Abstract
Transcription factors (TFs) and transcription coregulators (TCs) play important roles in regulating plant growth and development, physiological and metabolic processes, and responses to biotic and abiotic stresses. Genome-wide identification of TFs and TCs was performed in pineapple. The tissue-specific and diurnal expression of pineapple TFs and TCs was characterized via global transcriptomic analysis. A set of diurnal cycling TFs and TCs was identified using time-course gene expression analysis. The resources provide important information for studying developmental biology, stress physiology, and disease resistance in pineapple. The resources also provide essential information for understanding the circadian regulation of crassulacean acid metabolism (CAM) in pineapple.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Barak S, Tobin EM, Andronis C, Sugano S, Green RM (2000) All in good time: the Arabidopsis circadian clock. Trends Plant Sci 5:517ā522
Doherty CJ, Kay SA (2010) Circadian control of global gene expression patterns. Annu Rev Genet 44:419ā444
Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573ā581
Endo M, Shimizu H, Nohales MA, Araki T, Kay SA (2014) Tissue-specific clocks in Arabidopsis show asymmetric coupling. Nature 515:419ā422
Franci-Zorrilla JM, LĻpez-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R (2014) DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci 111:2367ā2372
Gates DJ, Strickler SR, Mueller LA, Olson BJSC, Smith SD (2016) Diversification of R2R3-MYB transcription factors in the tomato family solanaceae. J Mol Evol 83:26ā37
Gaudinier A, Tang M, Kliebenstein DJ (2015) Transcriptional networks governing plant metabolism. Curr Plant Biol 3ā4:56ā64
Ishihama A, Shimada T, Yamazaki Y (2016) Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic Acids Res 44:2058ā2074
James AB, Monreal JA, Nimmo GA, Kelly CL, Herzyk P, Jenkins GI, Nimmo HG (2008) The circadian clock in arabidopsis roots is a simplified slave version of the clock in shoots. Science 322:1832ā1835
Li S-B, Xie Z-Z, Hu C-G, Zhang J-Z (2016) A review of auxin response factors (ARFs) in plants. Front Plant Sci 7:47
Lin J-J, Yu C-P, Chang Y-M, Chen SC-C, Li W-H (2014) Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. BMC Genomics 15:818
Liu C, Xie T, Chen C, Luan A, Long J, Li C, Ding Y, He Y (2017) Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus). BMC Genomics 18:503
Michael TP, McClung CR (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in arabidopsis. Plant Physiol 132:629ā639
Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, Hazen SP, Shen R, Priest HD, Sullivan CM, Givan SA, Yanovsky M, Hong F, Kay SA, Chory J (2008) Network discovery pipeline elucidates conserved time-of-dayāspecific cis-regulatory modules. PLoS Genet 4:e14
Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE et al (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47:1435ā1442
Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran L-SP (2013) TreeTFDB: an integrative database of the transcription factors from six economically important tree crops for functional predictions and comparative and functional genomics. DNA Res 20:151ā162
Narlikar L, Ovcharenko I (2009) Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic 8:215ā230
PĆ©rez-RodrĆguez P, RiaƱo-PachĻn DM, CorrĆŖa LG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38:D822āD827
Riechmann JL, Heard J, Martin G, Reuber L, Jiang C-Z, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu GL (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105ā2110
Sharma A, Wai CM, Ming R, Yu Q (2017) Diurnal cycling transcription factors of pineapple revealed by genome-wide annotation and global transcriptomic analysis. Genome Biol Evol 9(9):2170ā2190. https://doi.org/10.1093/gbe/evx161
Su Z, Wang L, Li W, Zhao L, Huang X, Azam SM, Qin Y (2017) Genome-wide identification of auxin response factor (arf) genes family and its tissue-specific prominent expression in pineapple (Ananas comosus). Trop Plant Biol 10(2ā3):86ā96. https://doi.org/10.1007/s12042-017-9187-6
Takahashi N, Hirata Y, Aihara K, Mas P (2015) A hierarchical multi-oscillator network orchestrates the arabidopsis circadian system. Cell 163:148ā159
Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nat Genet 22:281ā285
Wai CM, VanBuren R, Zhang J, Huang L, Miao W, Edger PP, Yim WC, Priest HD, Meyers BC, Mockler T, Smith JAC, Cushman JC, Ming R (2017) Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple. Plant J 92(1):19ā30. https://doi.org/10.1111/tpj.13630
Walhout AJM (2006) Unraveling transcription regulatory networks by proteināDNA and proteināprotein interaction mapping. Genome Res 16:1445ā1454
Yilmaz A, Nishiyama MY Jr, Fuentes BG, Souza GM, Janies D, Gray J, Grotewold E (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol 149:171ā180
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
Ā© 2018 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Yu, Q., Sharma, A. (2018). Transcription Factors in theĀ Pineapple Genome. In: Ming, R. (eds) Genetics and Genomics of Pineapple. Plant Genetics and Genomics: Crops and Models, vol 22. Springer, Cham. https://doi.org/10.1007/978-3-030-00614-3_13
Download citation
DOI: https://doi.org/10.1007/978-3-030-00614-3_13
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-00613-6
Online ISBN: 978-3-030-00614-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)