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Genome-Wide Bioinformatics Analysis of DOF Transcription Factor Gene Family of Asparagus and Its Comparative Phylogenetic Assessment with Arabidopsis

Research Paper | December 1, 2020

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Humera Amin, Shumaila Dastgir, Muhammad Shafiq, Muhammad Arshad Javed, Muhammad Saleem Haider

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Int. J. Biosci.17( 6), 103-123, December 2020

DOI: http://dx.doi.org/10.12692/ijb/17.6.103-123


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Asparagus officinalis L has been cultivated and harvested from the wild for thousands of years for medicinal purposes. The family of DOF gene (DNA binding with One Finger) is highly conserved and member of this gene family plays an important role in many regulatory mechanisms in plants including plant growth and development. We identified 7 putative DOF genes through the genome mining of asparagus (A. officinalis L.) and distributed unevenly among 5 chromosomes. The DOF gene family in asparagus was phylogenetically analyzed with Arabidopsis thaliana DOF genes and classified into 5 subfamilies. The exon-intron organization of DOF gene in asparagus showed the presence of intron and AoDOF5 (2intron) contain a maximum no of introns. The DOF gene on chromosome in A.officinalis is observed in 4 chromosomes. Maximum 3 DOF genes were observed on chromosome 8 and a single DOF gene was found on other chromosomes. The segmental gene duplication was predominant over tandem duplication which might be the cause of DOF gene family expansion in A.officinalis. The cis-regulatory element analysis revealed the presence of light-responsive, abscisic acid responsiveness, endosperm-specific, anaerobic induction, root-specific expression, gibberellin-responsive, meristem-specific and stress-responsive elements. Comprehensive phylogenetic analysis of DOF genes of A.officinalis with Arabidopsis revealed several orthologs and paralogs assisting in understanding the putative functions of AoDOF genes. The bioinformatics-based genome-wide assessment of DOF gene family of A.officinalis   attempted in the present study could be a significant step for deciphering novel DOF genes based on genome-wide expression profiling.


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Genome-Wide Bioinformatics Analysis of DOF Transcription Factor Gene Family of Asparagus and Its Comparative Phylogenetic Assessment with Arabidopsis

Arnaiz A, Martinez M, Gonzalez-Melendi P, Grbic V, Diaz I, Santamaria ME. 2019. Plant Defenses Against Pests Driven by a Bidirectional Promoter. Frontiers in Plant Sciences 10, 930.

Bailey TL, Johnson J, Grant CE, Noble WS. 2015. The MEME suite. Nucleic acids research 43, W39-W49.

Bondarenko VS, Gelfand MS. 2016. Evolution of the Exon-Intron Structure in Ciliate Genomes. PLoS One 11, e0161476.

Bueso E, Munoz-Bertomeu J, Campos F, Martinez C, Tello C, Martinez-Almonacid I, Ballester P, Simon-Moya M, Brunaud V, Yenush L, Ferrandiz C, Serrano R. 2016. Arabidopsis COGWHEEL1 links light perception and gibberellins with seed tolerance to deterioration. The Plant Journal 87, 583-96.

Bulow L, Hehl R. 2016. Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes. Methods in Molecular Biology 1482, 233-45.

Cai X, Zhang Y, Zhang C, Zhang T, Hu T, Ye J, Zhang J, Wang T, Li H, Ye Z. 2013. Genome‐wide analysis of plant‐specific DOF transcription factor family in tomato. Journal of Integrative Plant Biology 55, 552-566.

Carbone F, Bruno L, Perrotta G, Bitonti MB, Muzzalupo I, Chiappetta A. 2019. Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome. PLoS One 14, e0221460.

Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. 2020. TBtools – an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant.

Chen H, Ahmad M, Rim Y, Lucas WJ, Kim J. Y. 2013. Evolutionary and molecular analysis of D of transcription factors identified a conserved motif for intercellular protein trafficking. New Phytologist 198, 1250-1260.

Chen R, Ni Z, Qin Y, Nie X. 2005. Isolation and characterization of TaDOF1 transcription factor in wheat (Triticum. aestivum. L) Full Length Research Paper. DNA Sequence 16, 358-363.

Cokol M, Nair R, Rost B. 2000. Finding nuclear localization signals. EMBO reports 1, 411-415.

Corrales AR, Nebauer SG, Carrillo L, Fernandez-Nohales P, Marques J, Renau Morata B, Granell A, Pollmann S, Vicente Carbajosa J, Molina RV, 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.

Diaz I, Martinez M, Isabel‐LaMoneda I, Rubio‐Somoza I, Carbonero P. 2005. The DOF protein, SAD, interacts with GAMYB in plant nuclei and activates transcription of endosperm‐specific genes during barley seed development. The Plant Journal 42, 652-662.

Dong C, Hu H, Xie J. 2016. Genome-wide analysis of the DNA-binding with one zinc finger (DOF) transcription factor family in bananas. Genome 59, 1085-1100.

Dong G, Ni Z, Yao Y, Nie X, Sun Q. 2007. Wheat DOF transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development. Plant Molecular Biology 63, 73-84.

Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J. 2014. Pfam: the protein families database. Nucleic acids research 42, D222-D230.

Fornara F. 2009. Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Europe PMC.

Fornara F, Panigrahi KC, Gissot L, Sauerbrunn N, Rühl M, Jarillo JA, Coupland, G. 2009. Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Developmental cell 17, 75-86.

Gardiner J. 2010. Expression of DOF genes identifies early stages of vascular development in Arabidopsis leaves. Europe PMC.

Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server. In “The proteomics protocols handbook”, pp. 571-607. Springer.

Goodstein D, Batra S, Carlson J, Hayes R, Phillips J, Shu S, Schmutz J, Rokhsar D. 2014. Phytozome Comparative Plant Genomics Portal.

Gupta S, Gupta SM, Gupta AK, Gaur VS, Kumar A. 2014. Fluctuation of DOF1/DOF2 expression ratio under the influence of varying nitrogen and light conditions: involvement in differential regulation of nitrogen metabolism in two genotypes of finger millet (Eleusine coracana L.). Gene 546, 327-35.

Gupta S, Malviya N, Kushwaha H, Nasim J, Bisht NC, Singh V, Yadav D. 2015. Insights into structural and functional diversity of DOF (DNA binding with one finger) transcription factor. Planta 241, 549-562.

Harkess A, Zhou J, Xu C, Bowers JE, Van der Hulst R, Ayyampalayam S, Mercati F, Riccardi P, McKain MR, Kakrana A, Tang, H, Ray J, Groenendijk J, Arikit S, Mathioni SM, Nakano M, Shan H, Telgmann-Rauber A, Kanno A, Yue Z, Chen H, Li W, Chen Y, Xu X, Zhang Y, Luo S, Gao J, Mao Z, Pires JC, Luo M, Kudrna, D, Wing RA, Meyers BC, Yi K, Kong H, Lavrijsen P, Sunseri F, Falavigna A, Ye Y, Leebens-Mack JH, Chen G. 2017. The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nature Communications 8, 1279.

Hartung AC, Nair MG, Putnam AR. 1990. Isolation and characterization of phytotoxic compounds from asparagus (Asparagus officinalis L .) roots. Journal of Chemical Ecology 16, 1707-18.

Hernando-Amado S, Gonzalez-Calle V, Carbonero P, 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.

Higo K, Ugawa Y, Iwamoto M, Higo H. 1998. PLACE: a database of plant cis-acting regulatory DNA elements. Nucleic Acids Research 26, 358-9.

Higo K, Ugawa Y, Iwamoto M, Korenaga T. 1999. Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Research 27, 297-300.

Horton P, Park KJ, Obayashi T, Nakai K. 2006. Protein subcellular localization prediction with WoLF PSORT. In “Proceedings of the 4th Asia-Pacific bioinformatics conference”, p 39-48. World Scientific.

Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G. 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31, 1296-7.

Imaizumi T. 2005. FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Europe PMC.

Iwamoto M. 2016. MicroRNA-targeted transcription factor gene RDD 1 promotes nutrient ion uptake and accumulation in rice. The Plant Journal.

Jones DM, Vandepoele K. 2020. Identification and evolution of gene regulatory networks: insights from comparative studies in plants. Current Opinion Plant Biology 54, 42-48.

Konishi M. 2007. Sequential activation of two DOF transcription factor gene promoters during vascular development in Arabidopsis thaliana. Europe PMC.

Koralewski TE, Krutovsky KV. 2011. Evolution of exon-intron structure and alternative splicing. PloS one 6, e18055.

Kumar S, Tamura K, Nei M. 1994. MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Computer Applications in  Biosciences 10, 189-91.

Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P. 2006. SMART 5: domains in the context of genomes and networks. Nucleic Acids Research 34, D257-60.

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P. 2004. SMART 4.0: towards genomic data integration. Nucleic Acids Research 32, D142-4.

Lijavetzky D, Carbonero P, Vicente-Carbajosa J. 2003. Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis DOF gene families. BMC evolutionary biology 3, 17.

Liu J, Cheng X, Liu P, Li D, Chen T, Gu X, Sun J. 2017. MicroRNA319-regulated TCPs interact with FBHs and PFT1 to activate CO transcription and control flowering time in Arabidopsis. PLoS Genetics 13, e1006833.

Ma J, Li MY, Wang F, Tang J, Xiong AS. 2015a. Genome-wide analysis of DOF family transcription factors and their responses to abiotic stresses in Chinese cabbage. BMC Genomics 16, 33.

Ma J, Li MY, Wang F, Tang J, Xiong AS. 2015b. Genome-wide analysis of DOF family transcription factors and their responses to abiotic stresses in Chinese cabbage. BMC Genomics 16, 33.

Malviya N, Gupta S, Singh V, Yadav M, Bisht N, Sarangi B, Yadav D. 2015. Genome wide in silico characterization of DOF gene families of pigeonpea (Cajanus cajan (L) Millsp.). Molecular biology reports 42, 535-552.

Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao, L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH. 2007. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Research 35, D237-40.

Mello B. 2018. Estimating timetrees with MEGA and the TimeTree resource. Molecular biology and evolution 35, 2334-2342.

Mena M, Cejudo FJ, Isabel-Lamoneda I, Carbonero P. 2002. A role for the DOF transcription factor BPBF in the regulation of gibberellin-responsive genes in barley aleurone. Plant Physiology 130, 111-9.

Miyashima S. 2019. Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Europe PMC.

Miyashima S, Roszak P, Sevilem I, Toyokura K, Blob B, Heo JO, Mellor N, Help-Rinta-Rahko H, Otero S, Smet W, Boekschoten M, Hooiveld G, Hashimoto K, Smetana O, Siligato R, Wallner ES, Mahonen AP, Kondo Y, Melnyk CW, Greb T, Nakajima K, Sozzani R, Bishopp A, De Rybel B, Helariutta Y. 2019. Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature 565, 490-494.

Moreno-Risueno MA, Martinez M, Vicente-Carbajosa J, Carbonero P. 2007. The family of DOF transcription factors: from green unicellular algae to vascular plants. Molecular Genetics and Genomics 277, 379-90.

Nasim J, Malviya N, Kumar R, Yadav D. 2016. Genome-wide bioinformatics analysis of DOF transcription factor gene family of chickpea and its comparative phylogenetic assessment with Arabidopsis and rice. Plant Systematics and Evolution 302, 1009-1026.

Negi J, Moriwaki K, Konishi M, Yokoyama R, Nakano T, Kusumi K, Hashimoto-Sugimoto, M, Schroeder JI, Nishitani K, Yanagisawa S. 2013. A DOF transcription factor, SCAP1, is essential for the development of functional stomata in Arabidopsis. Current Biology 23, 479-484.

Papi M, Sabatini S, Altamura MM, Hennig L,  Schafer E, Costantino P, Vittorioso P. 2002. Inactivation of the phloem-specific DOF zinc finger gene DAG1 affects response to light and integrity of the testa of Arabidopsis seeds. Plant Physiology 128, 411-7.

Qu D, Yan F, Li MA, Varotto C, Zhao ZY. 2016. Comparative analysis of MIR168 promoters in three plant species. Genet Mol Res 15.

Rombauts S, Déhais P, Van Montagu M, Rouzé P. 1999. PlantCARE, a plant cis-acting regulatory element database. Nucleic acids research 27, 295-296.

SKGSMLCKKT. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular biology and evolution, 1547-1549.

Samad AFA. 2017. MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network. Frontiers in Plant Science.

Schultz J, Copley RR, Doerks T, Ponting CP, Bork P. 2000. SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Research 28, 231-4.

Schultz J, Milpetz F, Bork P, Ponting CP. 1998. SMART, a simple modular architecture research tool: identification of signaling domains. Proceedings of the Natlional Academy Sciences of United States of America 95, 5857-64.

Skirycz A, Reichelt M, Burow M, Birkemeyer C, Rolcik J, Kopka J, Zanor MI, Gershenzon J, Strnad M, Szopa J, Mueller-Roeber B, Witt I. 2006. DOF transcription factor AtDOF1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. Plant Journal 47, 10-24.

Song A, Gao T, Li P, Chen S, Guan Z, Wu D, Xin J, Fan Q, Zhao K, Chen F. 2016 Transcriptome-Wide Identification and Expression Profiling of the DOF Transcription Factor Gene Family in Chrysanthemum morifolium. Frontiers in Plant Sciences 7, 199.

Spanudakis E. 2014. The role of microRNAs in the control of flowering time. Journal of Experimental Botany.

Sun Z, Guo T, Liu Y, Liu Q, Fang Y. 2015. The Roles of Arabidopsis CDF2 in Transcriptional and Posttranscriptional Regulation of Primary Micro RNAs. PLoS Genetics 11, e1005598.

Terzi  C. 2008. Regulation of Flowering Time by RNA Processing. Springer Link.

Thompson JD, Gibson TJ, Higgins DG. 2003. Multiple sequence alignment using ClustalW and ClustalX. Current protocols in bioinformatics, 2.3. 1-2.3. 22.

Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research 22, 4673-4680.

Wei Q, Wang W, Hu T, Hu H, Mao W, Zhu Q, Bao C. 2018. Genome-wide identification and characterization of DOF transcription factors in eggplant (Solanum melongena L.). Peer-reviewed Journal 6, e4481.

Wen CL, Cheng Q, Zhao L, Mao A, Yang J, Yu S, Weng Y, Xu Y. 2016. Identification and characterisation of DOF transcription factors in the cucumber genome. Scientific Reports 6, 23072.

Wu J, Fu L, Yi H. 2016. Genome-Wide Identification of the Transcription Factors Involved in Citrus Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type. PLoS One 11, e0154330.

Xu Y, Liu Z, Lou L, Su X. 2018. Identification of browning-related microRNAs and their targets reveals complex miRNA-mediated browning regulatory networks in Luffa cylindrica. Scientific Reports 8, 16242.

Yanagisawa S. 1995. A novel DNA-binding domain that may form a single zinc finger motif. Nucleic acids research 23, 3403-3410.

Yanagisawa S. 2000. DOF1 and DOF2 transcription factors are associated with expression of multiple genes involved in carbon metabolism in maize. Plant Journal 21, 281-8.

Yanagisawa S. 2002. The DOF family of plant transcription factors. Trends in plant science 7, 555-560.

Yanagisawa S, Akiyama A, Kisaka H, Uchimiya H, Miwa T. 2004. Metabolic engineering with DOF1 transcription factor in plants: improved nitrogen assimilation and growth under low-nitrogen conditions. Proceedings of the National Academy of Sciences 101, 7833-7838.

Yanagisawa S, Schmidt RJ. 1999. Diversity and similarity among recognition sequences of DOF  transcription factors. The Plant Journal 17, 209-214.

Yang J, Yang MF, Zhang WP, Chen F, Shen SH. 2011. A putative flowering-time-related DOF transcription factor gene, JcDOF3, is controlled by the circadian clock in Jatropha curcas. Plant Science 181, 667-674.

Yang X, Tuskan GA. 2006. Divergence of the DOF gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant physiology 142, 820-830.

Zhang H, Birch J, Pei J, Mohamed Ahmed IA, Yang H, Dias G, Abd El-Aty AM, Bekhit AE. 2019. Identification of Six Phytochemical Compounds from Asparagus officinalis L . Root Cultivars from New Zealand and China Using UAE-SPE-UPLC-MS/MS: Effects of Extracts on H(2)O(2)-Induced Oxidative Stress. Nutrients 11.

Zohary D, Spiegel-Roy P. 1975. Beginnings of fruit growing in the old world. Science 187, 319-27.

Zou HF, Zhang YQ, Wei W, Chen HW, Song  QX, Liu YF, Zhao MY, Wang F, Zhang BC, Lin Q, Zhang WK, Ma B, Zhou YH, Zhang JS, Chen SY. 2013. The transcription factor AtDOF4.2 regulates shoot branching and seed coat formation in Arabidopsis. Biochemical Journal 449, 373-88.