[1]

Coyne JA. 1992. Genetics and speciation. Nature 355:511−15

doi: 10.1038/355511a0
[2]

Hopkins R, Rausher MD. 2012. Pollinator-mediated selection on flower color allele drives reinforcement. Science 335:1090−92

doi: 10.1126/science.1215198
[3]

Siddique MA, Grossmann J, Gruissem W, Baginsky S. 2006. Proteome analysis of bell pepper (Capsicum annuum L.) chromoplasts. Plant and Cell Physiology 47:1663−73

doi: 10.1093/pcp/pcl033
[4]

Koes R, Verweij W, Quattrocchio F. 2005. Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends in Plant Science 10:236−42

doi: 10.1016/j.tplants.2005.03.002
[5]

Rodriguez-Concepcion M, Avalos J, Luisa Bonet ML, Boronat A, Gomez-Gomez L, et al. 2018. A global perspective on carotenoids: metabolism, biotechnology, and benefits for nutrition and health. Progress in Lipid Research 70:62−93

doi: 10.1016/j.plipres.2018.04.004
[6]

Lu C, Pu Y, Liu Y, Li Y, Qu J, et al. 2019. Comparative transcriptomics and weighted gene co-expression correlation network analysis (WGCNA) reveal potential regulation mechanism of carotenoid accumulation in Chrysanthemum × morifolium. Plant Physiology and Biochemistry 142:415−28

doi: 10.1016/j.plaphy.2019.07.023
[7]

Cui L, Zheng F, Zhang C, Gao S, Ye J, et al. 2025. The CONSTANS-LIKE SlCOL1 in tomato regulates the fruit chlorophyll content by stabilizing the GOLDEN2-LIKE protein. Journal of Integrative Agriculture 24:536−45

doi: 10.1016/j.jia.2024.11.022
[8]

Chen H, Ji H, Huang W, Zhang Z, Zhu K, et al. 2024. Transcription factor CrWRKY42 coregulates chlorophyll degradation and carotenoid biosynthesis in citrus. Plant Physiology 195:728−44

doi: 10.1093/plphys/kiae048
[9]

Hao Z, Liu S, Hu L, Shi J, Chen J. 2020. Transcriptome analysis and metabolic profiling reveal the key role of carotenoids in the petal coloration of Liriodendron tulipifera. Horticulture Research 7:70

doi: 10.1038/s41438-020-0287-3
[10]

Hao Q, Li T, Lu G, Wang S, Li Z, et al. 2025. Chlorophyllase (PsCLH1) and light-harvesting chlorophyll a/b binding protein 1 (PsLhcb1) and PsLhcb5 maintain petal greenness in Paeonia suffruticosa 'Lv Mu Yin Yu'. Journal of Advanced Research 73:173−85

doi: 10.1016/j.jare.2024.09.003
[11]

Zheng X, Lan J, Yu H, Zhang J, Zhang Y, et al. 2022. Arabidopsis transcription factor TCP4 represses chlorophyll biosynthesis to prevent petal greening. Plant Communications 3:100309

doi: 10.1016/j.xplc.2022.100309
[12]

Fang J, Liu S, Chen S, Deng H, Zhao L, et al. 2025. A R1-type MYB CmREVEILLE2 regulates light-mediated chlorophyll biosynthesis and green color formation in chrysanthemum flowers. Horticulture Advances 3:17

doi: 10.1007/s44281-025-00069-4
[13]

Lopez-Juez E, Pyke KA. 2005. Plastids unleashed: their development and their integration in plant development. The International Journal of Developmental Biology 49:557−77

doi: 10.1387/ijdb.051997el
[14]

Jarvis P, López-Juez E. 2013. Biogenesis and homeostasis of chloroplasts and other plastids. Nature Reviews Molecular Cell Biology 14:787−802

doi: 10.1038/nrm3702
[15]

Schweiggert RM, Steingass CB, Heller A, Esquivel P, Carle R. 2011. Characterization of chromoplasts and carotenoids of red- and yellow-fleshed papaya (Carica papaya L.). Planta 234:1031−44

doi: 10.1007/s00425-011-1457-1
[16]

Zeng Y, Du J, Wang L, Pan Z, Xu Q, et al. 2015. A comprehensive analysis of chromoplast differentiation reveals complex protein changes associated with plastoglobule biogenesis and remodeling of protein systems in sweet orange flesh. Plant Physiology 168:1648−65

doi: 10.1104/pp.15.00645
[17]

Suzuki M, Takahashi S, Kondo T, Dohra H, Ito Y, et al. 2015. Plastid proteomic analysis in tomato fruit development. PLoS One 10:e0137266

doi: 10.1371/journal.pone.0137266
[18]

Frey-Wyssling A, Kreutzer E. 1958. The submicroscopic development of chromoplasts in the fruit of Capsicum annuum L. Journal of Ultrastructure Research 1:397−411

doi: 10.1016/S0022-5320(58)90010-8
[19]

Toledo-Ortiz G, Huq E, Rodríguez-Concepción M. 2010. Direct regulation of phytoene synthase gene expression and carotenoid biosynthesis by phytochrome-interacting factors. Proceedings of the National Academy of Sciences of the United States of America 107:11626−31

doi: 10.1073/pnas.0914428107
[20]

Cazzonelli CI, Cuttriss AJ, Cossetto SB, Pye W, Crisp P, et al. 2009. Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8. The Plant Cell 21:39−53

doi: 10.1105/tpc.108.063131
[21]

Stanley L, Yuan YW. 2019. Transcriptional regulation of carotenoid biosynthesis in plants: so many regulators, so little consensus. Frontiers in Plant Science 10:1017

doi: 10.3389/fpls.2019.01017
[22]

Karlova R, Rosin FM, Busscher-Lange J, Parapunova V, Do PT, et al. 2011. Transcriptome and metabolite profiling show that APETALA2a is a major regulator of tomato fruit ripening. The Plant Cell 23:923−41

doi: 10.1105/tpc.110.081273
[23]

Dang Q, Sha H, Nie J, Wang Y, Yuan Y, et al. 2021. An apple (Malus domestica) AP2/ERF transcription factor modulates carotenoid accumulation. Horticulture Research 8:223

doi: 10.1038/s41438-021-00694-w
[24]

Lu S, Zhang Y, Zhu K, Yang W, Ye J, et al. 2018. The citrus transcription factor CsMADS6 modulates carotenoid metabolism by directly regulating carotenogenic genes. Plant Physiology 176:2657−76

doi: 10.1104/pp.17.01830
[25]

Chen J, Hao Z, Guang X, Zhao C, Wang P, et al. 2019. Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation. Nature Plants 5:18−25

doi: 10.1038/s41477-018-0323-6
[26]

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29:644−52

doi: 10.1038/nbt.1883
[27]

Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323

doi: 10.1186/1471-2105-12-323
[28]

Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550

doi: 10.1186/s13059-014-0550-8
[29]

Yu G, Wang LG, Han Y, He QY. 2012. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16:284−87

doi: 10.1089/omi.2011.0118
[30]

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32:268−74

doi: 10.1093/molbev/msu300
[31]

Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402−8

doi: 10.1006/meth.2001.1262
[32]

Cuong DM, Kim JK, Jeon J, Kim TJ, Park JS, et al. 2018. Expression of carotenoid biosynthetic genes and carotenoid biosynthesis during seedling development of Momordica charantia. Natural Product Communications 13:311−14

doi: 10.1177/1934578x1801300312
[33]

Sakuraba Y, Kim YS, Yoo SC, Hörtensteiner S, Paek NC. 2013. 7-Hydroxymethyl chlorophyll a reductase functions in metabolic channeling of chlorophyll breakdown intermediates during leaf senescence. Biochemical and Biophysical Research Communications 430:32−37

doi: 10.1016/j.bbrc.2012.11.050
[34]

Sakuraba Y, Schelbert S, Park SY, Han SH, Lee BD, et al. 2012. STAY-GREEN and chlorophyll catabolic enzymes interact at light-harvesting complex II for chlorophyll detoxification during leaf senescence in Arabidopsis. The Plant Cell 24:507−18

doi: 10.1105/tpc.111.089474
[35]

Luo Z, Zhang J, Li J, Yang C, Wang T, et al. 2013. A STAY-GREEN protein SlSGR1 regulates lycopene and β-carotene accumulation by interacting directly with SlPSY1 during ripening processes in tomato. New Phytologist 198:442−52

doi: 10.1111/nph.12175
[36]

Ren G, Zhou Q, Wu S, Zhang Y, Zhang L, et al. 2010. Reverse genetic identification of CRN1 and its distinctive role in chlorophyll degradation in Arabidopsis. Journal of Integrative Plant Biology 52:496−504

doi: 10.1111/j.1744-7909.2010.00945.x
[37]

Schelbert S, Aubry S, Burla B, Agne B, Kessler F, et al. 2009. Pheophytin pheophorbide hydrolase (pheophytinase) is involved in chlorophyll breakdown during leaf senescence in Arabidopsis. The Plant Cell 21:767−85

doi: 10.1105/tpc.108.064089
[38]

Egea I, Barsan C, Bian W, Purgatto E, Latché A, et al. 2010. Chromoplast differentiation: current status and perspectives. Plant and Cell Physiology 51:1601−11

doi: 10.1093/pcp/pcq136
[39]

Karniel U, Koch A, Zamir D, Hirschberg J. 2020. Development of zeaxanthin-rich tomato fruit through genetic manipulations of carotenoid biosynthesis. Plant Biotechnology Journal 18:2292−303

doi: 10.1111/pbi.13387
[40]

Lu S, Van Eck J, Zhou X, Lopez AB, O'Halloran DM, et al. 2006. The cauliflower Or gene encodes a DnaJ cysteine-rich domain-containing protein that mediates high levels of beta-carotene accumulation. The Plant Cell 18:3594−605

doi: 10.1105/tpc.106.046417
[41]

Kilcrease J, Collins AM, Richins RD, Timlin JA, O'Connell MA. 2013. Multiple microscopic approaches demonstrate linkage between chromoplast architecture and carotenoid composition in diverse Capsicum annuum fruit. The Plant Journal 76:1074−83

doi: 10.1111/tpj.12351
[42]

Vasquez-Caicedo AL, Heller A, Neidhart S, Carle R. 2006. Chromoplast morphology and beta-carotene accumulation during postharvest ripening of mango cv. 'Tommy Atkins'. Journal of Agricultural and Food Chemistry 54:5769−76

doi: 10.1021/jf060747u
[43]

Wang YH, Zhang YQ, Zhang RR, Zhuang FY, Liu H, et al. 2023. Lycopene ε-cyclase mediated transition of α-carotene and β-carotene metabolic flow in carrot fleshy root. The Plant Journal 115:986−1003

doi: 10.1111/tpj.16275
[44]

Ma Y, Liu N, Greisen P, Li J, Qiao K, et al. 2022. Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica. Nature Communications 13:572

doi: 10.1038/s41467-022-28277-w
[45]

Soltis PS, Folk RA, Soltis DE. 2019. Darwin review: angiosperm phylogeny and evolutionary radiations. Proceedings of the Royal Society B: Biological Sciences 286:20190099

doi: 10.1098/rspb.2019.0099
[46]

Jabbour F, Renner SS. 2012. Spurs in a spur: perianth evolution in the delphinieae (Ranunculaceae). International Journal of Plant Sciences 173:1036−54

doi: 10.1086/667613
[47]

Yang A, Zhong Y, Liu S, Liu L, Liu T, et al. 2019. New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east-west lineage split and genetic mixture within western subtropical China. PeerJ 7:e6355

doi: 10.7717/peerj.6355
[48]

Zhou Y, Li M, Zhao F, Zha H, Yang L, et al. 2016. Floral nectary morphology and proteomic analysis of nectar of Liriodendron tulipifera Linn. Frontiers in Plant Science 7:826

doi: 10.3389/fpls.2016.00826