Transcription Factors in the Pineapple Genome

  • Qingyi YuEmail author
  • Anupma Sharma
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 22)


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.


Ananas comosus Transcription factor Circadian clock Pineapple Diurnal expression 


  1. Barak S, Tobin EM, Andronis C, Sugano S, Green RM (2000) All in good time: the Arabidopsis circadian clock. Trends Plant Sci 5:517–522CrossRefGoogle Scholar
  2. Doherty CJ, Kay SA (2010) Circadian control of global gene expression patterns. Annu Rev Genet 44:419–444CrossRefGoogle Scholar
  3. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573–581CrossRefGoogle Scholar
  4. Endo M, Shimizu H, Nohales MA, Araki T, Kay SA (2014) Tissue-specific clocks in Arabidopsis show asymmetric coupling. Nature 515:419–422CrossRefGoogle Scholar
  5. Franci-Zorrilla JM, Lόpez-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 111:2367–2372CrossRefGoogle Scholar
  6. 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 83:26–37CrossRefGoogle Scholar
  7. Gaudinier A, Tang M, Kliebenstein DJ (2015) Transcriptional networks governing plant metabolism. Curr Plant Biol 3–4:56–64CrossRefGoogle Scholar
  8. Ishihama A, Shimada T, Yamazaki Y (2016) Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic Acids Res 44:2058–2074CrossRefGoogle Scholar
  9. 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 322:1832–1835CrossRefGoogle Scholar
  10. 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 7:47PubMedPubMedCentralGoogle Scholar
  11. 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 15:818CrossRefGoogle Scholar
  12. 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 18:503CrossRefGoogle Scholar
  13. Michael TP, McClung CR (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in arabidopsis. Plant Physiol 132:629–639CrossRefGoogle Scholar
  14. 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-day–specific cis-regulatory modules. PLoS Genet 4:e14CrossRefGoogle Scholar
  15. 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 47:1435–1442CrossRefGoogle Scholar
  16. 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 20:151–162CrossRefGoogle Scholar
  17. Narlikar L, Ovcharenko I (2009) Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic 8:215–230CrossRefGoogle Scholar
  18. Pérez-Rodríguez P, Riaño-Pachόn DM, Corrêa 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:D822–D827CrossRefGoogle Scholar
  19. 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 290:2105–2110CrossRefGoogle Scholar
  20. 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):2170–2190. Scholar
  21. 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(2–3):86–96. Scholar
  22. Takahashi N, Hirata Y, Aihara K, Mas P (2015) A hierarchical multi-oscillator network orchestrates the arabidopsis circadian system. Cell 163:148–159CrossRefGoogle Scholar
  23. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nat Genet 22:281–285CrossRefGoogle Scholar
  24. 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):19–30. Scholar
  25. Walhout AJM (2006) Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping. Genome Res 16:1445–1454CrossRefGoogle Scholar
  26. 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 149:171–180CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Texas A&M AgriLife Research Center at Dallas, Texas A&M University SystemDallasUSA
  2. 2.Department of Plant Pathology and MicrobiologyTexas A&M UniversityCollege StationUSA

Personalised recommendations