[1]

Barton NH. 2001. The role of hybridization in evolution. Molecular Ecology 10(3):551−68

doi: 10.1046/j.1365-294x.2001.01216.x
[2]

Duranton M, Pool JE. 2022. Interactions between natural selection and recombination shape the genomic landscape of introgression. Molecular Biology and Evolution 39(7):msac122

doi: 10.1093/molbev/msac122
[3]

Mitchell N, Whitney KD. 2019. Hybridization and diversification are positively correlated across vascular plant families. bioRxiv 724377

doi: 10.1101/724377
[4]

Lu L, Fritsch PW, Matzke NJ, Wang H, Kron KA, et al. 2019. Why is fruit colour so variable? Phylogenetic analyses reveal relationships between fruit‐colour evolution, biogeography and diversification. Global Ecology and Biogeography 28:891−903

doi: 10.1111/geb.12900
[5]

Messeder JVS, Carlo TA, Zhang G, Tovar JD, Arana C, et al. 2024. A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L. New Phytologist 243(2):765−80

doi: 10.1111/nph.19849
[6]

Milkovich M. 2023. Farms finding success with fruit diversification. Good Fruit Grower, Yakima, Washington, USA. https://goodfruit.com/farms-finding-success-with-fruit-diversification/
[7]

Gonzali S, Perata P. 2021. Fruit colour and novel mechanisms of genetic regulation of pigment production in tomato fruits. Horticulturae 7(8):259

doi: 10.3390/horticulturae7080259
[8]

Sinnott-Armstrong MA, Downie AE, Federman S, Valido A, Jordano P, et al. 2018. Global geographic patterns in the colours and sizes of animal-dispersed fruits. Global Ecology and Biogeography 27(11):1339−51

doi: 10.1111/geb.12801
[9]

Ranganath KG. 2022. Pigments that colour our fruits: An Overview. Erwerbs-Obstbau 64:535−47

doi: 10.1007/s10341-022-00698-3
[10]

Zhang X, Wang J, Li P, Sun C, Dong W. 2023. Integrative metabolome and transcriptome analyses reveals the black fruit coloring mechanism of Crataegus maximowiczii C. K. Schneid. Plant Physiology and Biochemistry 194:111−21

doi: 10.1016/j.plaphy.2022.11.008
[11]

Yang T, Ali M, Lin L, Li P, He H, et al. 2023. Recoloring tomato fruit by CRISPR/Cas9-mediated multiplex gene editing. Horticulture Research 10(1):uhac214

doi: 10.1093/hr/uhac214
[12]

Rajput R, Naik J, Stracke R, Pandey A. 2022. Interplay between R2R3 MYB-type activators and repressors regulates proanthocyanidin biosynthesis in banana (Musa acuminata). New Phytologist 236(3):1108−27

doi: 10.1111/nph.18382
[13]

Wang WQ, Moss SMA, Zeng L, Espley RV, Wang T, et al. 2022. The red flesh of kiwifruit is differentially controlled by specific activation-repression systems. New Phytologist 235(2):630−45

doi: 10.1111/nph.18122
[14]

Han K, Zhao Y, Sun Y, Li Y. 2023. NACs, generalist in plant life. Plant Biotechnology Journal 21(12):2433−57

doi: 10.1111/pbi.14161
[15]

Zhu K, Chen H, Mei X, Lu S, Xie H, et al. 2023. Transcription factor CsMADS3 coordinately regulates chlorophyll and carotenoid pools in Citrus hesperidium. Plant Physiology 193(1):519−36

doi: 10.1093/plphys/kiad300
[16]

Sun L, Huo J, Liu J, Yu J, Zhou J, et al. 2023. Anthocyanins distribution, transcriptional regulation, epigenetic and post-translational modification in fruits. Food Chemistry 411:135540

doi: 10.1016/j.foodchem.2023.135540
[17]

Kulczyński B, Gramza-Michałowska A. 2016. Goji berry (Lycium barbarum): composition and health effects – a review. Polish Journal of Food and Nutrition Sciences 66(2):67−75

doi: 10.1515/pjfns-2015-0040
[18]

Wang H, Li J, Tao W, Zhang X, Gao X, et al. 2018. Lycium ruthenicum studies: molecular biology, phytochemistry and pharmacology. Food Chemistry 240:759−66

doi: 10.1016/j.foodchem.2017.08.026
[19]

Zeng S, Wu M, Zou C, Liu X, Shen X, et al. 2014. Comparative analysis of anthocyanin biosynthesis during fruit development in two Lycium species. Physiologia Plantarum 150(4):505−16

doi: 10.1111/ppl.12131
[20]

Vulić JJ, Čanadanović-Brunet JM, Ćetković GS, Djilas SM, Tumbas Šaponjac VT, et al. 2016. Bioactive compounds and antioxidant properties of goji fruits (Lycium barbarum L.) cultivated in serbia. Journal of the American College of Nutrition 35(8):692−98

doi: 10.1080/07315724.2016.1142404
[21]

Wang Y, Chen H, Wu M, Zeng S, Liu Y, et al. 2015. Chemical and genetic diversity of wolfberry. In Lycium Barbarum and Human Health, eds. Chang RCC, So KF. Dordrecht, Netherlands: Springer. pp. 1−26 doi: 10.1007/978-94-017-9658-3_1
[22]

Liu Y, Zeng S, Sun W, Wu M, Hu W, et al. 2014. Comparative analysis of carotenoid accumulation in two goji (Lycium barbarum L. and L. ruthenicum Murr.) fruits. BMC Plant Biology 14:269

doi: 10.1186/s12870-014-0269-4
[23]

Qiao F, Zhang K, Zhou L, Qiu QS, Chen Z, et al. 2022. Analysis of flavonoid metabolism during fruit development of Lycium chinense. Journal of Plant Physiology 279:153856

doi: 10.1016/j.jplph.2022.153856
[24]

Tang Hao, Zhang Defang, Ma Yunting, Shi Wenjun, Xiaowen L. 2023. Variation in leaves and fruit characteristics for lycium babarum, lycium ruthenicum and their hybrid zone. Science and Technology of Qinghai Agriculture and Forestry 4:70−74
[25]

Tang H, Zhang D. 2025. Hybridization and introgression of two sympatric Lycium species revealed by simple sequence repeat (SSR) markers. Genetic Resources and Crop Evolution 72:1717−28

doi: 10.1007/s10722-024-02048-6
[26]

Jiang F, Lv S, Zhang Z, Chen Q, Mai J, et al. 2023. Integrated metabolomics and transcriptomics analysis during seed germination of waxy corn under low temperature stress. BMC Plant Biology 23:190

doi: 10.1186/s12870-023-04195-x
[27]

Wang H, Liu C, Xie X, Niu M, Wang Y, et al. 2023. Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection. Immunity 56(6):1410−1428.e8

doi: 10.1016/j.immuni.2023.05.007
[28]

Wu J, He D, Wang Y, Liu S, Du Y, et al. 2025. An integrated transcriptome, metabolome, and microbiome dataset of Populus under nutrient-poor conditions. Scientific Data 12:717

doi: 10.1038/s41597-025-05029-1
[29]

Yi Z, Zhu ZJ. 2020. Overview of tandem mass spectral and metabolite databases for metabolite identification in metabolomics. In Computational Methods and Data Analysis for Metabolomics, ed. Li S. New York, USA: Humana. pp. 139–48 doi: doi.org/10.1007/978-1-0716-0239-3_8
[30]

Shahzad K, Nawaz H, Majeed MI, Nazish R, Rashid N, et al. 2022. Classification of tuberculosis by surface-enhanced Raman spectroscopy (SERS) with principal component analysis (PCA) and partialleast squares – discriminant analysis (PLS-DA). Analytical Letters 55:1731−44

doi: 10.1080/00032719.2021.2024218
[31]

Mishra P, Singh U, Pandey CM, Mishra P, Pandey G, et al. 2019. Application of student's t-test, analysis of variance, and covariance. Annals of Cardiac Anaesthesia 22(4):407−11

doi: 10.4103/aca.ACA_94_19
[32]

Chen Q, Bao L, Yue Z, Wang L, Fan Z, et al. 2023. Adverse events after the transjugular intrahepatic portal shunt are linked to serum metabolomic changes following the procedure. Frontiers in Molecular Biosciences 10:1168782

doi: 10.3389/fmolb.2023.1168782
[33]

Thole V, Bassard JE, Ramírez-González R, Trick M, Ghasemi Afshar B, et al. 2019. RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics. BMC Genomics 20:995

doi: 10.1186/s12864-019-6183-2
[34]

Xiao Y, Liu J, Wei J, Xiao Z, Li J, et al. 2023. Improved high-quality reference genome of red drum facilitates the processes of resistance-related gene exploration. Scientific Data 10:774

doi: 10.1038/s41597-023-02699-7
[35]

Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7):923−30

doi: 10.1093/bioinformatics/btt656
[36]

Wu T, Hu E, Xu S, Chen M, Guo P, et al. 2021. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. The innovation 2(3):100141

doi: 10.1016/j.xinn.2021.100141
[37]

Huang LQ, Zhang YZ, Zheng B, He Y. 2017. Lycium barbarum polysaccharide attenuates cisplatininduced apoptosis in ovary granulosa cells via alleviation of endoplasmic reticulum stress. Tropical Journal of Pharmaceutical Research 16(4):827−35

doi: 10.4314/tjpr.v16i4.12
[38]

Gong L, Yang Y, Chen Y, Shi J, Song Y, et al. 2016. LbCML38 and LbRH52, two reference genes derived from RNA-Seq data suitable for assessing gene expression in Lycium barbarum L. Scientific Reports 6:37031

doi: 10.1038/srep37031
[39]

Zang Y, Zha J, Wu X, Zheng Z, Ouyang J, et al. 2019. In vitro naringenin biosynthesis from p-coumaric acid using recombinant enzymes. Journal of Agricultural and Food Chemistry 67(49):13430−36

doi: 10.1021/acs.jafc.9b00413
[40]

Lim SH, Park B, Kim DH, Park S, Yang JH, et al. 2020. Cloning and functional characterization of dihydroflavonol 4-reductase gene involved in anthocyanin biosynthesis of Chrysanthemum. International Journal of Molecular Sciences 21(21):7960

doi: 10.3390/ijms21217960
[41]

Qin S, Liu Y, Cui B, Cheng J, Liu S, et al. 2022. Isolation and functional diversification of dihydroflavonol 4-Reductase gene HvDFR from Hosta ventricosa indicate its role in driving anthocyanin accumulation. Plant Signaling & Behavior 17(1):2010389

doi: 10.1080/15592324.2021.2010389
[42]

Jang H, Kim H, Cho A, Yu HJ, Huh SM, et al. 2025. Structure and evolution of the Forsythieae genome elucidated by chromosome-level genome comparison of Abeliophyllum distichum and Forsythia ovata (Oleaceae). Communications Biology 8:254

doi: 10.1038/s42003-025-07683-y
[43]

Saini RK, Ranjit A, Sharma K, Prasad P, Shang X, et al. 2022. Bioactive compounds of citrus fruits: a review of composition and health benefits of carotenoids, flavonoids, limonoids, and terpenes. Antioxidants 11(2):239

doi: 10.3390/antiox11020239
[44]

Liang MH, Xie H, Chen HH, Liang ZC, Jiang JG. 2020. Functional identification of two types of carotene hydroxylases from the green alga Dunaliella bardawil rich in lutein. ACS Synthetic Biology 9(6):1246−53

doi: 10.1021/acssynbio.0c00070
[45]

Rana S, Bhat WW, Dhar N, Pandith SA, Razdan S, et al. 2014. Molecular characterization of two A-type P450s, WsCYP98A and WsCYP76A from withania somnifera (L.) dunal: expression analysis and withanolide accumulation in response to exogenous elicitations. BMC Biotechnology 14:89

doi: 10.1186/s12896-014-0089-5
[46]

Zi J, Peters RJ. 2013. Characterization of CYP76AH4 clarifies phenolic diterpenoid biosynthesis in the Lamiaceae. Organic & Biomolecular Chemistry 11(44):7650−52

doi: 10.1039/c3ob41885e
[47]

Ratanasut K, Wongkhamprai B, Maknoi S. 2011. Expression of a CYP76AB1 correlates with the sequential white-blue-white colour transition of Vanda coerulea petals. Biologia Plantarum 55:353−56

doi: 10.1007/s10535-011-0053-3
[48]

Sun R, Liu S, Zheng Y. 2025. Genome-wide identification of the pigment formation-regulating CYP450 family gives new insights into color improvement in Bougainvillea. Scientia Horticulturae 341:113997

doi: 10.1016/j.scienta.2025.113997
[49]

Zhou Z, Gao H, Ming J, Ding Z, Lin X, et al. 2020. Combined Transcriptome and Metabolome analysis of Pitaya fruit unveiled the mechanisms underlying Peel and pulp color formation. BMC Genomics 21:734

doi: 10.1186/s12864-020-07133-5
[50]

Miettinen K, Dong L, Navrot N, Schneider T, Burlat V, et al. 2014. The seco-iridoid pathway from Catharanthus roseus. Nature Communications 5:3606

doi: 10.1038/ncomms4606
[51]

Höfer R, Dong L, André F, Ginglinger JF, Lugan R, et al. 2013. Geraniol hydroxylase and hydroxygeraniol oxidase activities of the CYP76 family of cytochrome P450 enzymes and potential for engineering the early steps of the (seco)iridoid pathway. Metabolic Engineering 20:221−32

doi: 10.1016/j.ymben.2013.08.001
[52]

Zhao S, Yan F, Liu Y, Sun M, Wang Y, et al. 2024. Glycine max acyl-acyl carrier protein thioesterase B gene overexpression alters lipid content and fatty acid profile of Arabidopsis seeds. Functional Plant Biology 51(2):FP23001

doi: 10.1071/fp23001
[53]

Liao W, Guo R, Qian K, Shi W, Whelan J, et al. 2024. The acyl–acyl carrier protein thioesterases GmFATA1 and GmFATA2 are essential for fatty acid accumulation and growth in soybean. The Plant Journal 118(3):823−38

doi: 10.1111/tpj.16638
[54]

Ikeda M, Kanao Y, Yamanaka M, Sakuraba H, Mizutani Y, et al. 2008. Characterization of four mammalian 3-hydroxyacyl-CoA dehydratases involved in very long-chain fatty acid synthesis. FEBS Letters 582(16):2435−40

doi: 10.1016/j.febslet.2008.06.007
[55]

Lee K, Lee JG, Min K, Choi JH, Lim S, et al. 2021. Transcriptome analysis of the fruit of two strawberry cultivars 'sunnyberry' and 'kingsberry' that show different susceptibility to Botrytis cinerea after harvest. International Journal of Molecular Sciences 22(4):1518

doi: 10.3390/ijms22041518
[56]

Kawano-Kawada M, Kakinuma Y, Sekito T. 2018. Transport of amino acids across the vacuolar membrane of yeast: its mechanism and physiological role. Biological and Pharmaceutical Bulletin 41(10):1496−501

doi: 10.1248/bpb.b18-00165
[57]

Qian W, Miki D, Zhang H, Liu Y, Zhang X, et al. 2012. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336(6087):1445−48

doi: 10.1126/science.1219416
[58]

Duan CG, Wang X, Xie S, Pan L, Miki D, et al. 2017. A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation. Cell research 27:226−40

doi: 10.1038/cr.2016.147