Chen WJ, Zhu T. Networks of transcription factors with roles in environmental stress response. Trends Plant Sci. 2004;9(12):591–6.
Article
CAS
PubMed
Google Scholar
Lai X, Stigliani A, Vachon G, Carles C, Smaczniak C, Zubieta C, Kaufmann K, Parcy F. Building transcription factor binding site models to understand gene regulation in plants. Mol Plant. 2019;12(6):743–63.
Article
CAS
PubMed
Google Scholar
Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martinez-Garcia JF, Bilbao-Castro JR, Robertson DL. Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiol. 2010;153(3):1398–412.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang R, Zhao P, Kong N, Lu R, Pei Y, Huang C, Ma H, Chen Q. Genome-wide identification and characterization of the potato bHLH transcription factor family. Genes. 2018;9(1):54.
Article
PubMed Central
CAS
Google Scholar
Tian S, Li L, Wei M, Yang F. Genome-wide analysis of basic helix-loop-helix superfamily members related to anthocyanin biosynthesis in eggplant (Solanum melongena L.). PeerJ. 2019;7:e7768.
Article
PubMed
PubMed Central
Google Scholar
Pires N, Dolan L. Origin and diversification of basic-helix-loop-helix proteins in plants. Mol Biol Evol. 2010;27(4):862–74.
Article
CAS
PubMed
Google Scholar
Yingqi H, Ahmad N, Yuanyuan T, Jianyu L, Liyan W, Gang W, Xiuming L, Yuanyuan D, Fawei W, Weican L, Wang G, Liu X, Dong Y, Wang F, Liu W, Li X, Zhao X, Yao N, Li H. Genome-wide identification, expression analysis, and subcellular localization of Carthamus tinctorius bHLH transcription factors. Int J Mol Sci. 2019;20:3044.
Article
CAS
Google Scholar
Lin Y-J, Li M-J, Hsing H-C, Chen T-K, Yang T-T, Ko S-S. Spike activator 1, encoding a bHLH, mediates axillary bud development and spike initiation in Phalaenopsis aphrodite. Int J Mol Sci. 2019;20:5406.
Article
CAS
PubMed Central
Google Scholar
Liu Y, Li X, Li K, Liu H, Lin C. Multiple bHLH proteins form heterodimers to mediate CRY2-dependent regulation of flowering-time in Arabidopsis. PLoS Genet. 2013;9(10):e1003861.
Article
PubMed
PubMed Central
CAS
Google Scholar
Robinson KA, Lopes JM. Survey and summary: Saccharomyces cerevisiae basic helix-loop-helix proteins regulate diverse biological processes. Nucleic Acids Res. 2000;28(7):1499–505.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ke YZ, Wu YW, Zhou HJ, Chen P, Wang MM, Liu MM, Li PF, Yang J, Li JN, Du H. Genome-wide survey of the bHLH super gene family in Brassica napus. BMC Plant Biol. 2020;20(1):115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurt F, Filiz E. Genome-wide and comparative analysis of bHLH38, bHLH39, bHLH100 and bHLH101 genes in Arabidopsis, tomato, rice, soybean and maize: insights into iron (Fe) homeostasis. Biometals. 2018;31(4):489–504.
Article
CAS
PubMed
Google Scholar
Bao S, Hua C, Huang G, Cheng P, Gong X, Shen L, Yu H. Molecular basis of natural variation in photoperiodic flowering responses. Dev Cell. 2019;50(1):90–101 e103.
Article
CAS
PubMed
Google Scholar
Liu B, Yang Z, Gomez A, Liu B, Lin C, Oka Y. Signaling mechanisms of plant cryptochromes in Arabidopsis thaliana. J Plant Res. 2016;129(2):137–48.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen M, Chory J. Phytochrome signaling mechanisms and the control of plant development. Trends Cell Biol. 2011;21(11):664–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Q, Lin C. Mechanisms of cryptochrome-mediated photoresponses in plants. Annu Rev Plant Biol. 2020;71:103–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fantini E, Sulli M, Zhang L, Aprea G, Jiménez-Gómez JM, Bendahmane A, Perrotta G, Giuliano G, Facella P. Pivotal roles of cryptochromes 1a and 2 in tomato development and physiology. Plant Physiol. 2019;179(2):732–48.
Article
CAS
PubMed
Google Scholar
Liu H, Yu X, Li K, Klejnot J, Yang H, Lisiero D, Lin C. Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science. 2008;322(5907):1535–9.
Article
CAS
PubMed
Google Scholar
Ahmad M, Cashmore AR. HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature. 1993;366(6451):162–6.
Article
CAS
PubMed
Google Scholar
Cao S, He S, Lv H, Zhang J, Aslam M, Cheng H, Hu A, Cao G, Zhang X, Yu Y, et al. Genome-wide analysis of the Cryptochrome gene family in plants. Trop Plant Biol. 2020;13(1):117–26.
Article
CAS
Google Scholar
Huang Y, Baxter R, Smith BS, Partch CL, Colbert CL, Deisenhofer J. Crystal structure of cryptochrome 3 from Arabidopsis thaliana and its implications for photolyase activity. Proc Natl Acad Sci U S A. 2006;103(47):17701–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gartner W. In-Planta expression: searching for the genuine chromophores of Cryptochrome-3 from Arabidopsis thaliana. Photochem Photobiol. 2017;93(1):382–4.
Article
PubMed
CAS
Google Scholar
Liu H, Wang Q, Liu Y, Zhao X, Imaizumi T, Somers DE, Tobin EM, Lin C. Arabidopsis CRY2 and ZTL mediate blue-light regulation of the transcription factor CIB1 by distinct mechanisms. Proc Natl Acad Sci U S A. 2013;110(43):17582–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Q, Su T, He W, Ren H, Liu S, Chen Y, Gao L, Hu X, Lu H, Cao S, et al. Photooligomerization determines photosensitivity and photoreactivity of plant cryptochromes. Mol Plant. 2020;13:398–413.
Article
CAS
PubMed
Google Scholar
Liu Y, Li X, Ma D, Chen Z, Wang JW, Liu H. CIB1 and CO interact to mediate CRY2 dependent regulation of flowering. EMBO Rep. 2018;19(10):e45762.
Article
PubMed
PubMed Central
CAS
Google Scholar
Toledo-Ortiz G, Huq E, Quail PH. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell. 2003;15(8):1749–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol Biol Evol. 2003;20(5):735–47.
Article
CAS
PubMed
Google Scholar
Zhang T, Lv W, Zhang H, Ma L, Li P, Ge L, Li G. Genome-wide analysis of the basic helix-loop-helix (bHLH) transcription factor family in maize. BMC Plant Biol. 2018;18(1):235.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, et al. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet. 2015;47(12):1435–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ferre-D'Amare AR, Prendergast GC, Ziff EB, Burley SK. Recognition by max of its cognate DNA through a dimeric b/HLH/Z domain. Nature. 1993;363(6424):38–45.
Article
CAS
PubMed
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao Y, Zhang YY, Liu H, Zhang XS, Ni R, Wang PY, Gao S, Lou HX, Cheng AX. Functional characterization of a liverworts bHLH transcription factor involved in the regulation of bisbibenzyls and flavonoids biosynthesis. BMC Plant Biol. 2019;19(1):497.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin C, Shalitin D. Cryptochrome structure and signal transduction. Annu Rev Plant Biol. 2003;54:469–96.
Article
CAS
PubMed
Google Scholar
Amasino RM, Michaels SD. The timing of flowering. Plant Physiol. 2010;154(2):516–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hou N, Cao Y, Li F, Yuan W, Bian H, Wang J, Zhu M, Han N. Epigenetic regulation of miR396 expression by SWR1-C and the effect of miR396 on leaf growth and developmental phase transition in Arabidopsis. J Exp Bot. 2019;70(19):5217–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
D'Amico-Damião V, Carvalho RF. Cryptochrome-related abiotic stress responses in plants. Front Plant Sci. 2018;9:1897.
Article
PubMed
PubMed Central
Google Scholar
Liu H, Liu B, Zhao C, Pepper M, Lin C. The action mechanisms of plant cryptochromes. Trends Plant Sci. 2011;16(12):684–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Delgado D, Ballesteros I, Torres-Contreras J, Mena M, Fenoll C. Dynamic analysis of epidermal cell divisions identifies specific roles for COP10 in Arabidopsis stomatal lineage development. Planta. 2012;236(2):447–61.
Article
CAS
PubMed
Google Scholar
Kang CY, Lian HL, Wang FF, Huang JR, Yang HQ. Cryptochromes, phytochromes, and COP1 regulate light-controlled stomatal development in Arabidopsis. Plant Cell. 2009;21(9):2624–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mao J, Zhang YC, Sang Y, Li QH, Yang HQ. From the cover: a role for Arabidopsis cryptochromes and COP1 in the regulation of stomatal opening. Proc Natl Acad Sci U S A. 2005;102(34):12270–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aslam M, Fakher B, Jakada BH, Zhao L, Cao S, Cheng Y, Qin Y. Genome-wide identification and expression profiling of CBL-CIPK gene family in pineapple (Ananas comosus) and the role of AcCBL in abiotic and biotic stress response. Biomolecules. 2019;9(7):293.
Article
CAS
PubMed Central
Google Scholar
Clough SJ, Bent AF. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1998;16(6):735–43.
Article
CAS
PubMed
Google Scholar
Letunic I, Bork P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res. 2018;46(D1):D493–6.
Article
CAS
PubMed
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2015;31(8):1296–7.
Article
PubMed
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen P, Li Y, Zhao L, Hou Z, Yan M, Hu B, Liu Y, Azam SM, Zhang Z, Rahman ZU, et al. Genome-wide identification and expression profiling of ATP-Binding Cassette (ABC) transporter gene family in pineapple (Ananas comosus (L.) Merr.) reveal the role of AcABCG38 in pollen development. Front Plant Sci. 2017;8:2150.
Article
PubMed
PubMed Central
Google Scholar
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc. 2012;7(3):562–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dai X, Bai Y, Zhao L, Dou X, Liu Y, Wang L, Li Y, Li W, Hui Y, Huang X, et al. H2A.Z represses gene expression by modulating promoter nucleosome structure and enhancer histone modifications in Arabidopsis. Mol Plant. 2017;10(10):1274–92.
Article
CAS
PubMed
Google Scholar
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25(4):402–8.
Article
CAS
PubMed
Google Scholar
Wang L, Li Y, Jin X, Liu L, Dai X, Liu Y, Zhao L, Zheng P, Wang X, Liu Y, et al. Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development. Communications Biology. 2020;3(1):500.
Article
CAS
PubMed
PubMed Central
Google Scholar