robe, K., Gao, F., Grant‐Grant, S., Boucherez, J., Bellegarde, F., Maghiaoui, A., Marcelin, R., Izquierdo, E., & Benhamed, M .(2019).Transcriptional integration of the responses to iron availability in Arabidopsis by the bHLH factor ILR3. New Phytologist, 223(3), 1433-1446. https://doi.org/10.1111/nph.15753 

Wang, R., Zhao, P., Kong, N., Lu, R., Pei, Y., Huang, C., Ma, H., & Chen, Q. (2018). Genome-wide identification and characterization of the potato bHLH transcription factor family. Genes, 9(1), 54. https://doi.org/10.3390/genes9010054

Wang, X., Sun, W., Fang, S., Dong, B., Li, J., Lv, Z., Li, W., & Chen, W. (2023). AaWRKY6 contributes to artemisinin accumulation during growth in Artemisia annua. Plant science, 335, 111789. https://doi.org/10.1016/j.plantsci.2023.111789

Wu, Y., Wang, Y., Shi, H., Hu, H., Yi, L., & Hou, J. (2022). Time-course transcriptome and WGCNA analysis revealed the drought response mechanism of two sunflower inbred lines. PloS one, 17(4), e0265447.  https://doi.org/10.1371/journal.pone.0265447

Wu, Z., Li, L., Liu, H., Yan, X., Ma, Y., Li, Y., Chen, T., Wang, C., Xie, L., & Hao, X. (2021). AaMYB15, an R2R3-MYB TF in Artemisia annua, acts as a negative regulator of artemisinin biosynthesis. Plant science, 308, 110920. https://doi.org/10.1016/j.plantsci.2021.110920

Xiang, L., He, P., Shu, G., Yuan, M., Wen, M., Lan, X., Liao, Z., & Tang, Y. (2022). AabHLH112, a bHLH transcription factor, positively regulates sesquiterpenes biosynthesis in Artemisia annua. Frontiers in Plant Science, 13, 973591. https://doi.org/10.3389/fpls.2022.973591

Xu, F., Tang, J., Wang, S., Cheng, X., Wang, H., Ou, S., Gao, S., Li, B., Qian, Y., & Gao, C. (2022). Antagonistic control of seed dormancy in rice by two bHLH transcription factors. Nature genetics, 54(12), 1972-1982. https://doi.org/10.1038/s41588-022-01240-7

Zhang, F., Fu, X., Lv, Z., Lu, X., Shen, Q., Zhang, L., Zhu, M., Wang, G., Sun, X., & Liao, Z. (2015). A basic leucine zipper transcription factor, AabZIP1, connects abscisic acid signaling with artemisinin biosynthesis in Artemisia annua. Molecular plant, 8(1), 163-175. ttps://doi.org/10.1016/j.molp.2014.12.004

Zhang, Z., Chen, J., Liang, C., Liu, F., Hou, X., & Zou, X. (2020). Genome-wide identification and characterization of the bHLH transcription factor family in pepper (Capsicum annuum L.). Frontiers in Genetics, 11, 570156. https://doi.org/10.3389/fgene.2020.570156

Zhou, L., Lu, Y., Huang, J., Sha, Z., Mo, W., Xue, J., Ma, S., Shi, W., Yang, Z., & Gao, J. (2021). Arabidopsis CIB3 regulates photoperiodic flowering in an FKF1-dependent way. Bioscience, Biotechnology, and Biochemistry, 85(4), 765-774. https://doi.org/10.1093/bbb/zbaa120

Zhou, X., Liao, Y., Kim, S.-U., Chen, Z., Nie, G., Cheng, S., Ye, J., & Xu, F. (2020). Genome-wide identification and characterization of bHLH family genes from Ginkgo biloba. Scientific reports, 10(1), 13723. https://doi.org/10.1038/s41598-020-69305-3