Ain-Ali Q U, Mushtaq N, Amir R, Gul A, Tahir M, Munir F. 2021. Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum. PLoS ONE, 16, e0261215.

Alessio V M, Cavaçana N, Dantas L L D B, Lee N, Hotta C T, Imaizumi T, Menossi M. 2018. The FBH family of bHLH transcription factors controls ACC synthase expression in sugarcane. Journal of Experimental Botany, 69, 2511–2525.

Bailey T L, Johnson J, Grant C E, Noble W S. 2015. The MEME suite. Nucleic Acids Research, 43, W39–W49.

Boeckmann B, Bairoch A, Apweiler R, Blatter M C, Estreicher A, Gasteiger E, Martin M J, Michoud K, O’Donovan C, Phan I, Pilbout S, Schneider M. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research, 31, 365–370.

Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martínez-García J F, Bilbao-Castro J R, Robertson D L. 2010. Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiology, 153, 1398–1412.

Chen C B, Li F P, Xie F F, Chen J X, Hua Q Z, Chen J Y, Wu Z J, Zhang Z K, Zhang R, Zhao J T, Hu G B, Qin Y H. 2022. Pitaya genome and multiomics database (PGMD): A comprehensive and integrative resource of Selenicereus undatus. Genes, 13, 745.

Chen J Y, Xie F F, Cui Y Z, Chen C B, Lu W J, Hu X D, Hua Q Z, Zhao J, Wu Z J, Gao D, Zhang Z K, Jiang W K, Sun Q M, Hu G B, Qin Y H. 2021. A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis. Horticulture Research, 8, 164.

Chen Y C, Rajagopala S V, Stellberger T, Uetz P. 2010. Exhaustive benchmarking of the yeast two-hybrid system. Nature Methods, 7, 667–668.

Chu Y C, Chang J C. 2020. Regulation of floral bud development and emergence by ambient temperature under a long-day photoperiod in white-fleshed pitaya (Hylocereus undatus). Scientia Horticulturae, 271, 109479.

Falcon S, Gentleman R. 2007. Using GOstats to test gene lists for GO term association. Bioinformatics, 23, 257–258.

Feller A, Machemer K, Braun E L, Grotewold E. 2011. Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. The Plant Journal, 66, 94–116.

Gasteiger E, Hoogland C, Gattiker A, Duvaud S E, Wilkins M R, Appel R D, Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server. In: Walker J M, eds., The Proteomics Protocols Handbook. Humana press, Totowa, NJ. pp. 571–607.

Goodstein D M, Shu S, Howson R, Neupane R, Hayes R D, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar D S. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40, D1178–D1186.

Ito S, Song Y H, Josephson-Day A R, Miller R J, Breton G, Olmstead R G, Imaizumi T. 2012. FLOWERING BHLH transcriptional activators control expression of the photoperiodic flowering regulator CONSTANS in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 109, 3582–3587.

Jiang Y L, Liao Y Y, Lin T S, Lee C L, Yen C R, Yang W J. 2012. The photoperiod-regulated bud formation of red pitaya (Hylocereus sp.). Hortscience, 47, 1063–1067.

Katoh K, Rozewicki J, Yamada K D. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics, 20, 1160–1166.

Kim D, Langmead B, Salzberg S L. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12, 357–360.

Krueger F. 2015. Trim Galore!: A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. [2023-6-3]. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A. 2009. Circos: An information aesthetic for comparative genomics. Genome Research, 19, 1639–1645.

Le Bellec F, Vaillant F, Imbert E. 2006. Pitahaya (Hylocereus spp.): A new fruit crop, a market with a future. Fruits, 61, 237–250.

Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts, S. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30, 325–327.

Letunic I, Bork P. 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Research, 49, W293–W296.

Li X Y. 2011. Infiltration of Nicotiana benthamiana protocol for transient expression via Agrobacterium. Bio-protocol, 1, e95.

Liao Y, Smyth G K, Shi W. 2014. featureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923–930.

Lin L, Fan J L, Li P P, Liu D X, Ren S C, Lin K Y, Fang Y J, Lin C, Wang Y P, Wu J. 2022. The Sclerotinia sclerotiorum-inducible promoter pBnGH17D7 in Brassica napus: isolation, characterization, and application in host-induced gene silencing. Journal of Experimental Botany, 73, 6663–6677.

Lu S N, Wang J Y, Chitsaz F, Derbyshire M K, Geer R C, Gonzales N R, Gwadz M, Hurwitz D, Marchler G H, Song J S, Thanki N, Yamashita R A, Yang M Z, Zhang D C, Zhang C J, Lanczycki C J, Marchler-Bauer A. 2020. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Research, 48, D265–D268.

Minh B Q, Schmidt H A, Chernomor O, Schrempf D, Woodhams M D, Von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution, 37, 1530–1534.

Mistry J, Finn R D, Eddy S R, Bateman A, Punta M. 2013. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Research, 41, e121.

Morgan M, Falcon S, Gentleman R. 2018. GSEABase: Gene set enrichment data structures and methods. R package version 1.64.0. [2023-6-3]. https://bioconductor.org/packages/release/bioc/html/GSEABase.html

Nair S K, Burley S K. 2000. Recognizing DNA in the library. Nature, 404, 715–717.

Okada M, Lanzatella C, Saha M C, Bouton J, Wu R, Tobias C M. 2010. Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions. Genetics, 185, 745–760.

Popescu S C, Popescu G V, Bachan S, Zhang Z M, Gerstein M, Snyder M, Dinesh-Kumar, S P. 2009. MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes & Development, 23, 80–92.

Sanagi M, Aoyama S, Kubo A, Lu Y, Sato Y, Ito S, Abe M, Mitsuda N, Ohme-Takagi M, Kiba T, Nakagami H, Rolland F, Yamaguchi J, Imaizumi T, Sato T. 2021. Low nitrogen conditions accelerate flowering by modulating the phosphorylation state of FLOWERING BHLH 4 in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 118, e2022942118.

Schmittgen T D, Livak K J. 2008. Analyzing real-time PCR data by the comparative CT method. Nature Protocols, 3, 1101–1108.

Takahashi Y, Ebisu Y, Kinoshita T, Doi M, Okuma E, Murata Y, Shimazaki K I. 2013. bHLH transcription factors that facilitate K+ uptake during stomatal opening are repressed by abscisic acid through phosphorylation. Science Signaling, 6, ra48.

Takahashi Y, Kinoshita T, Matsumoto M, Shimazaki K I. 2016. Inhibition of the Arabidopsis bHLH transcription factor by monomerization through abscisic acid‐induced phosphorylation. The Plant Journal, 87, 559–567.

Thumuluri V, Almagro Armenteros J J, Johansen A R, Nielsen H, Winther O. 2022. DeepLoc 2.0: multi-label subcellular localization prediction using protein language models. Nucleic Acids Research, 50, W228–W234.

Tian H N, Guo H Y, Dai X M, Cheng Y X, Zheng K J, Wang X P, Wang S. 2015. An ABA down-regulated bHLH transcription repressor gene, bHLH129 regulates root elongation and ABA response when overexpressed in Arabidopsis. Scientific Reports, 5, 17587.

Toledo-Ortiz G, Huq E, Quail P H. 2003. The Arabidopsis basic/helix-loop-helix transcription factor family. The Plant Cell, 15, 1749–1770.

Törönen P, Medlar A, Holm L. 2018. PANNZER2: A rapid functional annotation web server. Nucleic Acids Research, 46, W84–W88.

Wang L P, Yu G, Macho A P, Lozano-Durán R. 2021. Split-luciferase complementation imaging assay to study protein–protein interactions in Nicotiana benthamiana. Bio-protocol, 11, e4237.

Wang Y P, Tang H B, DeBarry J D, Tan X, Li J P, Wang X Y, Lee T, Jin H Z, Marler B, Guo H, Kissinger J C, Paterson A H. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 40, e49.

Wu L C, Hsu H W, Chen Y C, Chiu C C, Lin Y I, Ho J A A. 2006. Antioxidant and antiproliferative activities of red pitaya. Food Chemistry, 95, 319–327.

Yin J, Chang X X, Kasuga T, Bui M, Reid M S, Jiang C Z. 2015. A basic helix-loop-helix transcription factor, PhFBH4, regulates flower senescence by modulating ethylene biosynthesis pathway in petunia. Horticulture Research, 2, 15059.

Yoo S K, Chung K S, Kim J, Lee J H, Hong S M, Yoo S J, Yoo S Y, Lee J S, Ahn J H. 2005. CONSTANS activates SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 through FLOWERING LOCUS T to promote flowering in Arabidopsis. Plant Physiology, 139, 770–778.

Zhang S C, Ma J Q, Zou H Y, Zhang L, Li S H, Wang Y P. 2020. The combination of blue and red LED light improves growth and phenolic acid contents in Salvia miltiorrhiza Bunge. Industrial Crops and Products, 158, 112959.

Zhang X R, Henriques R, Lin S S, Niu Q W, Chua N H. 2006. Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. Nature Protocols, 1, 641–646.

Zhang Z. 2022. KaKs_Calculator 3.0: Calculating selective pressure on coding and non-coding sequences. Genomics, Proteomics and Bioinformatics, 20, 536–540.

Zhang Z, Xiao J F, Wu J Y, Zhang H Y, Liu G M, Wang X M, Dai L. 2012. ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments. Biochemical and Biophysical Research Communications, 419, 779–781.

Zhao Y, Zhang G H, Tang Q Y, Song W L, Gao Q Q, Xiang G S, Li X, Liu G Z, Fan W, Li X N, Yang S C, Zhai C X. 2022. EbMYBP1, a R2R3-MYB transcription factor, promotes flavonoid biosynthesis in Erigeron breviscapus. Frontiers in Plant Science, 13, 946827.

Zinzen R P, Girardot C, Gagneur J, Braun M, Furlong E E. 2009. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature, 462, 65–70.