84
Views
0
CrossRef citations to date
0
Altmetric
Article

Transcriptomics-based identification of transcription factors in the halophyte Apocynum venetum L.

, , , &
Pages 336-351 | Received 31 Jul 2023, Accepted 03 Nov 2023, Published online: 22 Nov 2023

References

  • Andrási, N., Pettkó-Szandtner, A., & Szabados, L. (2021). Diversity of plant heat shock factors: Regulation, interactions, and functions. Journal of Experimental Botany, 72(5), 1558–1575. https://doi.org/10.1093/jxb/eraa576
  • An, X. H., Tian, Y., Chen, K. Q., Liu, X. J., Liu, D. D., Xie, X. B., Cheng, C. G., Cong, P. H., & Hao, Y. J. (2015). MdMYB9 and MdMYB11 are involved in the regulation of the JA-induced biosynthesis of anthocyanin and proanthocyanidin in apples. Plant & Cell Physiology, 56(4), 650–662. https://doi.org/10.1093/pcp/pcu205
  • Ariyarathne, M. A., & Wone, B. W. M. (2022). Overexpression of the selaginella lepidophylla bHLH transcription factor enhances water-use efficiency, growth, and development in Arabidopsis. Plant Science: An International Journal of Experimental Plant Biology, 315, 111129. https://doi.org/10.1016/j.plantsci.2021.111129
  • Bailey, T. L., Johnson, J., Grant, C. E., & Noble, W. S. (2015). The MEME Suite. Nucleic Acids Research, 43(W1), W39–W49. https://doi.org/10.1093/nar/gkv416
  • Baillo, E. H., Kimotho, R. N., Zhang, Z., & Xu, P. (2019). Transcription factors associated with abiotic and biotic stress tolerance and their potential for crops improvement. Genes (Basel), 10(10), 771. https://doi.org/10.3390/genes10100771
  • Banikamali, M., Soltanloo, H., Ramezanpour, S. S., Yamchi, A., & Sorahinobar, M. (2020). Identification of salinity responsive genes in lavender through cDNA-AFLP. Biotechnology Reports (Amsterdam, Netherlands), 28, e00520. https://doi.org/10.1016/j.btre.2020.e00520
  • Bansal, J., Gupta, K., Rajkumar, M. S., Garg, R., & Jain, M. (2021). Draft genome and transcriptome analyses of halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors. Physiologia Plantarum, 173(4), 1309–1322. https://doi.org/10.1111/ppl.13284
  • Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10(1), 421. https://doi.org/10.1186/1471-2105-10-421
  • Chen, C., Chen, J., Shi, J., Chen, S., Zhao, H., Yan, Y., Jiang, Y., Gu, L., Chen, F., & Liu, X. (2019). A strategy for quality evaluation of salt-treated Apocyni Veneti Folium and discovery of efficacy-associated markers by fingerprint-activity relationship modeling. Scientific Reports, 9(1), 16666. https://doi.org/10.1038/s41598-019-52963-3
  • Cheng, C., Wang, J., Hou, W., Malik, K., Zhao, C., Niu, X., Liu, Y., Huang, R., Li, C., & Nan, Z. (2021). Elucidating the molecular mechanisms by which seed-borne endophytic fungi, epichloë gansuensis, increases the tolerance of achnatherum inebrians to NaCl stress. International Journal of Molecular Sciences, 22(24), 13191. https://doi.org/10.3390/ijms222413191
  • Chen, C., Liu, H., Wang, C., Liu, Z., Liu, X., Zou, L., Zhao, H., Yan, Y., Shi, J., & Chen, S. (2019). Metabolomics characterizes metabolic changes of Apocyni Veneti Folium in response to salt stress. Plant Physiology and Biochemistry, 144, 187–196. https://doi.org/10.1016/j.plaphy.2019.09.043
  • Chen, C., Wang, C., Liu, Z., Liu, X., Zou, L., Shi, J., Chen, S., Chen, J., & Tan, M. (2018). Variations in physiology and multiple bioactive constituents under salt stress provide insight into the quality evaluation of Apocyni Veneti Folium. International Journal of Molecular Sciences, 19(10), 3042. https://doi.org/10.3390/ijms19103042
  • Colinas, M., & Goossens, A. (2018). Combinatorial transcriptional control of plant specialized metabolism. Trends in Plant Science, 23(4), 324–336. https://doi.org/10.1016/j.tplants.2017.12.006
  • Flowers, T. J., Galal, H. K., & Bromham, L. (2010). Evolution of halophytes: Multiple origins of salt tolerance in land plants. Functional Plant Biology, 37, 604–612. https://doi.org/10.1071/FP09269
  • Gao, Q., Song, W., Li, X., Xiang, C., Chen, G., Xiang, G., Liu, X., Zhang, G., Li, X., Yang, S., Zhai, C., & Zhao, Y. (2022). Genome-wide identification of bHLH transcription factors: Discovery of a candidate regulator related to flavonoid biosynthesis in erigeron breviscapus. Frontiers in Plant Science, 13, 977649. https://doi.org/10.3389/fpls.2022.977649
  • Glaubitz, U., Li, X., Schaedel, S., Erban, A., Sulpice, R., Kopka, J., Hincha, D. K., & Zuther, E. (2017). Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles. Plant, Cell & Environment, 40(1), 121–137. https://doi.org/10.1111/pce.12850
  • Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., diPalma, F., Birren, B. W., Nusbaum, C. … Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7), 644–652. https://doi.org/10.1038/nbt.1883
  • Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., MacManes, M. D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T. … Regev, A. (2013). De Novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8), 1494–1512. https://doi.org/10.1038/nprot.2013.084
  • Haider, S., Raza, A., Iqbal, J., Shaukat, M., & Mahmood, T. (2022). Analyzing the regulatory role of heat shock transcription factors in plant heat stress tolerance: A brief appraisal. Molecular Biology Reports, 49, 5771–5785. https://doi.org/10.1007/s11033-022-07190-x
  • Inukai, S., Kock, K. H., & Bulyk, M. L. (2017). Transcription factor–DNA binding: Beyond binding site motifs. Current Opinion in Genetics & Development, 43, 110–119. https://doi.org/10.1016/j.gde.2017.02.007
  • Jia, N., Wang, J. J., Liu, J., Jiang, J., Sun, J., Yan, P., Sun, Y., Wan, P., Ye, W., & Fan, B. (2021). DcTT8, a bHLH transcription factor, regulates anthocyanin biosynthesis in dendrobium candidum. Plant Physiology and Biochemistry, 162, 603–612. https://doi.org/10.1016/j.plaphy.2021.03.006
  • Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences: CABIOS, 8, 275–282. https://doi.org/10.1093/bioinformatics/8.3.275
  • Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870–1874. https://doi.org/10.1093/molbev/msw054
  • Li, Y., Chen, Y., Zhou, L., You, S., Deng, H., Chen, Y., Alseekh, S., Yuan, Y., Fu, R., Zhang, Z., Su, D., Fernie, A. R., Bouzayen, M., Ma, T., Liu, M., & Zhang, Y. (2020). MicroTom metabolic network: Rewiring tomato metabolic regulatory network throughout the growth cycle. Molecular Plant, 13(8), 1203–1218. https://doi.org/10.1016/j.molp.2020.06.005
  • Li, L., Li, M., Qi, X., Tang, X., & Zhou, Y. (2018). De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis. PeerJ, 6, e5681. https://doi.org/10.7717/peerj.5681
  • Li, Y., Liu, F., Li, P., Wang, T., Zheng, C., & Hou, B. (2020a). An Arabidopsis cytokinin-modifying glycosyltransferase UGT76C2 improves drought and salt tolerance in rice. Frontiers in Plant Science, 11, 560696. https://doi.org/10.3389/fpls.2020.560696
  • Li, Y., Liu, F., Li, P., Wang, T., Zheng, C., & Hou, B. (2020b). An Arabidopsis cytokinin-modifying glycosyltransferase UGT76C2 improves drought and salt tolerance in rice. Frontiers in Plant Science, 11, 560696. https://doi.org/10.3389/fpls.2020.560696
  • Li, P., Li, Y. J., Zhang, F. J., Zhang, G. Z., Jiang, X. Y., Yu, H. M., & Hou, B. K. (2017). The Arabidopsis UDP-glycosyltransferases UGT79B2 and UGT79B3, contribute to cold, salt and drought stress tolerance via modulating anthocyanin accumulation. The Plant Journal: For Cell and Molecular Biology, 89(1), 85–103. https://doi.org/10.1111/tpj.13324
  • Li, M., Sun, L., Gu, H., Cheng, D., Guo, X., Chen, R., Wu, Z., Jiang, J., Fan, X., & Chen, J. (2021). Genome-wide characterization and analysis of bHLH transcription factors related to anthocyanin biosynthesis in spine grapes (Vitis davidii). Scientific Reports, 11(1), 6863–6863. https://doi.org/10.1038/s41598-021-85754-w
  • Liu, Q., Tang, J., Wang, W., Zhang, Y., Yuan, H., & Huang, S. (2018). Transcriptome analysis reveals complex response of the medicinal/ornamental halophyte iris halophila pall. to high environmental salinity. Ecotoxicology & Environmental Safety, 165, 250–260. https://doi.org/10.1016/j.ecoenv.2018.09.003
  • Long, G., Zhao, C., Zhao, P., Zhou, C., Ntirenganya, E., & Zhou, Y. (2020). Transcriptomic response to cold of thermophilous medicinal plant marsdenia tenacissima. Gene, 742, 144602. https://doi.org/10.1016/j.gene.2020.144602
  • Mergner, J., Frejno, M., List, M., Papacek, M., Chen, X., Chaudhary, A., Samaras, P., Richter, S., Shikata, H., Messerer, M., Lang, D., Altmann, S., Cyprys, P., Zolg, D. P., Mathieson, T., Bantscheff, M., Hazarika, R. R., Schmidt, T. … Kuster, B. (2020). Mass-spectrometry-based draft of the Arabidopsis proteome. Nature, 579(7799), 409–414. https://doi.org/10.1038/s41586-020-2094-2
  • Naik, J., Misra, P., Trivedi, P. K., & Pandey, A. (2022). Molecular components associated with the regulation of flavonoid biosynthesis. Plant Science: An International Journal of Experimental Plant Biology, 317, 111196. https://doi.org/10.1016/j.plantsci.2022.111196
  • Parida, A. K., & Das, A. B. (2005). Salt tolerance and salinity effects on plants: A review. Ecotoxicology & Environmental Safety, 60(3), 324–349. https://doi.org/10.1016/j.ecoenv.2004.06.010
  • Shoji, T. (2019). The recruitment Model of metabolic evolution: Jasmonate-responsive transcription factors and a conceptual model for the evolution of metabolic pathways. Frontiers in Plant Science, 10, 560. https://doi.org/10.3389/fpls.2019.00560
  • Shoji, T., & Yuan, L. (2021). ERF gene clusters: Working together to regulate metabolism. Trends in Plant Science, 26(1), 23–32. https://doi.org/10.1016/j.tplants.2020.07.015
  • Tebani, A., Gummesson, A., Zhong, W., Koistinen, I. S., Lakshmikanth, T., Olsson, L. M., Boulund, F., Neiman, M., Stenlund, H., Hellström, C., Karlsson, M. J., Arif, M., Dodig-Crnković, T., Mardinoglu, A., Lee, S., Zhang, C., Chen, Y., Olin, A. … Fagerberg, L. (2020). Integration of molecular profiles in a longitudinal wellness profiling cohort. Nature Communications, 11(1), 4487. https://doi.org/10.1038/s41467-020-18148-7
  • van Zelm, E., Zhang, Y., & Testerink, C. (2020). Salt tolerance mechanisms of plants. Annual Review of Plant Biology, 71(1), 403–433. https://doi.org/10.1146/annurev-arplant-050718-100005
  • Voelckel, C., Gruenheit, N., & Lockhart, P. (2017). Evolutionary transcriptomics and proteomics: Insight into plant adaptation. Trends in Plant Science, 22(6), 462–471. https://doi.org/10.1016/j.tplants.2017.03.001
  • Wang, C., Chen, L., Cai, Z., Chen, C., Liu, Z., Liu, S., Zou, L., Tan, M., Chen, J., Liu, X., Mei, Y., Wei, L., Liang, J., & Chen, J. (2021). Metabolite profiling and transcriptome analysis explains difference in accumulation of bioactive constituents in licorice (Glycyrrhiza uralensis) under salt stress. Frontiers in Plant Science, 12, 727882. https://doi.org/10.3389/fpls.2021.727882
  • Wei, Z., Cheng, Y., Zhou, C., Li, D., Gao, X., Zhang, S., & Chen, M. (2019). Genome-wide identification of direct targets of the TTG1–bHLH–MYB complex in regulating trichome formation and flavonoid accumulation in Arabidopsis Thaliana. International Journal of Molecular Sciences, 20(20), 5014. https://doi.org/10.3390/ijms20205014
  • Wu, P., Cogill, S., Qiu, Y., Li, Z., Zhou, M., Hu, Q., Chang, Z., Noorai, R. E., Xia, X., Saski, C., Raymer, P., & Luo, H. (2020). Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum). BMC Genomics, 21(1), 131. https://doi.org/10.1186/s12864-020-6508-1
  • Xiang, M., Ding, W., Wu, C., Wang, W., Ye, S., Cai, C., Hu, X., Wang, N., Bai, W., Tang, X., Zhu, C., Yu, X., Xu, Q., Zheng, Y., Ding, Z., Lin, C., & Zhu, Q. (2021). Production of purple Ma bamboo (dendrocalamus latiflorus Munro) with enhanced drought and cold stress tolerance by engineering anthocyanin biosynthesis. Planta, 254(3), 50. https://doi.org/10.1007/s00425-021-03696-z
  • Xie, X. B., Li, S., Zhang, R. F., Zhao, J., Chen, Y. C., Zhao, Q., Yao, Y. X., You, C. X., Zhang, X. S., & Hao, Y. J. (2012). The bHLH transcription factor MdbHLH3 promotes anthocyanin accumulation and fruit colouration in response to low temperature in apples. Plant, Cell & Environment, 35(11), 1884–1897. https://doi.org/10.1111/j.1365-3040.2012.02523.x
  • Xie, Z., Nolan, T. M., Jiang, H., & Yin, Y. (2019). AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in arabidopsis. Frontiers in Plant Science, 10, 228. https://doi.org/10.3389/fpls.2019.00228
  • Xie, W., Zhang, X., Wang, T., & Hu, J. (2012). Botany, traditional uses, phytochemistry and pharmacology of Apocynum venetum L. (Luobuma): A review. Journal of Ethnopharmacology, 141(1), 1–8. https://doi.org/10.1016/j.jep.2012.02.003
  • Yao, P. F., Li, C. L., Zhao, X. R., Li, M. F., Zhao, H. X., Guo, J. Y., Cai, Y., Chen, H., & Wu, Q. (2017). Overexpression of a tartary buckwheat gene, FtbHLH3, enhances drought/oxidative stress tolerance in transgenic Arabidopsis. Frontiers in Plant Science, 8, 625. https://doi.org/10.3389/fpls.2017.00625
  • Ye, W., Wang, T., Wei, W., Lou, S., Lan, F., Zhu, S., Li, Q., Ji, G., Lin, C., Wu, X., & Ma, L. (2020). The Full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte. Plant & Cell Physiology, 61(5), 882–896. https://doi.org/10.1093/pcp/pcaa013
  • Zander, M., Lewsey, M. G., Clark, N. M., Yin, L., Bartlett, A., Saldierna Guzmán, J. P., Hann, E., Langford, A. E., Jow, B., Wise, A., Nery, J. R., Chen, H., Bar-Joseph, Z., Walley, J. W., Solano, R., & Ecker, J. R. (2020). Integrated multi-omics framework of the plant response to jasmonic acid. Nature Plants, 6(3), 290–302. https://doi.org/10.1038/s41477-020-0605-7
  • Zhang, Y., De Stefano, R., Robine, M., Butelli, E., Bulling, K., Hill, L., Rejzek, M., Martin, C., & Schoonbeek, H. J. (2015). Different reactive oxygen species scavenging properties of flavonoids determine their abilities to extend the shelf life of tomato. Plant Physiology, 169, 1568–1583. https://doi.org/10.1104/pp.15.00346
  • Zhang, H., Li, G., Hu, D., Zhang, Y., Zhang, Y., Shao, H., Zhao, L., Yang, R., & Guo, X. (2020). Functional characterization of maize heat shock transcription factor gene ZmHsf01 in thermotolerance. PeerJ, 8, e8926. https://doi.org/10.7717/peerj.8926
  • Zhang, K., Sun, Y., Li, M., & Long, R. (2021). CrUGT87A1, a UDP-sugar glycosyltransferases (UGTs) gene from Carex rigescens, increases salt tolerance by accumulating flavonoids for antioxidation in Arabidopsis thaliana. Plant Physiology and Biochemistry, 159, 28–36. https://doi.org/10.1016/j.plaphy.2020.12.006
  • Zhang, L., Wang, Y., Zhang, Q., Jiang, Y., Zhang, H., & Li, R. (2020). Overexpression of HbMBF1a, encoding multiprotein bridging factor 1 from the halophyte hordeum brevisubulatum, confers salinity tolerance and ABA insensitivity to transgenic Arabidopsis thaliana. Plant Molecular Biology, 102(1–2), 1–17. https://doi.org/10.1007/s11103-019-00926-7
  • Zhang, X., Xu, W., Ni, D., Wang, M., & Guo, G. (2020). Genome-wide characterization of tea plant (camellia sinensis) hsf transcription factor family and role of CsHsfA2 in heat tolerance. BMC Plant Biology, 20(1), 244. https://doi.org/10.1186/s12870-020-02462-9
  • Zou, C., Chen, A., Xiao, L., Muller, H. M., Ache, P., Haberer, G., Zhang, M., Jia, W., Deng, P., Huang, R., Lang, D., Li, F., Zhan, D., Wu, X., Zhang, H., Bohm, J., Liu, R., Shabala, S. … Zhang, H. (2017). A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value. Cell Research, 27(11), 1327–1340. https://doi.org/10.1038/cr.2017.124

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.