[1]

Christenhusz MJM, Byng JW. 2016. The number of known plants species in the world and its annual increase. Phytotaxa 261:201−17

doi: 10.11646/phytotaxa.261.3.1
[2]

Schmitzer V, Veberic R, Osterc G, Stampar F. 2010. Color and phenolic content changes during flower development in groundcover rose. Journal of the American Society for Horticultural Science 135:195−202

doi: 10.21273/JASHS.135.3.195
[3]

Kay QON, Daoud HS, Stirton CH. 1981. Pigment distribution, light reflection and cell structure in petals. Botanical Journal of the Linnean Society 83:57−83

doi: 10.1111/j.1095-8339.1981.tb00129.x
[4]

Jaakola L. 2013. New insights into the regulation of anthocyanin biosynthesis in fruits. Trends in Plant Science 18:477−83

doi: 10.1016/j.tplants.2013.06.003
[5]

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
[6]

Shi M, Xie D. 2014. Biosynthesis and metabolic engineering of anthocyanins in Arabidopsis thaliana. Recent Patents On Biotechnology 8:47−60

doi: 10.2174/1872208307666131218123538
[7]

Alsmairat NG, Al-Ajlouni MG, Ayad JY, Othman YA, St. Hilaire R. 2018. Composition of soilless substrates affect the physiology and fruit quality of two strawberry (Fragaria × ananassa Duch.) cultivars. Journal of Plant Nutrition 41:2356−64

doi: 10.1080/01904167.2018.1510508
[8]

Khasawneh AER, Alsmairat N, Othman YA, Ayad JY, Al-Qudah T, et al. 2021. Influence of nitrogen source on physiology, yield and fruit quality of young apricot trees. Journal of Plant Nutrition 44:2597−608

doi: 10.1080/01904167.2021.1918718
[9]

Aaby K, Skrede G, Wrolstad RE. 2005. Phenolic composition and antioxidant activities in flesh and achenes of strawberries (Fragaria ananassa). Journal of Agricultural and Food Chemistry 53:4032−40

doi: 10.1021/jf048001o
[10]

Li Y, Cao K, Zhu G, Fang W, Chen C, et al. 2019. Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history. Genome Biology 20:36

doi: 10.1186/s13059-019-1648-9
[11]

Cheng R, Cheng Y, Lü J, Chen J, Wang Y, et al. 2018. The gene PbTMT4 from pear (Pyrus bretschneideri) mediates vacuolar sugar transport and strongly affects sugar accumulation in fruit. Physiologia Plantarum 164:307−19

doi: 10.1111/ppl.12742
[12]

Sweetman C, Deluc LG, Cramer GR, Ford CM, Soole KL. 2009. Regulation of malate metabolism in grape berry and other developing fruits. Phytochemistry 70:1329−44

doi: 10.1016/j.phytochem.2009.08.006
[13]

He J, Giusti MM. 2010. Anthocyanins: natural colorants with health-promoting properties. Annual Review of Food Science and Technology 1:163−87

doi: 10.1146/annurev.food.080708.100754
[14]

Zeng Y, Song J, Zhang M, Wang H, Zhang Y, et al. 2020. Comparison of in vitro and in vivo antioxidant activities of six flavonoids with similar structures. Antioxidants 9:732

doi: 10.3390/antiox9080732
[15]

Ummenhofer CC, Meehl GA. 2017. Extreme weather and climate events with ecological relevance: a review. Philosophical Transactions of the Royal Society B 372:20160135

doi: 10.1098/rstb.2016.0135
[16]

Zhou K, Hu L, Li Y, Chen X, Zhang Z, et al. 2019. MdUGT88F1-mediated phloridzin biosynthesis regulates apple development and Valsa canker resistance. Plant Physiology 180:2290−305

doi: 10.1104/pp.19.00494
[17]

Yoshida T, Mogami J, Yamaguchi-Shinozaki K. 2014. ABA-dependent and ABA-independent signaling in response to osmotic stress in plants. Current Opinion in Plant Biology 21:133−39

doi: 10.1016/j.pbi.2014.07.009
[18]

Maxam AM, Gilbert W. 1977. A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America 74:560−64

doi: 10.1073/pnas.74.2.56
[19]

Sanger F, Nicklen S, Coulson AR. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America 74:5463−67

doi: 10.1073/pnas.74.12.5463
[20]

van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. 2018. The third revolution in sequencing technology. Trends in Genetics 34:666−81

doi: 10.1016/j.tig.2018.05.008
[21]

Xue S, Shi T, Luo W, Ni X, Iqbal S, et al. 2019. Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina. Horticulture Research 6:89

doi: 10.1038/s41438-019-0171-1
[22]

Zhao K, Zhou Y, Zheng Y, Chen B, Wei Z. 2019. The chloroplast genome of Prunus dielsiana (Rosaceae). Mitochondrial DNA Part B 4:4033−34

doi: 10.1080/23802359.2019.1688723
[23]

Ge D, Dong J, Guo L, Yan M, Zhao X, et al. 2020. The complete mitochondrial genome sequence of cultivated apple (Malus domestica cv. 'Yantai Fuji 8'). Mitochondrial DNA Part B 5:1317−18

doi: 10.1080/23802359.2020.1733447
[24]

Li Y, Liu Y, Wu P, Zhou S, Wang L, et al. 2020. The complete chloroplast genome sequence of Malus toringoides (Rosaceae). Mitochondrial DNA Part B 5:2787−89

doi: 10.1080/23802359.2020.1780977
[25]

Cheng L, Wang Y, Yang J, He Y, Li G, et al. 2020. Characterization of the complete chloroplast genome of Pyrus pyrifolia 'Yunhongli No. 1'. Mitochondrial DNA Part B 5:3100−02

doi: 10.1080/23802359.2020.1800429
[26]

Liu Y, Song Q, Kang W, Yang F, Yan W. 2021. The complete chloroplast genome sequence of Rubus sachalinensis Lévl. Mitochondrial DNA Part B 6:1621−22

doi: 10.1080/23802359.2021.1926354
[27]

Li J, Liu L, Wang H, Li C, Zuo W, et al. 2021. The complete chloroplast genome of a medical herb, Potentilla parvifolia Fisch. (Rosaceae), from Qinghai-Tibet Plateau in China. Mitochondrial DNA Part B 6:349−50

doi: 10.1080/23802359.2020.1866447
[28]

He S, Xie J, Yang Y, Yang T. 2020. Chloroplast genome for Crataegus pinnatifida (Rosaceae) and phylogenetic analyses with its coordinal species. Mitochondrial DNA Part B 5:2097−2098

doi: 10.1080/23802359.2019.1667273
[29]

Bai L, Ye Y, Chen Q, Tang H. 2017. The complete chloroplast genome sequence of the white strawberry Fragaria pentaphylla. Conservation Genetics Resources 9:659−61

doi: 10.1007/s12686-017-0713-5
[30]

Zhao X, Yan M, Ding Y, Huo Y, Yuan Z. 2019. Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium 'Summit'. PeerJ 7:e8210

doi: 10.7717/peerj.8210
[31]

Jian H, Zhang Y, Yan H, Qiu X, Wang Q, et al. 2018. The complete chloroplast genome of a key ancestor of modern roses, Rosa chinensis var. spontanea, and a comparison with congeneric species. Molecules 23:389

doi: 10.3390/molecules23020389
[32]

Li C, Lin F, An D, Wang W, Huang R. 2018. Genome sequencing and assembly by long reads in plants. Genes 9:6

doi: 10.3390/genes9010006
[33]

Delseny M, Han B, Hsing YI. 2010. High throughput DNA sequencing: the new sequencing revolution. Plant Science 179:407−22

doi: 10.1016/j.plantsci.2010.07.019
[34]

Rang FJ, Kloosterman WP, de Ridder J. 2018. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biology 19:90

doi: 10.1186/s13059-018-1462-9
[35]

Garalde DR, Snell EA, Jachimowicz D, Sipos B, Lloyd JH, et al. 2018. Highly parallel direct RNA sequencing on an array of nanopores. Nature Methods 15:201−06

doi: 10.1038/nmeth.4577
[36]

Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, et al. 2013. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics 45:487−94

doi: 10.1038/ng.2586
[37]

Tan Q, Li S, Zhang T, Chen M, Wen B, et al. 2021. Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach. Horticulture Research 8:213

doi: 10.1038/s41438-021-00648-2
[38]

VanBuren R, Bryant D, Bushakra JM, Vining KJ, Edger PP, et al. 2016. The genome of black raspberry (Rubus occidentalis). The Plant Journal 87:535−47

doi: 10.1111/tpj.13215
[39]

VanBuren R, Wai CM, Colle M, Wang J, Sullivan S, et al. 2018. A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. GigaScience 7:giy094

doi: 10.1093/gigascience/giy094
[40]

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289−93

doi: 10.1126/science.1181369
[41]

He S, Weng D, Zhang Y, Kong Q, Wang K, et al. 2023. A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa. Horticulture Research 10:uhad183

doi: 10.1093/hr/uhad183
[42]

Zhou Y, Xiong J, Shu Z, Dong C, Gu T, et al. 2023. The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry. Horticulture Research 10:uhad027

doi: 10.1093/hr/uhad027
[43]

Sun M, Yao C, Shu Q, He Y, Chen G, et al. 2023. Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution. Horticulture Research 10:uhad201

doi: 10.1093/hr/uhad201
[44]

Gao Y, Yang Q, Yan X, Wu X, Yang F, et al. 2021. High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy. Horticulture Research 8:197

doi: 10.1038/s41438-021-00632-w
[45]

Shirasawa K, Itai A, Isobe S. 2021. Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety 'Nijisseiki'. DNA Research 28:dsab001

doi: 10.1093/dnares/dsab001
[46]

Yi X, Yu X, Chen J, Zhang M, Liu S, et al. 2020. The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species. Horticulture Research 7:165

doi: 10.1038/s41438-020-00382-1
[47]

Wang J, Liu W, Zhu D, Zhou X, Hong P, et al. 2020. A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology. PeerJ 8:e9114

doi: 10.7717/peerj.9114
[48]

Jiu S, Chen B, Dong X, Lv Z, Wang Y, et al. 2023. Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L. Horticulture Research 10:uhad62

doi: 10.1093/hr/uhad062
[49]

Griesmann M, Chang Y, Liu X, Song Y, Haberer G, et al. 2018. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science 361:eaat1743

doi: 10.1126/science.aat1743
[50]

Su W, Jing Y, Lin S, Yue Z, Yang X, et al. 2021. Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. Proceedings of the National Academy of Sciences of the United States of America 118:e2101767118

doi: 10.1073/pnas.2101767118
[51]

Edger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, et al. 2018. Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. GigaScience 7:gix124

doi: 10.1093/gigascience/gix124
[52]

Zhang J, Lei Y, Wang B, Li S, Yu S, et al. 2020. The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation. Plant Biotechnology Journal 18:1908−24

doi: 10.1111/pbi.13351
[53]

Feng C, Wang J, Harris AJ, Folta KM, Zhao M, et al. 2021. Tracing the diploid ancestry of the cultivated octoploid strawberry. Molecular Biology and Evolution 38:478−85

doi: 10.1093/molbev/msaa238
[54]

Sun R, Li S, Chang L, Dong J, Zhong C, et al. 2022. Chromosome-level genome assembly of Fragaria pentaphylla using PacBio and Hi-C technologies. Frontiers in Genetics 13:873711

doi: 10.3389/fgene.2022.873711
[55]

Cao K, Peng Z, Zhao X, Li Y, Liu K, et al. 2022. Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. BMC Biology 20:139

doi: 10.1186/s12915-022-01342-y
[56]

Zheng T, Li P, Zhuo X, Liu W, Qiu L, et al. 2021. The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume. New Phytologist 235:141−56

doi: 10.1111/nph.17894
[57]

Callahan AM, Zhebentyayeva TN, Humann JL, Saski CA, Galimba KD, et al. 2021. Defining the 'HoneySweet' insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica). Horticulture Research 8:8

doi: 10.1038/s41438-020-00438-2
[58]

Daccord N, Celton J, Linsmith G, Becker C, Choisne N, et al. 2017. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics 49:1099−106

doi: 10.1038/ng.3886
[59]

Chen X, Li S, Zhang D, Han M, Jin X, et al. 2019. Sequencing of a wild apple (Malus baccata) genome unravels the differences between cultivated and wild apple species regarding disease resistance and cold tolerance. G3 Genes|Genomes|Genetics 9:2051−60

doi: 10.1534/g3.119.400245
[60]

D'Amico-Willman KM, Ouma WZ, Meulia T, Sideli GM, Gradziel TM, et al. 2022. Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D. A. Webb] cultivar 'Nonpareil'. G3 Genes|Genomes|Genetics 12:jkac065

doi: 10.1093/g3journal/jkac065
[61]

Zhu Q, Wang Y, Yao N, Ni X, Wang C, et al. 2023. Chromosome-level genome assembly of an endangered plant Prunus mongolica using PacBio and Hi-C technologies. DNA Research 30:dsad012

doi: 10.1093/dnares/dsad012
[62]

Soyturk A, Sen F, Uncu AT, Celik I, Uncu AO. 2021. De novo assembly and characterization of the first draft genome of quince (Cydonia oblonga Mill.). Scientific Reports 11:3818

doi: 10.1038/s41598-021-83113-3
[63]

Zhang T, Qiao Q, Du X, Zhang X, Hou Y, et al. 2022. Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe). Journal of Integrative Plant Biology 64:1487−501

doi: 10.1111/jipb.13318
[64]

Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, et al. 2018. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nature Plants 4:473−84

doi: 10.1038/s41477-018-0166-1
[65]

Zang F, Ma Y, Tu X, Huang P, Wu Q, et al. 2021. A high-quality chromosome-level genome of wild Rosa rugosa. DNA Research 28:dsab017

doi: 10.1093/dnares/dsab017
[66]

Wang L, Lei T, Han G, Yue J, Zhang X, et al. 2021. The chromosome-scale reference genome of Rubus chingii Hu provides insight into the biosynthetic pathway of hydrolysable tannins. The Plant Journal 107:1466−77

doi: 10.1111/tpj.15394
[67]

Yang Y, Zhang K, Xiao Y, Zhang L, Huang Y, et al. 2022. Genome assembly and population resequencing reveal the geographical divergence of Shanmei (Rubus corchorifolius). Genomics, Proteomics & Bioinformatics 20:1106−18

doi: 10.1016/j.gpb.2022.05.003
[68]

Brůna T, Aryal R, Dudchenko O, Sargent DJ, Mead D, et al. 2023. A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist"). G3 Genes|Genomes|Genetics 13:jkac289

doi: 10.1093/g3journal/jkac289
[69]

Chen F, Dong W, Zhang J, Guo X, Chen J, et al. 2018. The sequenced angiosperm genomes and genome databases. Frontiers in Plant Science 9:418

doi: 10.3389/fpls.2018.00418
[70]

Jung S, Lee T, Cheng CH, Buble K, Zheng P, et al. 2019. 15 years of GDR: new data and functionality in the Genome Database for Rosaceae. Nucleic Acids Research 47:D1137−D1145

doi: 10.1093/nar/gky1000
[71]

Pan Z, Xu D, Zhang J, Lin F, Wu B, et al. 2009. Reviews in comparative genomic research based on orthologs. Hereditas 31:457−63

doi: 10.3724/SP.J.1005.2009.00457
[72]

Zhang J. 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18:292−98

doi: 10.1016/s0169-5347(03)00033-8
[73]

Murat F, Armero A, Pont C, Klopp C, Salse J. 2017. Reconstructing the genome of the most recent common ancestor of flowering plants. Nature Genetics 49:490−96

doi: 10.1038/ng.3813
[74]

Pincot DDA, Poorten TJ, Hardigan MA, Harshman JM, Acharya CB, et al. 2018. Genome-wide association mapping uncovers Fw1, a dominant gene conferring resistance to fusarium wilt in strawberry. G3 Genes|Genomes|Genetics 8:1817−28

doi: 10.1534/g3.118.200129
[75]

Tazawa J, Oshino H, Kon T, Kasai S, Kudo T, et al. 2019. Genetic characterization of flesh browning trait in apple using the non-browning cultivar 'Aori 27'. Tree Genetics & Genomes 15:49

doi: 10.1007/s11295-019-1356-3
[76]

Kunihisa M, Hayashi T, Hatsuyama Y, Fukasawa-Akada T, Uenishi H, et al. 2021. Genome-wide association study for apple flesh browning: detection, validation, and physiological roles of QTLs. Tree Genetics & Genomes 17:11

doi: 10.1007/s11295-021-01492-0
[77]

Nan H, Ludlow RA, Lu M, An H. 2021. Genome-wide analysis of Dof genes and their response to abiotic stress in rose (Rosa chinensis). Frontiers in Genetics 12:538733

doi: 10.3389/fgene.2021.538733
[78]

Li P, Zheng T, Zhuo X, Zhang M, Yong X, et al. 2021. Photoperiod- and temperature-mediated control of the ethylene response and winter dormancy induction in Prunus mume. Horticultural Plant Journal 7:232−42

doi: 10.1016/j.hpj.2021.03.005
[79]

Zhang Q, Zhang H, Sun L, Fan G, Ye M, et al. 2018. The genetic architecture of floral traits in the woody plant Prunus mume. Nature Communications 9:1702

doi: 10.1038/s41467-018-04093-z
[80]

Chen L, Xue L, Li S. 2021. Genome-wide association study of flower color trait in Prunus persica f. versicolor. Acta Horticulturae Sinica 48:553−65

[81]

Nie C, Zhang Y, Zhang X, Xia W, Sun H, et al. 2023. Genome assembly, resequencing and genome-wide association analyses provide novel insights into the origin, evolution and flower colour variations of flowering cherry. The Plant Journal 114:519−33

doi: 10.1111/tpj.16151
[82]

Cao K, Yang X, Li Y, Zhu G, Fang W, et al. 2021. New high-quality peach (Prunus persica L. Batsch) genome assembly to analyze the molecular evolutionary mechanism of volatile compounds in peach fruits. The Plant Journal 108:281−95

doi: 10.1111/tpj.15439
[83]

Jiang L, Geng D, Zhi F, Li Z, Yang Y, et al. 2022. A genome-wide association study provides insights into fatty acid synthesis and metabolism in Malus fruits. Journal of Experimental Botany 73:7467−76

doi: 10.1093/jxb/erac372
[84]

Nishio S, Hayashi T, Shirasawa K, Saito T, Terakami S, et al. 2021. Genome-wide association study of individual sugar content in fruit of Japanese pear (Pyrus spp.). BMC Plant Biology 21:378

doi: 10.1186/s12870-021-03130-2
[85]

Dos Reis MV, Rouhana LV, Sadeque A, Koga L, Clough SJ, et al. 2020. Genome-wide expression of low temperature response genes in Rosa hybrida L. Plant Physiology and Biochemistry 146:238−48

doi: 10.1016/j.plaphy.2019.11.021
[86]

Lou X, Wang H, Ni X, Gao Z, Iqbal S. 2018. Integrating proteomic and transcriptomic analyses of loquat (Eriobotrya japonica Lindl.) in response to cold stress. Gene 677:57−65

doi: 10.1016/j.gene.2018.07.022
[87]

Zhuang D, Ma C, Xue L, Li Z, Wang C, et al. 2021. Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress. BMC Plant Biology 21:472

doi: 10.1186/s12870-021-03246-5
[88]

Wang X, Song Z, Ti Y, Liu Y, Li Q. 2022. Physiological response and transcriptome analysis of Prunus mume to early salt stress. Journal of Plant Biochemistry and Biotechnology 31:330−42

doi: 10.1007/s13562-021-00680-2
[89]

Li W, Fu L, Geng Z, Zhao X, Liu Q, et al. 2020. Physiological characteristic changes and full-length transcriptome of Rose (Rosa chinensis) roots and leaves in response to drought stress. Plant and Cell Physiology 61:2153−66

doi: 10.1093/pcp/pcaa137
[90]

Li Z, Xing W, Luo P, Zhang F, Jin X, et al. 2019. Comparative transcriptome analysis of Rosa chinensis 'Slaters' crimson China' provides insights into the crucial factors and signaling pathways in heat stress response. Plant Physiology and Biochemistry 142:312−31

doi: 10.1016/j.plaphy.2019.07.002
[91]

Liu X, Cao X, Shi S, Zhao N, Li D, et al. 2018. Comparative RNA-Seq analysis reveals a critical role for brassinosteroids in rose (Rosa hybrida) petal defense against Botrytis cinerea infection. BMC Genetics 19:62

doi: 10.1186/s12863-018-0668-x
[92]

Bai Y, Liu H, Lyu H, Su L, Xiong J, et al. 2022. Development of a single-cell atlas for woodland strawberry (Fragaria vesca) leaves during early Botrytis cinerea infection using single cell RNA-seq. Horticulture Research 9:uhab055

doi: 10.1093/hr/uhab055
[93]

Xue L, Wang J, Zhao J, Zheng Y, Wang H, et al. 2019. Study on cyanidin metabolism in petals of pink-flowered strawberry based on transcriptome sequencing and metabolite analysis. BMC Plant Biology 19:423

doi: 10.1186/s12870-019-2048-8
[94]

Han M, Yin J, Zhao Y, Sun X, Meng J, et al. 2020. How the color fades from Malus halliana flowers: transcriptome sequencing and DNA methylation analysis. Frontiers in Plant Science 11:576054

doi: 10.3389/fpls.2020.576054
[95]

Han Y, Wan H, Cheng T, Wang J, Yang W, et al. 2017. Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis. Scientific Reports 7:43382

doi: 10.1038/srep43382
[96]

Sheng L, Xia W, Zang S, Zeng Y, Yuan X, et al. 2018. Transcriptome-sequencing analyses reveal putative genes related to flower color variation in Chinese Rosa rugosa. Acta Physiologiae Plantarum 40:62

doi: 10.1007/s11738-018-2635-6
[97]

Li M, Zhang H, Yang Y, Wang H, Xue Z, et al. 2022. Rosa1, a transposable element-like insertion, produces red petal coloration in rose through altering RcMYB114 transcription. Frontiers in Plant Science 13:857684

doi: 10.3389/fpls.2022.857684
[98]

Manivannan A, Han K, Lee SY, Lee HE, Hong JP, et al. 2021. Genome-wide analysis of MYB10 transcription factor in Fragaria and identification of QTLs associated with fruit color in octoploid strawberry. International Journal of Molecular Sciences 22:12587

doi: 10.3390/ijms222212587
[99]

Yang H, Tian C, Li X, Gong H, Zhang A. 2021. Transcriptome co-expression network analysis identifies key genes and regulators of sweet cherry anthocyanin biosynthesis. Horticulturae 7:123

doi: 10.3390/horticulturae7060123
[100]

Li H, Duan S, Sun W, Wang S, Zhang J, et al. 2022. Identification, through transcriptome analysis, of transcription factors that regulate anthocyanin biosynthesis in different parts of red-fleshed apple 'May' fruit. Horticultural Plant Journal 8:11−21

doi: 10.1016/j.hpj.2021.07.001
[101]

Zhao Y, Li A, Qi S, Su K, Guo Y. 2022. Identification of candidate genes related to anthocyanin biosynthesis in red sarcocarp hawthorn (Crataegus pinnatifida). Scientia Horticulturae 298:110987

doi: 10.1016/j.scienta.2022.110987
[102]

Mei Z, Li Z, Lu X, Zhang S, Liu W, et al. 2023. Supplementation of natural light duration promotes accumulation of sugar and anthocyanins in apple (Malus domestica Borkh.) fruit. Environmental and Experimental Botany 205:105133

doi: 10.1016/j.envexpbot.2022.105133
[103]

Liang Y, Jing Y, Shen S. 2004. Advances in plant proteomics. Chinese Journal of Plant Ecology 28:114−25

doi: 10.17521/cjpe.2004.0017
[104]

Ghosh D, Xu J. 2014. Abiotic stress responses in plant roots: a proteomics perspective. Frontiers in Plant Science 5:6

doi: 10.3389/fpls.2014.00006
[105]

Dafny-Yelin M, Guterman I, Menda N, Ovadis M, Shalit M, et al. 2005. Flower proteome: changes in protein spectrum during the advanced stages of rose petal development. Planta 222:37−46

doi: 10.1007/s00425-005-1512-x
[106]

Koehler G, Wilson RC, Goodpaster JV, Sønsteby A, Lai X, et al. 2012. Proteomic study of low-temperature responses in strawberry cultivars (Fragaria × ananassa ) that differ in cold tolerance. Plant Physiology 159:1787−805

doi: 10.1104/pp.112.198267
[107]

Xu Y, Yang S, Jia R, Zhao X, He L, et al. 2020. Physiological and proteomics analysis on freezing tolerance of Rosa beggeriana branches during overwintering. Journal of Plant Genetic Resources 21:1568−76

doi: 10.13430/j.cnki.jpgr.20200612003
[108]

Sevilla E, Andreu P, Fillat MF, Peleato ML, Marín JA, et al. 2022. Identification of early salt-stress-responsive proteins in vitro Prunus cultured excised roots. Plants 11:2101

doi: 10.3390/plants11162101
[109]

He X, Meng H, Wang H, He P, Chang Y, et al. 2022. Quantitative proteomic sequencing of F 1 hybrid populations reveals the function of sorbitol in apple resistance to Botryosphaeria dothidea. Horticulture Research 9:uhac115

doi: 10.1093/hr/uhac115
[110]

Wu X, Ni X, Zhou Y, Gong Q, Gao Z. 2015. Comparative proteomic analysis of floral color variegation in Japanese apricot ( Prunus mume 'Fuban Tiaozhi'). Journal of Beijing Forestry University 37:74−81

[111]

Zhou Y, Wu X, Zhang Z, Gao Z. 2015. Comparative proteomic analysis of floral color variegation in peach. Biochemical and Biophysical Research Communications 464:1101−06

doi: 10.1016/j.bbrc.2015.07.084
[112]

Lu J, Xu Y, Fan Y, Wang Y, Zhang G, et al. 2019. Proteome and ubiquitome changes during rose petal senescence. International Journal of Molecular Sciences 20:6108

doi: 10.3390/ijms20246108
[113]

Yin P, Zhen Y, Li S. 2019. Identification and functional classification of differentially expressed proteins and insight into regulatory mechanism about flower color variegation in peach. Acta Physiologiae Plantarum 41:95

doi: 10.1007/s11738-019-2886-x
[114]

Wang P, Sun X, Xie Y, Li M, Chen W, et al. 2014. Melatonin regulates proteomic changes during leaf senescence in Malus hupehensis. Journal of Pineal Research 57:291−307

doi: 10.1111/jpi.12169
[115]

Huan C, Xu Y, An X, Yu M, Ma R, et al. 2019. iTRAQ-based protein profiling of peach fruit during ripening and senescence under different temperatures. Postharvest Biology and Technology 151:88−97

doi: 10.1016/j.postharvbio.2019.01.017
[116]

Li Q, Yang S, Zhang R, Liu S, Zhang C, et al. 2022. Characterization of honey peach (Prunus persica (L.) Batsch) aroma variation and unraveling the potential aroma metabolism mechanism through proteomics analysis under abiotic stress. Food Chemistry 386:132720

doi: 10.1016/j.foodchem.2022.132720
[117]

Antunes ACN, dos S Acunha T, Perin EC, Rombaldi CV, Galli V, et al. 2019. Untargeted metabolomics of strawberry (Fragaria × ananassa 'Camarosa') fruit from plants grown under osmotic stress conditions. Journal of the Science of Food and Agriculture 99:6973−80

doi: 10.1002/jsfa.9986
[118]

Sun T, Zhang J, Zhang Q, Li X, Li M, et al. 2021. Transcriptome and metabolome analyses revealed the response mechanism of apple to different phosphorus stresses. Plant Physiology and Biochemistry 167:639−50

doi: 10.1016/j.plaphy.2021.08.040
[119]

Sun T, Zhang J, Zhang Q, Li X, Li M, et al. 2021. Integrative physiological, transcriptome, and metabolome analysis reveals the effects of nitrogen sufficiency and deficiency conditions in apple leaves and roots. Environmental and Experimental Botany 192:104633

doi: 10.1016/j.envexpbot.2021.104633
[120]

Dong B, Zheng Z, Zhong S, Ye Y, Wang Y, et al. 2022. Integrated transcriptome and metabolome analysis of color change and low-temperature response during flowering of Prunus mume. International Journal of Molecular Sciences 23:12831

doi: 10.3390/ijms232112831
[121]

Xu G, Li L, Zhou J, Lyu D, Zhao D, et al. 2023. Comparison of transcriptome and metabolome analysis revealed differences in cold resistant metabolic pathways in different apple cultivars under low temperature stress. Horticultural Plant Journal 9:183−98

doi: 10.1016/j.hpj.2022.09.002
[122]

Lu J, Zhang Q, Lang L, Jiang C, Wang X, et al. 2021. Integrated metabolome and transcriptome analysis of the anthocyanin biosynthetic pathway in relation to color mutation in miniature roses. BMC Plant Biology 21:257

doi: 10.1186/s12870-021-03063-w
[123]

Su M, Damaris RN, Hu Z, Yang P, Deng J. 2021. Metabolomic analysis on the petal of 'Chen Xi' rose with light-induced color changes. Plants 10:2065

doi: 10.3390/plants10102065
[124]

Cheng X, Feng Y, Chen D, Luo C, Yu X, et al. 2022. Evaluation of Rosa germplasm resources and analysis of floral fragrance components in R. rugosa. Frontiers in Plant Science 13:1026763

doi: 10.3389/fpls.2022.1026763
[125]

Li T, Zhao X, Cao X. 2023. Volatile metabolome and aroma differences of six cultivars of Prunus mume blossoms. Plants 12:308

doi: 10.3390/plants12020308
[126]

Zou S, Wu J, Shahid MQ, He Y, Lin S, et al. 2020. Identification of key taste components in loquat using widely targeted metabolomics. Food Chemistry 323:126822

doi: 10.1016/j.foodchem.2020.126822
[127]

Wang X, Wu L, Qiu J, Qian Y, Wang M. 2023. Comparative metabolomic analysis of the nutritional aspects from ten cultivars of the strawberry fruit. Foods 12:1153

doi: 10.3390/foods12061153
[128]

Horikawa K, Hirama T, Shimura H, Jitsuyama Y, Suzuki T. 2019. Visualization of soluble carbohydrate distribution in apple fruit flesh utilizing MALDI-TOF MS imaging. Plant Science 278:107−12

doi: 10.1016/j.plantsci.2018.08.014
[129]

Wang J, Yang E, Chaurand P, Raghavan V. 2021. Visualizing the distribution of strawberry plant metabolites at different maturity stages by MALDI-TOF imaging mass spectrometry. Food Chemistry 345:128838

doi: 10.1016/j.foodchem.2020.128838
[130]

Zhang L, Saber FR, Rocchetti G, Zengin G, Hashem MM, et al. 2021. UHPLC-QTOF-MS based metabolomics and biological activities of different parts of Eriobotrya japonica. Food Research International 143:110242

doi: 10.1016/j.foodres.2021.110242
[131]

Zhang S, Liu Z, Li X, Abubaker MA, Liu X, et al. 2022. Comparative study of three raspberry cultivar (Rubus idaeus L.) leaves metabolites: metabolome profiling and antioxidant activities. Applied Sciences 12:990

doi: 10.3390/app12030990
[132]

Cambeiro-Pérez N, Figueiredo-González M, Pérez-Gregorio MR, Bessa-Pereira C, De Freitas V, et al. 2022. Unravelling the immunomodulatory role of apple phenolic rich extracts on human THP-1- derived macrophages using multiplatform metabolomics. Food Research International 155:111037

doi: 10.1016/j.foodres.2022.111037
[133]

Jia X, Zhu Y, Hu Y, Zhang R, Cheng L, et al. 2019. Integrated physiologic, proteomic, and metabolomic analyses of Malus halliana adaptation to saline–alkali stress. Horticulture Research 6:91

doi: 10.1038/s41438-019-0172-0
[134]

Chen Y, Deng C, Xu Q, Chen X, Jiang F, et al. 2022. Integrated analysis of the metabolome, transcriptome and miRNome reveals crucial roles of auxin and heat shock proteins in the heat stress response of loquat fruit. Scientia Horticulturae 294:110764

doi: 10.1016/j.scienta.2021.110764
[135]

Wang F, Ge S, Xu X, Xing Y, Du X, et al. 2021. Multiomics analysis reveals new insights into the apple fruit quality decline under high nitrogen conditions. Journal of Agricultural and Food Chemistry 69:5559−72

doi: 10.1021/acs.jafc.1c01548
[136]

Zhuo X, Zheng T, Li S, Zhang Z, Zhang M, et al. 2021. Identification of the PmWEEP locus controlling weeping traits in Prunus mume through an integrated genome-wide association study and quantitative trait locus mapping. Horticulture Research 8:131

doi: 10.1038/s41438-021-00573-4
[137]

Jing D, Chen W, Hu R, Zhang Y, Xia Y, et al. 2020. An integrative analysis of transcriptome, proteome and hormones reveals key differentially expressed genes and metabolic pathways involved in flower development in loquat. International Journal of Molecular Sciences 21:5107

doi: 10.3390/ijms21145107
[138]

Yuan X, Ma K, Zhang M, Wang J, Zhang Q. 2021. Integration of transcriptome and methylome analyses provides insight into the pathway of floral scent biosynthesis in Prunus mume. Frontiers in Genetics 12:779557

doi: 10.3389/fgene.2021.779557
[139]

Zhang M, Yang Q, Yuan X, Yan X, Wang J, et al. 2021. Integrating genome-wide association analysis with transcriptome sequencing to identify candidate genes related to blooming time in Prunus mume. Frontiers in Plant Science 12:690841

doi: 10.3389/fpls.2021.690841
[140]

Ma W, Li B, Zheng L, Peng Y, Tian R, et al. 2021. Combined profiling of transcriptome and DNA methylome reveal genes involved in accumulation of soluble sugars and organic acid in apple fruits. Foods 10:2198

doi: 10.3390/foods10092198
[141]

Ji X, Ren J, Lang S, Wang D, Zhu L, et al. 2020. Differential regulation of anthocyanins in Cerasus humilis fruit color revealed by combined transcriptome and metabolome analysis. Forests 11:1065

doi: 10.3390/f11101065
[142]

Wang Y. 2021. A draft genome, resequencing, and metabolomes reveal the genetic background and molecular basis of the nutritional and medicinal properties of loquat (Eriobotrya japonica (Thunb.) Lindl). Horticulture Research 8:231

doi: 10.1038/s41438-021-00657-1
[143]

Campoy JA, Sun H, Goel M, Jiao WB, Folz-Donahue K, et al. 2020. Gamete binning: chromosome-level and haplotype-resolved genome assembly enabled by high-throughput single-cell sequencing of gamete genomes. Genome Biology 21:306

doi: 10.1186/s13059-020-02235-5