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Transcriptome sequencing analysis revealing the potential mechanism of seed germination in Pulsatilla chinensis (Bunge) Regel

Published online by Cambridge University Press:  11 May 2023

Yanjing Dong
Affiliation:
Jiangxi University of Chinese Medicine, 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
Shouwen Zhang*
Affiliation:
Jiangxi University of Chinese Medicine, 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
Qian Qin
Affiliation:
Jiangxi University of Chinese Medicine, 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
Yating Cai
Affiliation:
Jiangxi University of Chinese Medicine, 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
Danyang Wu
Affiliation:
Jiangxi University of Chinese Medicine, 1688 Meiling Avenue, Xinjian District, Nanchang, Jiangxi 330004, China
*
*Author For Correspondence: Shou-wen Zhang, E-mail: 546572890@qq.com

Abstract

Pulsatilla chinensis (Bunge) Regel has been widely used in the pharmaceutical industry. With the deepening of clinical application, the research on its plant resources has attracted much attention. However, the underlying molecular mechanisms of distinct germination during Pulsatilla seed development are still mostly unknown. Therefore, in this study, four germination stages of P. chinensis seeds, with obvious differences in seed appearance traits, were used as materials. Transcriptome sequencing technology was used to analyse the molecular mechanisms of seed germination. A total of 27,601 differentially expressed genes (DEGs) (six different groups) were determined. KEGG enrichment analysis revealed that the up-regulated DEGs were enriched in phenylpropanoid biosynthesis, photosynthesis, photosynthesis–antenna proteins, plant hormone signal transduction, flavonoid biosynthesis and other pathways. A total of 87 DEGs was enriched in phytohormone signal transduction pathways, including auxin (25), abscisic acid (13), gibberellin (6), ethylene (9) and cytokinin (7). Furthermore, a protein–protein interaction network was constructed using these DEGs. Some DEGs were validated by qRT-PCR analysis. This comprehensive analysis provided basic information on the key genes of plant hormone signal transduction pathways involved in the seed germination process of P. chinensis (Bunge) Regel.

Type
Research Paper
Copyright
Copyright © The Author(s), 2023. Published by Cambridge University Press

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References

Alberts, B (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291294.CrossRefGoogle ScholarPubMed
Ashburner, M, Ball, CA, Blake, JA, Botstein, D, Butler, H, Cherry, JM, Davis, AP, Dolinski, K, Dwight, SS, Eppig, JT, Harris, MA, Hill, DP, Issel-Tarver, L, Kasarskis, A, Lewis, S, Matese, JC, Richardson, JE, Ringwald, M, Rubin, GM and Sherlock, G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25, 2529.CrossRefGoogle ScholarPubMed
Belin, C, Megies, C, Hauserová, E and Lopez-Molina, L (2009) Abscisic acid represses growth of the Arabidopsis embryonic axis after germination by enhancing auxin signaling. Plant Cell 21, 22532268.CrossRefGoogle ScholarPubMed
Charbonnier, S, Gallego, O and Gavin, A-C (2008) The social network of a cell: recent advances in interactome mapping. Biotechnology Annual Review 14, 128.CrossRefGoogle ScholarPubMed
Conesa, A, Madrigal, P, Tarazona, S, Gomez-Cabrero, D, Cervera, A, McPherson, A, Szcześniak, MW, Gaffney, DJ, Elo, LL, Zhang, X and Mortazavi, A (2016) Erratum to: a survey of best practices for RNA-seq data analysis. Genome Biology 17, 181.CrossRefGoogle ScholarPubMed
Daszkowska-Golec, A (2011) Arabidopsis seed germination under abiotic stress as a concert of action of phytohormones. Omics: A Journal of Integrative Biology 15, 763774.CrossRefGoogle ScholarPubMed
Delatte, B, Wang, F, Ngoc, LV, Collignon, E, Bonvin, E, Deplus, R, Calonne, E, Hassabi, B, Putmans, P, Awe, S, Wetzel, C, Kreher, J, Soin, R, Creppe, C, Limbach, PA, Gueydan, C, Kruys, V, Brehm, A, Minakhina, S, Defrance, M, Steward, R and Fuks, F (2016) RNA biochemistry. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 351, 282285.CrossRefGoogle ScholarPubMed
Doncheva, NT, Morris, JH, Gorodkin, J and Jensen, LJ (2019) Cytoscape StringApp: network analysis and visualization of proteomics data. Journal of Proteome Research 18, 623632.CrossRefGoogle ScholarPubMed
Du, W, Cheng, J, Cheng, Y, Wang, L, He, Y, Wang, Z and Zhang, H (2015) Physiological characteristics and related gene expression of after-ripening on seed dormancy release in rice. Plant Biology 17, 11561164.CrossRefGoogle ScholarPubMed
Durbak, A, Yao, H and McSteen, P (2012) Hormone signaling in plant development. Current Opinion in Plant Biology 15, 9296.CrossRefGoogle ScholarPubMed
Finkelstein, R, Reeves, W, Ariizumi, T and Steber, C (2008) Molecular aspects of seed dormancy. Annual Review of Plant Biology 59, 387415.CrossRefGoogle ScholarPubMed
Gao, J, Xue, J, Xue, Y, Liu, R, Ren, X, Wang, S and Zhang, X (2020) Transcriptome sequencing and identification of key callus browning-related genes from petiole callus of tree peony (Paeonia suffruticosa cv. Kao) cultured on media with three browning inhibitors. Plant Physiology and Biochemistry 149, 3649.CrossRefGoogle ScholarPubMed
Gazzarrini, S and Tsai, AY-L (2015) Hormone cross-talk during seed germination. Essays in Biochemistry 58, 151164.Google ScholarPubMed
Grabherr, MG, Haas, BJ, Yassour, M, Levin, JZ, Thompson, DA, Amit, I, Adiconis, X, Fan, L, Raychowdhury, R, Zeng, Q, Chen, Z, Mauceli, E, Hacohen, N, Gnirke, A, Rhind, N, di Palma, F, Birren, BW, Nusbaum, C, Lindblad-Toh, K, Friedman, N and Regev, A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29, 644652.CrossRefGoogle ScholarPubMed
Graeber, K, Nakabayashi, K, Miatton, E, Leubner-Metzger, G and Soppe, WJJ (2012) Molecular mechanisms of seed dormancy. Plant, Cell & Environment 35, 17691786.CrossRefGoogle ScholarPubMed
Gu, DZ, Zhang, LF, Wang, QS and Zhang, XS (2014) Study on seeds after-ripening regulation and key techniques for seedling of Pulsatilla cernua. Zhong Yao Cai 37, 11261129 (in Chinese).Google Scholar
Guan, SJ, Ge, TT, Xu, RR, Wang, N, Gao, J, Zhang, G, Peng, L, Zhang, YL and Xie, FP (2021) Transcriptome analysis of roots in Glycyrrhiza uralensis under salt, low phosphorus and drought stresses. Molecular Plant Breeding, 1–16. http://kns.cnki.net/kcms/detail/46.1068.S.20210401.0929.004.html.Google Scholar
Guo, S, Liu, J, Zheng, Y, Huang, M, Zhang, H, Gong, G, He, H, Ren, Y, Zhong, S, Fei, Z and Xu, Y (2011) Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. BMC Genomics 12, 454.CrossRefGoogle ScholarPubMed
Holdsworth, MJ, Bentsink, L and Soppe, WJJ (2008) Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New Phytologist 179, 3354.CrossRefGoogle ScholarPubMed
Huang, YG, Cui, SY, Yang, JX and Li, XG (1993) Causes and solutions of seed dormancy of wild medicinal plants. Journal of Jilin Agricultural University, 1993(S1):203207. doi:10.13327/j.jjlau.1993.s1.057.Google Scholar
Ibrahim, EA (2016) Seed priming to alleviate salinity stress in germinating seeds. Journal of Plant Physiology 192, 3846.CrossRefGoogle ScholarPubMed
Jensen, JK, Schultink, A, Keegstra, K, Wilkerson, CG and Pauly, M (2012) RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis. Molecular Plant 5, 984992.CrossRefGoogle ScholarPubMed
Jin, J, Tian, F, Yang, D-C, Meng, Y-Q, Kong, L, Luo, J and Gao, G (2017) PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research 45, D1040D1045.CrossRefGoogle Scholar
Kanehisa, M and Goto, S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28, 2730.CrossRefGoogle ScholarPubMed
Kang, N, Shen, W, Zhang, Y, Su, Z, Yang, S, Liu, Y and Xu, Q (2019) Anti-inflammatory and immune-modulatory properties of anemoside B4 isolated from Pulsatilla chinensis in vivo. Phytomedicine: International Journal of Phytotherapy and Phytopharmacology 64, 152934.CrossRefGoogle ScholarPubMed
Kang, H, Zhao, Z-l, Ni, L-h, Li, W-t, Zhao, S-j and Liu, T-h (2021) Transcriptome analysis and exploration of genes involved in the biosynthesis of iridoids in Gentiana crassicaulis (Gentianaceae). Acta Pharmaceutica Sinica 56, 20052014.Google Scholar
Keskin, O, Tuncbag, N and Gursoy, A (2016) Predicting protein-protein interactions from the molecular to the proteome level. Chemical Reviews 116, 48844909.CrossRefGoogle Scholar
Kim, SY, Warpeha, KM and Huber, SC (2019) The brassinosteroid receptor kinase, BRI1, plays a role in seed germination and the release of dormancy by cold stratification. Journal of Plant Physiology 241, 153031.CrossRefGoogle Scholar
Li, W and Godzik, A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 16581659.CrossRefGoogle ScholarPubMed
Li, HY and Piao, ZY (2010) Effects of different treatments on seed germination of Pulsatilla cernua. Acta Agriculturae Boreali-occidentalis Sinica 19, 175179.Google Scholar
Li, Q, Zhang, S and Wang, J (2014) Transcriptome analysis of callus from Picea balfouriana. BMC Genomics 15, 553.CrossRefGoogle ScholarPubMed
Li, R, Jia, Y, Yu, L, Yang, W, Chen, Z, Chen, H and Hu, X (2018) Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1. Plant Physiology and Biochemistry 123, 204212.CrossRefGoogle ScholarPubMed
Li, B, Peng, L, Wang, N, Sun, XC, He, YH, Song, ZX, Zhang, YQ, Tang, ZS and Huang, WJ (2020a) Transcriptome analysis of stems of Pinellia ternata under drought stress simulated by PEG. Chinese Traditional and Herbal Drugs 51, 55795589.Google Scholar
Li, Q-F, Zhou, Y, Xiong, M, Ren, X-Y, Han, L, Wang, J-D, Zhang, C-Q, Fan, X-L and Liu, Q-Q (2020b) Gibberellin recovers seed germination in rice with impaired brassinosteroid signalling. Plant Science: An International Journal of Experimental Plant Biology 293, 110435.CrossRefGoogle ScholarPubMed
Liping, G (2016) Study on dormancy and dormancy breaking of tree peony seeds. Master thesis, Northwest A&F University, China.Google Scholar
Liu, X, Zhang, H, Zhao, Y, Feng, Z, Li, Q, Yang, H-Q, Luan, S, Li, J and He, Z-H (2013) Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 110, 1548515490.CrossRefGoogle ScholarPubMed
Livak, KJ and Schmittgen, TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25, 402408.CrossRefGoogle ScholarPubMed
Love, MI, Huber, W and Anders, S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15, 550.CrossRefGoogle ScholarPubMed
Ma, L, Cui, G, Wang, X, Jia, W, Duan, Q, Du, W, Wang, J and Chen, F (2019) Selection and validation of reference genes for quantitative real-time PCR analysis in Iris bulleyana during flower color variation. Journal of Nuclear Agricultural Sciences 33, 17071716.Google Scholar
Meng, Y, Shuai, H, Luo, X, Chen, F, Zhou, W, Yang, W and Shu, K (2016) Karrikins: regulators involved in phytohormone signaling networks during seed germination and seedling development. Frontiers in Plant Science 7, 2021.Google ScholarPubMed
Mhamdi, A and Van Breusegem, F (2018) Reactive oxygen species in plant development. Development 145, 164376.CrossRefGoogle ScholarPubMed
Moravcová, Š, Tůma, J, Dučaiová, ZK, Waligórski, P, Kula, M, Saja, D, Słomka, A, Bąba, W and Libik-Konieczny, M (2018) Influence of salicylic acid pretreatment on seeds germination and some defence mechanisms of Zea mays plants under copper stress. Plant Physiology and Biochemistry 122, 1930.CrossRefGoogle ScholarPubMed
Nakashima, K and Yamaguchi-Shinozaki, K (2013) ABA signaling in stress-response and seed development. Plant Cell Reports 32, 959970.CrossRefGoogle ScholarPubMed
Pipatpongpinyo, W, Korkmaz, U, Wu, H, Kena, A, Ye, H, Feng, J and Gu, X-Y (2020) Assembling seed dormancy genes into a system identified their effects on seedbank longevity in weedy rice. Heredity 124, 135145.CrossRefGoogle ScholarPubMed
Qi, P-F, Jiang, Y-F, Guo, Z-R, Chen, Q, Ouellet, T, Zong, L-J, Wei, Z-Z, Wang, Y, Zhang, Y-Z, Xu, B-J, Kong, L, Deng, M, Wang, J-R, Chen, G-Y, Jiang, Q-T, Lan, X-J, Li, W, Wei, Y-M and Zheng, Y-L (2019) Transcriptional reference map of hormone responses in wheat spikes. BMC Genomics 20, 390.CrossRefGoogle ScholarPubMed
Rajjou, L, Duval, M, Gallardo, K, Catusse, J, Bally, J, Job, C and Job, D (2012) Seed germination and vigor. Annual Review of Plant Biology 63, 507533.CrossRefGoogle ScholarPubMed
Robles, JA, Qureshi, SE, Stephen, SJ, Wilson, SR, Burden, CJ and Taylor, JM (2012) Efficient experimental design and analysis strategies for the detection of differential expression using RNA-sequencing. BMC Genomics 13, 484.CrossRefGoogle ScholarPubMed
Seneviratne, M, Rajakaruna, N, Rizwan, M, Madawala, HMSP, Ok, YS and Vithanage, M (2019) Heavy metal-induced oxidative stress on seed germination and seedling development: a critical review. Environmental Geochemistry and Health 41, 18131831.CrossRefGoogle ScholarPubMed
Shi, WJ, Zhang, ZX, Yu, QY and Wei, Z (2005) Study on the germination characteristics of Pulsatilla chinensis seeds. Seed 4, 6062.Google Scholar
Shu, K, Liu, X-D, Xie, Q and He, Z-H (2016) Two faces of one seed: hormonal regulation of dormancy and germination. Molecular Plant 9, 3445.CrossRefGoogle ScholarPubMed
Shuai, H-w, Meng, Y-j, Luo, X-f, Chen, F, Qi, Y, Yang, W-y and Shu, K (2016) The roles of auxin in seed dormancy and germination. Hereditas 38, 314322.Google ScholarPubMed
Simão, FA, Waterhouse, RM, Ioannidis, P, Kriventseva, EV and Zdobnov, EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 32103212.CrossRefGoogle ScholarPubMed
Smith-Unna, R, Boursnell, C, Patro, R, Hibberd, JM and Kelly, S (2016) Transrate: reference-free quality assessment of de novo transcriptome assemblies. Genome Research 26, 11341144.CrossRefGoogle ScholarPubMed
Struk, S, Jacobs, A, Sánchez Martín-Fontecha, E, Gevaert, K, Cubas, P and Goormachtig, S (2019) Exploring the protein-protein interaction landscape in plants. Plant, Cell & Environment 42, 387409.CrossRefGoogle ScholarPubMed
Subbiah, V and Reddy, KJ (2010) Interactions between ethylene, abscisic acid and cytokinin during germination and seedling establishment in Arabidopsis. Journal of Biosciences 35, 451458.CrossRefGoogle ScholarPubMed
Vanstraelen, M and Benková, E (2012) Hormonal interactions in the regulation of plant development. Annual Review of Cell and Developmental Biology 28, 463487.CrossRefGoogle ScholarPubMed
Verma, V, Ravindran, P and Kumar, PP (2016) Plant hormone-mediated regulation of stress responses. BMC Plant Biology 16, 86.CrossRefGoogle ScholarPubMed
Vishal, B and Kumar, PP (2018) Regulation of seed germination and abiotic stresses by gibberellins and abscisic acid. Frontiers in Plant Science 9, 838.CrossRefGoogle ScholarPubMed
Vishweshwaraiah, YL, Prakash, B and Gowda, LR (2018) Expression profiling of the Dolichos lablab lectin during germination and development of the seed. Plant Physiology and Biochemistry 124, 1019.CrossRefGoogle ScholarPubMed
Walck, JL, Baskin, CC and Baskin, JMJB (1999) Seeds of Thalictrum mirabile (Ranunculaceae) require cold stratification for loss of nondeep simple morphophysiological dormancy. Canadian Journal of Botany 77, 17691776.CrossRefGoogle Scholar
Wang, Y, Zeng, X, Iyer, NJ, Bryant, DW, Mockler, TC and Mahalingam, R (2012) Exploring the switchgrass transcriptome using second-generation sequencing technology. PLoS ONE 7, e34225.CrossRefGoogle ScholarPubMed
Wang, F, Zhang, LM, Zhang, D, Yu, XM and Song, H (2013) Effect of different treatments on seed germination of Pulsatilla chinensis and Pulsatilla dahurica. Northern Horticulture 2, 6567 (in Chinese with English abstract).Google Scholar
Wang, Z, Chen, F, Li, X, Cao, H, Ding, M, Zhang, C, Zuo, J, Xu, C, Xu, J, Deng, X, Xiang, Y, Soppe, WJJ and Liu, Y (2016) Arabidopsis seed germination speed is controlled by SNL histone deacetylase-binding factor-mediated regulation of AUX1. Nature Communications 7, 13412.CrossRefGoogle ScholarPubMed
Xu, D (2020) COP1 and BBXs-HY5-mediated light signal transduction in plants. New Phytologist 228, 17481753.CrossRefGoogle ScholarPubMed
Yang, L, Liu, S and Lin, R (2020) The role of light in regulating seed dormancy and germination. Journal of Integrative Plant Biology 62, 13101326.CrossRefGoogle ScholarPubMed
Ying, L (2013) Study on seed dormancy and germination of Hovenia acerba Lindl. Master Thesis, Nanjing Forestry University, China.Google Scholar
Zhou, W, Chen, F, Meng, Y, Chandrasekaran, U, Luo, X, Yang, W and Shu, K (2020) Plant waterlogging/flooding stress responses: from seed germination to maturation. Plant Physiology and Biochemistry 148, 228236.CrossRefGoogle ScholarPubMed
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