Transcriptome-Wide Identification of WRKY Transcription Factors and Their Expression Profiles under Different Types of Biological and Abiotic Stress in Pinus massoniana Lamb
Abstract
:1. Introduction
2. Materials and Methods
2.1. Selection of PmWRKY Genes
2.2. Sequence Analysis
2.3. Subcellular Localization
2.4. Plant Material and Treatments
2.5. RNA-Seq Data Analysis of PmWRKY Genes
2.6. RNA Extraction and Quantitative Real-Time Reverse Transcription PCR
3. Results
3.1. Verification of WRKY Proteins in P. massoniana
3.2. Phylogenetic Analysis of PmWRKY Proteins
3.3. Compositions of PmWRKY Protein Motifs
3.4. Analysis of the Transcriptional Profiles of PmWRKY Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Reddy, V.A.; Purangaiah, M.; Sudhakar, C.; Lokesh, U.; Kirankumar, T.V.; Venkatesh, B.; Nareshkumar, A.; Kiranmai, K.; Gunupuru, L.R. Expression Analysis of WRKY Transcription Factor Genes in Response to Abiotic Stresses in Horsegram (Macrotyloma uniflorum(lam.) Verde.). Am. J. Mol. Biol. 2016, 6, 125–137. [Google Scholar]
- Zhang, L.L.; Cheng, J.; Sun, X.M.; Zhao, T.T.; Li, M.J. Overexpression of VaWRKY14 increases osmotic tolerance in Arabidopsis by modulating the expression of stress-related genes. Plant Cell Rep. 2018, 37, 1159–1172. [Google Scholar] [CrossRef] [PubMed]
- Eulgem, T.; Rushton, P.J.; Robatzek, S.; Somssich, I.E. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 2000, 5, 199–206. [Google Scholar] [CrossRef]
- Tao, X.; Chen, C.; Li, C.; Liu, J.; Liu, C.; He, Y. Genome-wide investigation of WRKY gene family in pineapple: Evolution and expression profiles during development and stress. BMC Genom. 2018, 19, 490. [Google Scholar]
- Li, M.Y.; Xu, Z.S.; Tian, C.; Huang, Y.; Wang, F.; Xiong, A.S. Genomic identification of WRKY transcription factors in carrot (Daucus carota) and analysis of evolution and homologous groups for plants. Sci. Rep. 2016, 6, 23101. [Google Scholar] [CrossRef] [Green Version]
- Song, A.P.; Li, P.L.; Jiang, J.F.; Chen, S.M.; Li, H.Y. Phylogenetic and Transcription Analysis of Chrysanthemum WRKY Transcription Factors. Int. J. Mol. Sci. 2014, 8, 15. [Google Scholar] [CrossRef] [Green Version]
- ülker, B.; Somssich, I.E. WRKY transcription factors: From DNA binding towards biological function. Curr. Opin. Plant Biol. 2004, 7, 491–498. [Google Scholar] [CrossRef] [Green Version]
- Devaiah, B.N.; Karthikeyan, A.S.; Raghothama, K.G. WRKY75 Transcription Factor Is a Modulator of Phosphate Acquisition and Root Development in Arabidopsis. Plant Physiol. 2007, 143, 1789–1801. [Google Scholar] [CrossRef] [Green Version]
- Amjad, A.M.; Farrukh, A.; Amjad, N.M.; Tuba, A.; Amjad, A.; Muhammad, I.Q.; Hussain, S.K.; Mamoon, R.H.; Gyuhwa, C.; Hwan, Y.S.; et al. Transcription WRKY11 and WRKY17 are involved in abiotic stress responses in Arabidopsis. J. Plant Physiol. 2018, 226, 12–21. [Google Scholar]
- Robatzek, S.; Somssich, I.E. A new member of the Arabidopsis WRKY transcription factor family, AtWRKY6, is associated with both senescence- and defence-related processes. Plant J. 2001, 28, 123–133. [Google Scholar] [CrossRef]
- Phukan, U.J.; Jeena, G.S.; Shukla, R.K. WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants. Front. Plant Sci. 2016, 7, 760. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Jing, L.; Günter, B.; Tapio, P.E. The WRKY70 transcription factor: A node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell 2004, 16, 319–331. [Google Scholar]
- Tang, L.Y.; Chen, Z.C.; Wang, Q.M.; Sun, J.J.; Yao, L.Q. Pinus Massoniana Morphological Architecture Analysis and 3D Visualization. J. Syst. Simul. 2006, S1, 315–318. [Google Scholar]
- Wang, Z.Q.; Ni, L.J.; Guo, J.B.; Liu, L.Q.; Li, H.G.; Yin, Y.L.; Gu, C.S. Phylogenetic and Transcription Analysis of Hibiscus hamabo Sieb. et Zucc. WRKY Transcription Factors. DNA Cell Biol. 2020, 39, 1141–1154. [Google Scholar] [CrossRef] [PubMed]
- Wu, F.; Sun, X.; Zou, B.; Zhu, P.; Ji, K. Transcriptional Analysis of Masson Pine (Pinus massoniana) under High CO2 Stress. Genes 2019, 10, 804. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- He, C.M.; Teixeira, D.S.J.A.; Tan, J.W.; Zhang, J.X.; Pan, X.P.; Li, M.Z.; Luo, J.P.; Duan, J.A. Genome-Wide Identification of the WRKY Family Genes and a Survey of Potential WRKY Target Genes in Dendrobium officinale. Sci. Rep. 2017, 7, 9200. [Google Scholar] [CrossRef] [Green Version]
- Yang, Z.H. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24, 1586–1591. [Google Scholar] [CrossRef] [Green Version]
- Kinuthia, K.B.; Fan, L.X.; Xu, L.; Wang, Y.; Zhu, X.W.; Tang, M.J.; Wang, R.H.; Zhang, F.; M’mbone, M.E.; Liu, L.W. Genome-wide characterization of the WRKY gene family in radish (Raphanus sativus L.) reveals its critical functions under different abiotic stresses. Plant Cell Rep. 2017, 36, 1757–1773. [Google Scholar]
- Bailey, T.L.; Boden, M.; Buske, F.A.; Frith, M.; Grant, C.E.; Clementi, L.; Ren, J.Y.; Li, W.W.; Noble, W.S. MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res. 2009, 37, W202–W208. [Google Scholar] [CrossRef]
- Fan, C.; Yao, H.; Qiu, Z.; Ma, H.; Zeng, B. Genome-wide analysis of Eucalyptus grandis WRKY genes family and their expression profiling in response to hormone and abiotic stress treatment. Gene 2018, 678, 38–48. [Google Scholar] [CrossRef]
- Li, Z.Q.; Wang, C.J.; Yang, A.G.; Ding, A.M.; Feng, Q.F.; Xu, J.; Jiao, H.P.; Shang, K.Y. Cloning and Subcellular Localization of DXS Gene in Tobacco. J. Anhui Agric. Sci. 2013, 41, 11957–11960. [Google Scholar]
- Zhu, P.H.; Ma, Y.Y.; Zhu, L.Z.; Chen, Y.; Ji, K.S. Selection of Suitable Reference Genes in Pinus massoniana Lamb. Under Different Abiotic Stresses for qPCR Normalization. Forests 2019, 10, 632. [Google Scholar] [CrossRef] [Green Version]
- Goyal, P.; Manzoor, M.M.; Vishwakarma, R.A.; Sharma, D.; Dhar, M.K.; Gupta, S. Comprehensive Transcriptome-Wide Identification and Screening of WRKY Gene Family Engaged in Abiotic Stress in Glycyrrhiza glabra. Sci. Rep. 2020, 10, 373. [Google Scholar] [CrossRef]
- Fu, Q.T.; Yu, D.Q. Expression profiles of AtWRKY25, AtWRKY26 and AtWRKY33 under abiotic stresses. Hereditas (Beijing) 2010, 32, 848–856. [Google Scholar] [CrossRef] [PubMed]
- Kloth, K.J.; Wiegers, G.L.; Busscher-Lange, J. AtWRKY22 promotes susceptibility to aphids and modulates salicylic acid and jasmonic acid signalling. J. Exp. Bot. 2016, 67, 3383–3396. [Google Scholar] [CrossRef] [Green Version]
- Wu, L.Y.; Zhou, B.; Li, Y.H. Roles of WRKY Transcription Factors in Abscisic Acid Signal Transduction. Mol. Plant Breed. 2014, 12, 404–410. [Google Scholar]
- Ulker, B.; Shahid, M.M.; Somssich, I.E. The WRKY70 transcription factor of Arabidopsis influences both the plant senescence and defense signaling pathways. Planta 2007, 226, 125–137. [Google Scholar] [CrossRef] [Green Version]
- Wenke, K.; Wanke, D.; Kilian, J.; Berendzen, K.; Harter, K.; Piechulla, B. Volatiles of two growth-inhibiting rhizobacteria commonly engage AtWRKY18 function. Plant J. Cell Mol. Biol. 2012, 70, 445–459. [Google Scholar] [CrossRef]
- Bailey, T.L.; Williams, N.; Misleh, C.; Li, W.W. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 2006, 34, W369–W373. [Google Scholar] [CrossRef]
- Banerjee, A.; Roychoudhury, A. WRKY proteins: Signaling and regulation of expression during abiotic stress responses. Sci. World J. 2015, 2015, 807560. [Google Scholar] [CrossRef] [Green Version]
- Xu, H.J.; Watanabe, K.A.; Zhang, L.Y.; Shen, Q.X.J. WRKY transcription factor genes in wild rice Oryza nivara. DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes 2016, 23, 311–323. [Google Scholar]
- Wu, Z.J.; Li, X.H.; Liu, Z.W.; Li, H.; Wang, Y.X.; Zhuang, J. Transcriptome-wide identification of Camellia sinensis WRKY transcription factors in response to temperature stress. Mol. Genet. Genom. MGG 2016, 291, 255–269. [Google Scholar] [CrossRef] [PubMed]
- Wei, K.F.; Chen, J.; Chen, Y.F.; Wu, L.J.; Xie, D.X. Molecular Phylogenetic and Expression Analysis of the Complete WRKY Transcription Factor Family in Maize. DNA Res. Int. J. Rapid Publ. Rep. Genes Genomes 2012, 19, 153–164. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Fei, C.; Yue, H.; Alessandro, V.; Wu, K.C.; Cai, H.Y.; Qin, Y.; Alison, M.; Lin, Z.G.; Zhang, L.S. The WRKY Transcription Factor Family in Model Plants and Crops. Crit. Rev. Plant Sci. 2017, 36, 311–335. [Google Scholar]
- Yu, N.; Cai, W.J.; Wang, S.; Shan, C.M.; Wang, L.J.; Chen, X.Y. Temporal control of trichome distribution by microRNA156-targeted SPL genes in Arabidopsis thaliana. Plant Cell 2010, 22, 2322–2335. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, L.; White, M.J.; MacRae, T.H. Transcription factors and their genes in higher plants functional domains, evolution and regulation. Eur. J. Biochem. 1999, 262, 247–257. [Google Scholar] [CrossRef]
- Zhang, Y.J.; Wang, L.J. The WRKY transcription factor superfamily: Its origin in eukaryotes and expansion in plants. BMC Evol. Biol. 2005, 5, 1. [Google Scholar]
- Yang, X.Z.; Li, H.; Yang, Y.C. Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus). PLoS ONE 2018, 13, 146–149. [Google Scholar] [CrossRef]
- Gu, Y.B.; Ji, Z.R.; Chi, F.M. Genome-wide identification and expression analysis of the WRKY gene family in peach. Hereditas (Beijing) 2016, 38, 77–93. [Google Scholar]
- Liu, T.T.; Fan, D.; Ran, L.Y. Highly efficient CRISPR/Cas9-mediated targeted mutagenesis of multiple genes in Populus. Hereditas (Beijing) 2015, 37, 1044–1052. [Google Scholar]
- Zeng, M.; Gao, W.J.; Shuai, P. Identification of WRKY Gene Family Members in Chinese Fir and Its Expression Analysis under Low Phosphorus Stress. J. Northeast For. Univ. 2019, 47, 12–20. [Google Scholar]
- Yao, L.; Wang, J.; Sun, J.; He, J.; Paek, K.Y.; Park, S.Y.; Huang, L.; Gao, W. A WRKY transcription factor, PgWRKY4X, positively regulates ginsenoside biosynthesis by activating squalene epoxidase transcription in Panax ginseng. Ind. Crop. Prod. 2020, 154, 112671. [Google Scholar] [CrossRef]
- Singh, D.; Debnath, P.; Roohi; Sane, A.P.; Sane, V.A. Expression of the tomato WRKY gene, SlWRKY23, alters root sensitivity to ethylene, auxin and JA and affects aerial architecture in transgenic Arabidopsis. Physiol. Mol. Biol. Plants Int. J. Funct. Plant Biol. 2020, 26, 1187–1199. [Google Scholar] [CrossRef] [PubMed]
- Sun, W.J.; Ma, Z.T.; Chen, H.; Liu, M.Y. Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development. PeerJ 2020, 8, e8727. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Cui, X.; Zhao, P.Y.; Liang, W.W.; Cheng, Q.; Mu, B.B.; Niu, F.F.; Yan, J.L.; Liu, C.L.; Hua, X.; Kav, N.N.V.; et al. A rapeseed WRKY transcription factor phosphorylated by CPK modulates cell death and leaf senescence by regulating the expression of ROS and SA-synthesis-related genes. J. Agric. Food Chem. 2020, 68, 7348–7359. [Google Scholar] [CrossRef]
- Sun, Y.D.; Yu, D.Q. Activated expression of AtWRKY53 negatively regulates osmotic tolerance by mediating stomatal movement. Plant Cell Rep. 2015, 34, 1295–1306. [Google Scholar] [CrossRef]
Gene ID | Gene | cDNA Length | Aa | MW(kDa) | pl | Group | WRKY Domain | Subcellular Localization | NLS |
---|---|---|---|---|---|---|---|---|---|
m.15387 | PmWRKY1 | 996 | 331 | 37.6 | 8.9 | IIb | WRKYGQK | Nucleus | |
m.7589 | PmWRKY2 | 1428 | 475 | 50.9 | 5.82 | IIc | WRKYGQK | Nucleus | |
m.7738 | PmWRKY3 | 1434 | 477 | 52.5 | 5.56 | III | WRKYGQK | Nucleus | |
m.6876 | PmWRKY4 | 1347 | 448 | 48.8 | 9.41 | IId | WRKYGQK | Nucleus | |
m.8763 | PmWRKY5 | 1092 | 364 | 40.4 | 9.68 | IId | WRKYGQK | Nucleus | |
m.256914 | PmWRKY6 | 783 | 261 | 29.8 | 6.49 | IIc | WRKYGQK | Nucleus | |
m.293152 | PmWRKY7 | 1134 | 377 | 41.0 | 4.75 | IIe | WRKYGQK | Nucleus | |
m.293159 | PmWRKY8 | 1269 | 422 | 45.7 | 4.68 | IIe | WRKYGQK | Nucleus | |
m.199902 | PmWRKY9 | 1377 | 458 | 50.1 | 6.22 | IIe | WRKYGQK | Nucleus | |
m.140205 | PmWRKY10 | 1359 | 452 | 50.5 | 6.43 | IIc | WRKYGQK | Nucleus | |
m.257305 | PmWRKY11 | 1332 | 443 | 48.0 | 6.47 | IIe | WRKYGQK | Nucleus | |
m.115513 | PmWRKY12 | 969 | 322 | 36.4 | 9.18 | IIc | WRKYGQK | Nucleus | |
m.62912 | PmWRKY13 | 1578 | 525 | 55.7 | 8.95 | I | WRKYGQK X2 | Nucleus | |
m.156607 | PmWRKY14 | 1095 | 364 | 40.4 | 9.68 | IId | WRKYGQK | Nucleus | |
m.423632 | PmWRKY15 | 330 | 233 | 26.2 | 9.89 | IId | WRKYGQK | Nucleus Cytoplasmic | |
m.423648 | PmWRKY16 | 546 | 181 | 20.1 | 9.55 | IId | WRKYGQK | Nucleus | |
m.59196 | PmWRKY17 | 843 | 280 | 32.3 | 6.83 | IIc | WRKYGQK | Nucleus | |
m.416602 | PmWRKY18 | 1041 | 346 | 37.4 | 9.42 | IId | WRKYGQK | Nucleus | |
m.318109 | PmWRKY19 | 1425 | 475 | 50.8 | 5.37 | IIe | WRKYGQK | Nucleus | |
m.198227 | PmWRKY20 | 2367 | 788 | 86.2 | 9.02 | I | WRKYGQK X2 | Nucleus | |
m.175245 | PmWRKY21 | 1914 | 637 | 70.1 | 6.77 | IIb | WRKYGQK | Nucleus | |
m.394091 | PmWRKY22 | 1380 | 459 | 50.2 | 6.28 | IIc | WRKYGQK | Nucleus | |
m.282372 | PmWRKY23 | 705 | 234 | 27.1 | 8.62 | IIb | WRKYGQK | Nucleus | |
m.282362 | PmWRKY24 | 651 | 216 | 24.9 | 9.66 | IIb | WRKYGQK | Nucleus | |
m.50488 | PmWRKY25 | 633 | 210 | 23.8 | 9.47 | IIb | WRKYGQK | Nucleus | |
m.50492 | PmWRKY26 | 417 | 138 | 15.7 | 9.99 | IIb | WRKYGQK | Nucleus | |
m.50499 | PmWRKY27 | 654 | 217 | 24.4 | 9.27 | IIb | WRKYGQK | Nucleus | |
m.50472 | PmWRKY28 | 756 | 251 | 28.6 | 9.43 | IIb | WRKYGQK | Nucleus | |
m.57136 | PmWRKY29 | 2202 | 733 | 79.5 | 6.39 | IIb | WRKYGQK | Nucleus | |
m.252813 | PmWRKY30 | 1293 | 430 | 47.5 | 5.74 | IIb | WRKYGQK | Nucleus | |
m.252861 | PmWRKY31 | 1929 | 642 | 69.4 | 6.06 | IIb | WRKYGQK | Nucleus |
Group | Subgroup | Gene Number | |
---|---|---|---|
PmWRKY | PtWRKY | ||
I | 2 | 5 | |
II | IIa | 0 | 0 |
IIb | 11 | 5 | |
IIc | 6 | 6 | |
IId | 6 | 4 | |
IIe | 5 | 1 | |
III | 1 | 0 | |
Total | 31 | 21 |
Motif | Width | Motif Sequence |
---|---|---|
1 | 32 | SEADIPSDGYRWRKYGQKPVKGSPYPRSYYRC |
2 | 41 | SSARGCPARKQVERCATDPSILITTYEGEHNHSWPLSANAS |
3 | 48 | WDCLEQGWEKDNKNAKFMDDQQLPSSKRTLNYFQSAQIENRINSSTDD |
4 | 15 | RVKKRVERTIDDPAI |
5 | 39 | QVEINRMKEENQNLKSMLSRMINNYHNLQMHMMSVMQQQ |
6 | 21 | KKHKVKGRRTIRVPRFIVSTR |
7 | 19 | VITTYEGQHTHPSPALLRS |
8 | 48 | ADTNRHQQLHPQMHYPPLQLQHLSPQPEVMFRNGYMQLDNSMSCTATI |
9 | 50 | RCAATCLGGVAALYPEKQENSCNQRNEGEFMFGTSIVKQELEDQLDFVQP |
10 | 50 | VRELLDTELKQKCRRKGDFMADAPRVDRLGGIDLSVKLEETENEEKLMTD |
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Yao, S.; Wu, F.; Hao, Q.; Ji, K. Transcriptome-Wide Identification of WRKY Transcription Factors and Their Expression Profiles under Different Types of Biological and Abiotic Stress in Pinus massoniana Lamb. Genes 2020, 11, 1386. https://doi.org/10.3390/genes11111386
Yao S, Wu F, Hao Q, Ji K. Transcriptome-Wide Identification of WRKY Transcription Factors and Their Expression Profiles under Different Types of Biological and Abiotic Stress in Pinus massoniana Lamb. Genes. 2020; 11(11):1386. https://doi.org/10.3390/genes11111386
Chicago/Turabian StyleYao, Sheng, Fan Wu, Qingqing Hao, and Kongshu Ji. 2020. "Transcriptome-Wide Identification of WRKY Transcription Factors and Their Expression Profiles under Different Types of Biological and Abiotic Stress in Pinus massoniana Lamb" Genes 11, no. 11: 1386. https://doi.org/10.3390/genes11111386