Genome-Wide Identification and Characterization of the <i>Dof</i> Transcription Factor Gene Family in <i>Phaseolus vulgaris</i> L. — Oak Academic Publishing
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Genome-Wide Identification and Characterization of the <i>Dof</i> Transcription Factor Gene Family in <i>Phaseolus vulgaris</i> L.
Programa de Pós-Graduacao em Biotecnologia Aplicada à Agricultura, Laboratório de Biologia Molecular, Universidade Paranaense (UNIPAR), Umuarama, Brazil
,
Programa de Pós-Graduacao em Biotecnologia Aplicada à Agricultura, Laboratório de Biologia Molecular, Universidade Paranaense (UNIPAR), Umuarama, Brazil
,
Programa de Pós-Graduacao em Agronomia, Universidade do Oeste Paulista (UNOESTE), Presidente Prudente, Brazil
,
Programa de Pós-Graduacao em Biotecnologia Aplicada à Agricultura, Laboratório de Biologia Molecular, Universidade Paranaense (UNIPAR), Umuarama, Brazil
1 Programa de Pós-Graduacao em Biotecnologia Aplicada à Agricultura, Laboratório de Biologia Molecular, Universidade Paranaense (UNIPAR), Umuarama, Brazil
2 Programa de Pós-Graduacao em Biotecnologia Aplicada à Agricultura, Laboratório de Biologia Molecular, Universidade Paranaense (UNIPAR), Umuarama, Brazil
3 Programa de Pós-Graduacao em Agronomia, Universidade do Oeste Paulista (UNOESTE), Presidente Prudente, Brazil
4 Programa de Pós-Graduacao em Biotecnologia Aplicada à Agricultura, Laboratório de Biologia Molecular, Universidade Paranaense (UNIPAR), Umuarama, Brazil
The Dof (DNA-binding with one finger) proteins are a class of plant-specific transcription factors that can trigger several processes involved in plant growth and development, as well as in stress responses. Here, we performed a systematic bioinformatics analysis to characterize all Dof genes in common bean, which included analysis of the genome sequence, conserved protein domains, chromosomal locations, subcellular locations, phylogenetic relationships, gene duplications, and gene expression profiles in different tissues. Bioinformatics analysis revealed 36 putative genes related to PvDof that were classified into seven subfamilies (A, B1, B2, C1, C2, D1, and, D2) by comparative phylogenetic analysis. Based on our genome duplication analysis, a total of 36 genes were found to be distributed on all 11 chromosomes, and they expanded through gene duplication in tandem, suggesti ng the involvement of segmental duplication events in the evolutionary process. Synteny events and phylogenetic comparisons of the Dof proteins of common bean with those of A. thaliana , O. sativa , and G. max L. led to the identification of several orthologous and paralogous genes, which provided further insight into the diversity of the evolutionary characteristics of genes of this family in other plant species. Expression profiles revealed that most of the PvDof genes were expressed in different tissues, indicating that PvDof genes may be involved in various physiological functions during plant development. The results of this study provide additional information and potential biotechnological resources for further understanding the molecular basis of this gene family and consequently improvement of common bean crops.
KeywordsCommon BeanDNA-Binding with One Finger (Dof)Domain ProteinsTran-scription Factor
Riechmann, J.L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O.J., Samaha, R.R., Creelman, R., Pilgrim, M., Broun, P., Zhang, J.Z., Ghandehari D., Sherman, B.K. and Yu, G. (2000) Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis among Eukaryotes. Science, 290, 2105-2110. https://doi.org/10.1126/science.290.5499.2105
Zheng, L., Liu, G., Meng, X., Liu, Y., Ji, X., Li, Y., Nie, X. and Wang Y. (2013) A WRKY Gene from Tamarix hispida, ThWRKY4, Mediates Abiotic Stress Responses by Modulating Reactive Oxygen Species and Expression of Stress-Responsive Genes. Plant Molecular Biology, 82, 303-320. https://doi.org/10.1007/s11103-013-0063-y
Wray, G.A., Hahn, M.W., Abouheif, E., Balhoff, J.P., Pizer, M., Rockman, M.V. and Romano, L.A. (2003) The Evolution of Transcriptional Regulation in Eukaryotes. Molecular Biology and Evolution, 20, 1377-1419. https://doi.org/10.1093/molbev/msg140
Yanagisawa, S. and Schmidt, R.J. (1999) Diversity and Similarity among Recognition Sequences of Dof Transcription Factors. The Plant Journal, 17, 209-214. https://doi.org/10.1046/j.1365-313X.1999.00363.x
Lijavetzky, D., Carbonero, P. and Vicente-Carbajosa, J. (2003) Genome Wide Comparative Phylogenetic Analysis of the Rice and Arabidopsis DofGene Families. BMC Evolutionary Biology, 3, 17. https://doi.org/10.1186/1471-2148-3-17
Park, D.H., Lim, P.O., Kim, J.S., Cho, D.S., Hong, S.H. and Nam, H.G. (2003) The Arabidopsis COG1 Gene Encodes a Dof Domain Transcription Factor and Negatively Regulates Phytochrome Signaling. The Plant Journal, 34, 161-171. https://doi.org/10.1046/j.1365-313X.2003.01710.x
Kushwaha, H., Gupta, S., Singh, V.K. and Rastogi, S. (2011) Genome Wide Identification of DofTranscription Factor Gene Family in Sorghum and Its Comparative Phylogenetic Analysis with Rice and Arabidopsis. Molecular Biology Reports, 38, 5037-5053. https://doi.org/10.1007/s11033-010-0650-9
Hernando-Amado, S., González-Calle, V., Carbonero, P. and Barrero-Sicilia, C. (2012) The Family of Dof Transcription Factors in Brachypodium distachyon: Phylogenetic Comparison with Rice and Barley DOFs and Expression Profiling. BMC Plant Biology, 12, 202. https://doi.org/10.1186/1471-2229-12-202
Cai, X., Zhang, Y., Zhang, C., Zhang, T., Hu, T., Ye, J., Zhang, J., Wang, T., Li, H. and Ye, Z. (2013) Genome-Wide Analysis of Plant-Specific Dof Transcription Factor Family in Tomato. Journal of Integrative Plant Biology, 55, 552-566. https://doi.org/10.1111/jipb.12043
Jin, Z., Chandrasekaran, U. and Liu, A. (2014) Genome-Wide Analysis of the Dof Transcription Factors in Castor Bean (Ricinus communis L.). Genes &Genomics, 36, 527-537. https://doi.org/10.1007/s13258-014-0189-6
Malviya, N., Gupta, S., Singh, V.K., Yadav, M.K., Bisht, N.C., Sarangi, B.K. and Yadav, D. (2014) Genome Wide in Silico Characterization of Dof Gene Families of Pigeonpea (Cajanus Cajan (L) Millsp.). Molecular Biology Reports, 42, 535-552. https://doi.org/10.1007/s11033-014-3797-y
Wang, T., Yue, J.-J., Wang, X.-J., Xu, L., Li, L.-B. and Gu, X.-P. (2016) Genome-Wide Identification and Characterization of the Dof Gene Family in Moso Bamboo (Phyllostachys heterocycla var. pubescens). Genes & Genomics, 38, 733. https://doi.org/10.1007/s13258-016-0418-2
Song, A., Gao, T., Li, P., Chen, S., Guan, Z., Wu, D., Xin, J., Fan, Q., Zhao, K. and Chen, F. (2016) Transcriptome-Wide Identification and Expression Profiling of the DOF Transcription Factor Gene Family in Chrysanthemum morifolium. Frontiers in Plant Science, 7, 199. https://doi.org/10.3389/fpls.2016.00199
Wu, Z., Cheng, J., Cui, J., Xu, X., Liang, G., Luo, X., Chen, X., Tang, X., Hu, K. and Qin, C. (2016) Genome-Wide Identification and Expression Profile of Dof Transcription Factor Gene Family in Pepper (Capsicum annuum L.). Frontiers in Plant Science, 7, 574. https://doi.org/10.3389/fpls.2016.00574
Wang, H., Zhao, S., Gao, Y. and Yang, J. (2017) Characterization of Dof Transcription Factors and Their Responses to Osmotic Stress in Poplar (Populus trichocarpa). PLoS ONE, 12, e0170210. https://doi.org/10.1371/journal.pone.0170210
Umemura, Y., Ishiduka, T., Yamamoto, R. and Esaka, M. (2004) The Dof domain, a Zinc Finger DNA-Binding Domain Conserved only in Higher Plants, Truly Functions as a Cys2/Cys2 Zn Finger Domain. The Plant Journal, 37, 741-749. https://doi.org/10.1111/j.1365-313X.2003.01997.x
Yanagisawa, S. (2004) Dof Domain Proteins: Plant-Specific Transcription Factors Associated with Diverse Phenomena Unique to Plants. Plant & Cell Physiology, 45, 386-391. https://doi.org/10.1093/pcp/pch055
Noguero, M., Atif, R.M., Ochatt, S. and Thompson, R.D. (2013) The Role of the DNA-Binding One Zinc Finger (DOF) Transcription Factor Family in Plants. Plant Science, 209, 32-45. https://doi.org/10.1016/j.plantsci.2013.03.016
Gabriele, S., Rizza, A., Martone, J., Circelli, P., Costantino, P. and Vittorioso, P. (2010) The Dof Protein DAG1 Mediates PIL5 Activity on Seed Germination by Negatively Regulating GA Biosynthetic Gene Atga3ox1. The Plant Journal, 61, 312-323. https://doi.org/10.1111/j.1365-313X.2009.04055.x
Rueda-Romero, P., Barrero-Sicilia, C., Gómez-Cadenas, A., Carbonero, P. and Onate-Sánchez, L. (2012) Arabidopsis thaliana DOF6 Negatively Affects Germination in Non-after-Ripened Seeds and Interacts with TCP14. Journal of Experimental Botany, 63, 1937-1949. https://doi.org/10.1093/jxb/err388
Negi, J., Moriwaki, K., Konishi, M., Yokoyama, R., Nakano, T., Kusumi, K., Hashimoto-Sugimoto, M., Schroeder, J.I., Nishitani, K. and Yanagisawa, S. (2013) A Dof Transcription Factor, SCAP1, Is Essential for the Development of Functional Stomata in Arabidopsis. Current Biology, 23, 479-484. https://doi.org/10.1016/j.cub.2013.02.001
Le Hir, R. and Bellini, C. (2013) The Plant-Specific Dof Transcription Factors Family: New Players Involved in Vascular System Development and Functioning in Arabidopsis. Frontiers in Plant Science, 29, 164.
Kang, W.-H., Kim, S., Lee, H.-A., Choi, D. and Yeom, S.-I. (2016) Genome-wide Analysis of DofTranscription Factors Reveals Functional Characteristics during Development and Response to Biotic Stresses in Pepper. Scientific Reports, 6, 33332. https://doi.org/10.1038/srep33332
Corrales, A.R., Nebauer, S.G., Carrillo, L., Fernández-Nohales, P., Marqués, J., Renau-Morata, B., Granell, A., Pollmann, S., Vicente-Carbajosa, J., Molina, R.V. and Medina, J. (2014) Characterization of Tomato Cycling Dof Factors Reveals Conserved and New Functions in the Control of Flowering Time and Abiotic Stress Responses. Journal of Experimental Botany, 65, 995-1012. https://doi.org/10.1093/jxb/ert451
Cai, X., Zhang, C., Shu, W., Ye, Z., Li, H. and Zhang, Y. (2016) The Transcription Factor SlDof22 Involved in Ascorbate Accumulation and Salinity Stress in Tomato. Biochemical and Biophysical Research Communications, 474, 736-741. https://doi.org/10.1016/j.bbrc.2016.04.148
Broughton, W.J., Hernandez, G., Blair, M., Beebe, S., Gepts, P. andVenderleyden, J. (2003) Bean (PhaseolusSpp)—Model Food Legumes. Plant and Soil, 252, 55-128. https://doi.org/10.1023/A:1024146710611
Gepts, P., Aragao, F., De Barros, E., Blair, M.W., Brondani, R., Broughton, W., Galasso, I., Hernández, G., Kami, J., Lariguet, P., McClean, P., Melotto, M., Miklas, P., Pauls, P., Pedrosa-Harand, A., Porch, T., Sánchez, F., Sparvoli, F. and Yu, K.(2008) Genomics of PhaseolusBeans, a Major Source of Dietary Protein and Micronutrients in the Tropics. In: Moore, P.H. and Ming, R., Eds.,Genomics of Tropical Crop Plants, Springer, Berlin, 113-143. https://doi.org/10.1007/978-0-387-71219-2_5
MAPA (2015) Ministério da Agriculta, Pecuária e Abastecimento. http://www.agricultura.gov.br/vegetal/culturas/feijao
Beebe, S.E., Rao, I.M., Blair, M.W. and Acosta-Gallegos, J.A. (2013) Phenotyping Common Beans for Adaptation to Drought. Frontiers in Physiology, 4, 35. https://doi.org/10.3389/fphys.2013.00035
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acids Research, 25, 3389-3402. https://doi.org/10.1093/nar/25.17.3389
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson. J.D., Gibson, T.J. and Higgins, D.G. (2007) Clustal W and Clustal X Version 2.0. Bioinformatic, 23, 2947-2948. https://doi.org/10.1093/bioinformatics/btm404
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology Evolution, 30, 2725-2729. https://doi.org/10.1093/molbev/mst197
Bailey, T.L., Williams, N., Misleh, C. and Li, W.W. (2006) MEME: Discovering and Analyzing DNA and Protein Sequence Motifs. Nucleic Acids Research, 34, W369-W373. https://doi.org/10.1093/nar/gkl198
Hu, B., Jin, J., Guo, A.-Y., Zhang, H., Luo, J. and Gao, G. (2015) GSDS 2.0: An Upgraded Gene Feature Visualization Server. Bioinformatics, 31, 1296-1297. https://doi.org/10.1093/bioinformatics/btu817
Voorrips, R.E. (2002) MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs. The Journal of Hered, 93, 77-78. https://doi.org/10.1093/jhered/93.1.77
Hu, R., Qi, G., Kong, Y., Kong, D., Gao, Q. and Zhou, G. (2010) Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa. BMC Plant Biology, 10, 145. https://doi.org/10.1186/1471-2229-10-145
Schmutz, J., McClean, P.E., Mamidi, S., Wu, G.A., Cannon, S.B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Torres-Torres, M., Geffroy, V., Moghaddam, S.M., Gao, D., Abernathy, B., Barry, K., Blair, M., Brick, M.A., Chovatia, M., Gepts, P., Goodstein, D.M., Gonzales, M., Hellsten, U., Hyten, D.L., Jia, G., Kelly, J.D., Kudrna, D., Lee, R., Richard, M.M., Miklas, P.N., Osorno, J.M., Rodrigues, J., Thareau, V., Urrea, C.A., Wang, M., Yu, Y., Zhang, M., Wing, R.A., Cregan, P.B., Rokhsar, D.S. and Jackson, S.A. (2014) A Reference Genome for Common Bean and Genome-Wide Analysis of Dual Domestications. Nature Genetics, 46, 707-713. https://doi.org/10.1038/ng.3008
Lee, T.-H., Tang, H., Wang, X. and Paterson, A.H. (2013) PGDD: A Database of Gene and Genome Duplication in Plants. Nucleic Acids Research, 41, D1152-D1158. https://doi.org/10.1093/nar/gks1104
Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J. and Marra, M.A. (2009) Circos: An Information Aesthetic for Comparative Genomics. Genome Research, 19, 1639-1645. https://doi.org/10.1101/gr.092759.109
Guo, Y. and Qiu, L.-J. (2013) Genome-Wide Analysis of the Dof Transcription Factor Gene Family Reveals Soybean-Specific Duplicable and Functional Characteristics. PLoS ONE, 8, e76809. https://doi.org/10.1371/journal.pone.0076809
Yanagisawa, S. (2002) The Dof Family of Plant Transcription Factors. Trends in Plant Science, 7, 555-560. https://doi.org/10.1016/S1360-1385(02)02362-2
Chen, M., Liu, X., Huan, L., Sun, M., Liu, L., Chen, Gao, D. and Li, L. (2017) Genome-Wide Analysis of Dof Family Genes and their Expression during Bud Dormancy in Peach (Prunus persica). Scientia Horticulturae, 214, 18-26. https://doi.org/10.1016/j.scienta.2016.11.014
Gupta, S., Kushwaha, H., Singh, V.K., Bisht, N.C., Sarangi, B.K. and Yadav, D. (2014) Genome Wide in Silico Characterization of Dof TranscriptionFactor Gene Family of Sugarcane and Its Comparative Phylogenetic Analysis with Arabidopsis, Rice and Sorghum. Sugar Tech, 16, 372-384. https://doi.org/10.1007/s12355-013-0288-8
Silva, D.C., Falavigna, V.S., Fasoli, M., Buffon, V., Porto, D.D., Pappas Jr, G.J., Pezzotti, M., Pasquali, G. and Revers, L.F. (2016) Transcriptome Analyses of the Dof-Like Gene Family in Grapevine Reveal Its Involvement in Berry, Flower and Seed Development. Horticulture Research, 3, 16042. https://doi.org/10.1038/hortres.2016.42
Bennett, M.D. And Leitch, I.J. (1995) Nuclear DNA Amounts in Angiosperms. Annals of Botany, 76, 2, 113-176. https://doi.org/10.1006/anbo.1995.1085
Huala, E., Dickerman, A.W., Garcia-Hernandez, M., Weems, D., Reiser, L., LaFond, F., Hanley, D., Kiphart, D., Zhuang, M., Huang, W., Mueller, L.A., Bhattacharyya, D., Bhaya, D., Sobral, B.W., Beavis, W., Meinke, D.W., Town, C.D., Somerville, C. and Rhee, S.Y. (2001) The Arabidopsis Information Resource (TAIR): A Comprehensive Database and Web-Based Information Retrieval, Analysis, and Visualization System for a Model Plant. Nucleic Acids Research, 29, 102-105. https://doi.org/10.1093/nar/29.1.102
Wen, C.-L., Cheng, Q., Zhao, L., Mao, A., Yang, J., Yu, S., Weng, Y. and Xu, Y. (2016) Identification and Characterisation of Dof Transcription Factors in the Cucumber Genome. Scientific Reports, 6, 23072. https://doi.org/10.1038/srep23072
Zhang, Y., Mao, L., Wang, H., Brocker, C., Yin, X., Vasiliou, V., Fei, Z. and Wang, X. (2012) Genome-Wide Identification and Analysis of Grape Aldehyde Dehydrogenase (ALDH) Gene Superfamily. PLoS ONE, 7, e32152.
Liu, Y., Yang, H., Chen, W., Qian, Y., Ma, Q., Cheng, B. and Zhu, S. (2011) Genome-Wide Analysis of the Auxin Response Factor (ARF) Gene Family in Maize (Zea mays). Plant Growth Regulation, 63, 225-234. https://doi.org/10.1007/s10725-010-9519-0
Lynch, M. and Conery, J.S. (2000) The Evolutionary Fate and Consequences of Duplicate Genes. Science, 290, 1151-1155. https://doi.org/10.1126/science.290.5494.1151
Lavin, M., Herendeen, P.S. and Wojciechowski, M.F. (2005) Evolutionary Rates Analysis of Leguminosae Implicates a Rapid Diversification of Lineages during the Tertiary. Systematic Biology, 54, 575-594. https://doi.org/10.1080/10635150590947131
Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., Hyten, D.L., Song, Q., Thelen, J.J., Cheng, J., Xu, D., Hellsten, U., May, G.D., Yu, Y., Sakurai, T., Umezawa, T., Bhattacharyya, M.K., Sandhu, D., Valliyodan, B., Lindquist, E., Peto, M., Grant, D., Shu, S., Goodstein, D., Barry, K., Futrell-Griggs, M., Abernathy, Brian., Du, J., Tian, Z., Zhu, L., Gill, N., Joshi, T., Libault, M., Sethuraman, A., Zhang, X.-C., Shinozaki, K., Nguyen, H.T., Wing, R.A., Cregan, P., Specht, J., Grimwood, J., Rokhsar, D., Stacey, G., Shoemaker, R.C. and Jackson, S.A. (2010) Genome Sequence of the Palaeopolyploid Soybean. Nature, 463, 178-183. https://doi.org/10.1038/nature08670
Kim, H.-S., Kim, S. J., Abbasi, N., Bressan, R.A., Yun, D.-J., Yoo, S.-D., Kwon, S.-Y. and Choi, S.-B. (2010) The DOF Transcription Factor Dof5.1 Influences Leaf Axial Patterning by Promoting Revoluta Transcription in Arabidopsis. The Plant Journal, 64, 524-535. https://doi.org/10.1111/j.1365-313X.2010.04346.x