Cao K, Zheng Z, Wang L, Liu X, Zhu G, Fang W, Cheng S, Zeng P, Chen C, Wang X, Xie M, Zhong X, Wang X, Zhao P, Bian C, Zhu Y, Zhang J, Ma G, Chen C, Li Y, Hao F, Li Y, Huang G, Li Y, Li H, Guo J, Xu X, Wang J. Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. Genome Biol. 2014;15(7):415.
PubMed
PubMed Central
Google Scholar
Monti LL, Bustamante CA, Osorio S, Gabilondo J, Borsani J, Lauxmann MA, Maulión E, Valentini G, Budde CO, Fernie AR, Lara MV, Drincovich MF. Metabolic profiling of a range of peach fruit varieties reveals high metabolic diversity and commonalities and differences during ripening. Food Chem. 2016;190:879–88.
Article
CAS
PubMed
Google Scholar
Verde I, Jenkins J, Dondini L, Micali S, Pagliarani G, Vendramin E, Paris R, Aramini V, Gazza L, Rossini L, Bassi D, Troggio M, Shu S, Grimwood J, Tartarini S, Dettori MT, Schmutz J. The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity. BMC Genomics. 2017;18(1):225.
Aranzana MJ, Decroocq V, Dirlewanger E, Eduardo I, Gao ZS, Gasic K, Iezzoni A, Jung S, Peace C, Prieto H, Tao R. Prunus genetics and applications after de novo genome sequencing: achievements and prospects. Horticulture Research. 2019;6(1):1–25.
Article
Google Scholar
Giovannoni J, Nguyen C, Ampofo B, Zhong S, Fei Z. The epigenome and transcriptional dynamics of fruit ripening. Annu Rev Plant Biol. 2017;68:61–84.
Article
CAS
PubMed
Google Scholar
Wu X, Jiang L, Yu M, An X, Ma R, Yu Z. Proteomic analysis of changes in mitochondrial protein expression during peach fruit ripening and senescence. J Proteome. 2016;147:197–211.
Article
CAS
Google Scholar
Gapper NE, McQuinn RP, Giovannoni JJ. Molecular and genetic regulation of fruit ripening. Plant Mol Biol. 2013;82(6):575–91.
Article
CAS
PubMed
Google Scholar
Sánchez G, Venegas-Calerón M, Salas JJ, Monforte A, Badenes ML, Granell A. An integrative "omics" approach identifies new candidate genes to impact aroma volatiles in peach fruit. BMC Genomics. 2013;14:343.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang JJ, Liu HR, Gao J, Huang YJ, Zhang B, Chen KS. Two ω-3 FADs are associated with peach fruit volatile formation. Int J Mol Sci. 2016;17(4):464.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang L, Li H, Gao L, Qi Y, Fu W, Li X, Zhou X, Gao Q, Gao Z, Jia H. Acyl-CoA oxidase 1 is involved in γ-decalactone release from peach (Prunus persica) fruit. Plant Cell Rep. 2017;36(6):829–42.
Article
CAS
PubMed
Google Scholar
Tadiello A, Ziosi V, Negri AS, Noferini M, Fiori G, Busatto N, Espen L, Costa G, Trainotti L. On the role of ethylene, auxin and a GOLVEN-like peptide hormone in the regulation of peach ripening. BMC Plant Biol. 2016;16:44.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang X, Ding Y, Wang Y, Pan L, Niu L, Lu Z, Cui G, Zeng W, Wang Z. Genes involved in ethylene signal transduction in peach (Prunus persica) and their expression profiles during fruit maturation. Sci Hortic. 2017;224:306–16.
Article
CAS
Google Scholar
Zeng W, Niu L, Wang Z, Wang X, Wang Y, Pan L, Lu Z, Cui G, Weng W, Wang M, Meng X. Application of an antibody chip for screening differentially expressed proteins during peach ripening and identification of a metabolon in the SAM cycle to generate a peach ethylene biosynthesis model. Hortic Res. 2020;7(1):1–4.
Article
CAS
Google Scholar
Trainotti L, Zanin D, Casadoro G. A cell wall-oriented genomic approach reveals a new and unexpected complexity of the softening in peaches. J Exp Bot. 2003;54(389):1821–32.
Article
CAS
PubMed
Google Scholar
Cao S, Liang M, Shi L, Shao J, Song C, Bian K, Chen W, Yang Z. Accumulation of carotenoids and expression of carotenogenic genes in peach fruit. Food Chem. 2017;214:137–46.
Article
CAS
PubMed
Google Scholar
Cao K, Ding T, Mao D, Zhu G, Fang W, Chen C, Wang X, Wang L. Transcriptome analysis reveals novel genes involved in anthocyanin biosynthesis in the flesh of peach. Plant Physiol Biochem. 2017;123:94–102.
Article
PubMed
CAS
Google Scholar
Famiani F, Farinelli D, Moscatello S, Battistelli A, Leegood RC, Walker RP. The contribution of stored malate and citrate to the substrate requirements of metabolism of ripening peach (Prunus persica L. Batsch) flesh is negligible. Implications for the occurrence of phosphoenolpyruvate carboxykinase and gluconeogenesis. Plant Physiol Biochem. 2016;101:33–42.
Article
CAS
PubMed
Google Scholar
Vimolmangkang S, Zheng H, Peng Q, Jiang Q, Wang H, Fang T, Liao L, Wang L, He H, Han Y. Assessment of sugar components and genes involved in the regulation of sucrose accumulation in peach fruit. J Agric Food Chem. 2016;64(35):6723–9.
Article
CAS
PubMed
Google Scholar
Desnoues E, Génard M, Quilot-Turion B, Baldazzi V. A kinetic model of sugar metabolism in peach fruit reveals a functional hypothesis of a markedly low fructose-to-glucose ratio phenotype. Plant J. 2018;94(4):685–98.
Article
CAS
PubMed
Google Scholar
Bianchi VJ, Rubio M, Trainotti L, Verde I, Bonghi C, Martínez-Gómez P. Prunus transcription factors: breeding perspectives. Front Plant Sci. 2015;6:443.
Article
PubMed
PubMed Central
Google Scholar
Pegoraro C, Tadiello A, Girardi CL, Chaves FC, Quecini V, de Oliveira AC, Trainotti L, Rombaldi CV. Transcriptional regulatory networks controlling woolliness in peach in response to preharvest gibberellin application and cold storage. BMC Plant Biol. 2015;15:279.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pons C, Martí C, Forment J, Crisosto CH, Dandekar AM, Granell A. A genetic genomics-expression approach reveals components of the molecular mechanisms beyond the cell wall that underlie peach fruit woolliness due to cold storage. Plant Mol Biol. 2016;92(4–5):483–503.
Article
CAS
PubMed
Google Scholar
Nilo-Poyanco R, Vizoso P, Sanhueza D, Balic I, Meneses C, Orellana A, Campos-Vargas R. A Prunus persica genome-wide RNA-seq approach uncovers major differences in the transcriptome among chilling injury sensitive and non-sensitive varieties. Physiol Plant. 2019;166(3):772–93.
Article
CAS
PubMed
Google Scholar
Abdallah C, Dumas-Gaudot E, Renaut J, Sergeant K. Gel-based and gel-free quantitative proteomics approaches at a glance. Int J Plant Genomics. 2012. https://doi.org/10.1155/2012/494572JF.
Gapper NE, Giovannoni JJ, Watkins CB. Understanding development and ripening of fruit crops in an 'omics' era. Hortic Res. 2014;1:14034.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nilo-Poyanco R, Saffie C, Lilley K, Baeza-Yates R, Cambiazo V, Campos-Vargas R, González M, Meisel LA, Retamales J, Silva H, Orellana A. Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). BMC Genomics. 2010;11:43.
Article
CAS
Google Scholar
Nilo-Poyanco R, Campos-Vargas R, Orellana A. Assessment of Prunus persica fruit softening using a proteomics approach. J Proteome. 2012;75(5):1618–38.
Article
CAS
Google Scholar
Campos-Vargas R, Becerra O, Baeza-Yates R, Cambiazo V, Gonzalez M, Meisel L, Orellana A, Retamales J, Silva H, Defilippi BG. Seasonal variation in the development of chilling injury in 'O'Henry' peaches. Sci Hortic-Amsterdam. 2006;110(1):79–83.
Article
Google Scholar
Pan L, Zeng W, Niu L, Lu Z, Liu H, Cui G, Zhu Y, Chu J, Li W, Fang W, Cai Z, Li G, Wang Z. PpYUC11, a strong candidate gene for the stony hard phenotype in peach (Prunus persica L. Batsch), participates in IAA biosynthesis during fruit ripening. J Exp Bot. 2015;66(22):7031–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Monti LL, Bustamante CA, Budde CO, Gabilondo J, Müller GL, Lara MV, Drincovich MF. Metabolomic and proteomic profiling of spring lady peach fruit with contrasting woolliness phenotype reveals carbon oxidative processes and proteome reconfiguration in chilling-injured fruit. Postharvest Biol Tec. 2019;151:142–51.
Article
CAS
Google Scholar
Guy HR. Amino acid scale: hydrophobicity scale based on free energy of transfer (kcal/mole). Biophys J. 1985;47:61–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lü P, Yu S, Zhu N, Chen YR, Zhou B, Pan Y, Tzeng D, Fabi JP, Argyris J, Garcia-Mas J, Ye N, Zhang J, Grierson D, Xiang J, Fei Z, Giovannoni J, Zhong S. Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nat Plants. 2018;4(10):784–91.
Article
PubMed
CAS
Google Scholar
D'Ambrosio C, Arena S, Rocco M, Verrillo F, Novi G, Viscosi V, Marra M, Scaloni A. Proteomic analysis of apricot fruit during ripening. J Proteome. 2013;78:39–57.
Article
CAS
Google Scholar
Bianco L, Lopez L, Scalone AG, Di Carli M, Desiderio A, Benvenuto E, Perrotta G. Strawberry proteome characterization and its regulation during fruit ripening and in different genotypes. J Proteome. 2009;72(4):586–607.
Article
CAS
Google Scholar
Tanou G, Minas IS, Socossa F, Belghazi M, Xanthopoulou A, Ganopoulos I, Madesis P, Fernie A, Molassiotis A. Exploring priming responses involved in peach fruit acclimation to cold stress. Sci Rep. 2017;7:11358.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu X, Mason AM, Yu M, Ma R, Yu Z. Quantitative proteomic analysis of pre-and post-harvest peach fruit ripening based on iTRAQ technique. Acta Physiol Plant. 2017;39(8):181.
Article
CAS
Google Scholar
Huan C, Xu Y, An X, Yu M, Ma R, Zheng X. Yu Z iTRAQ-based protein profiling of peach fruit during ripening and senescence under different temperatures. Postharvest Biol Tec. 2019;151:88–97.
Article
CAS
Google Scholar
Jiang L, Kang R, Feng L, Yu Z, Luo H. iTRAQ-based quantitative proteomic analysis of peach fruit (Prunus persica L.) at different ripening and postharvest storage stages. Postharvest Biol Tec. 2020;164:111137.
Papavasileiou A, Tanou G, Samaras A, Samiotaki M, Molassiotis A, Karaoglanidis G. Proteomic analysis upon peach fruit infection with Monilinia fructicola and M laxa identify responses contributing to brown rot resistance Sci Rep 2020; 10:7807.
Asara JM, Christofk HR, Freimark LM, Cantley LC. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics. 2008;8(5):994–9.
Article
CAS
PubMed
Google Scholar
Lindemann C, Thomanek N, Hundt F, Lerari T, Meyer HE, Wolters D, Marcus K. Strategies in relative and absolute quantitative mass spectrometry based proteomics. Biol Chem. 2017;398(5–6):687–99.
Article
CAS
PubMed
Google Scholar
Zhao Q, Liu C. Chloroplast Chaperonin: An intricate protein folding machine for photosynthesis. Front Mol Biosci. 2018;4:98.
Article
PubMed
PubMed Central
CAS
Google Scholar
Velasco D, Hough J, Aradhya M, Ross-Ibarra J. Evolutionary Genomics of Peach and Almond Domestication. G3 (Bethesda). 2016;6(12):3985–3993.
Qian M, Zhang Y, Yan X, Han M, Li J, Li F, Li F, Zhang D, Zhao C. Identification and expression analysis of polygalacturonase family members during peach fruit softening. Int J Mol Sci. 2016;17(11):1933.
Article
CAS
PubMed Central
Google Scholar
Hayama H, Shimada T, Fujii H, Ito A, Kashimura Y. Ethylene-regulation of fruit softening and softening-related genes in peach. J Exp Bot. 2006;57(15):4071–7.
Article
CAS
PubMed
Google Scholar
Zhu Y, Zeng W, Wang X, Pan L, Niu L, Lu Z, Cui G, Wang Z. Characterization and transcript profiling of PME and PMEI gene families during peach fruit maturation. J Am Soc Hortic Sci. 2017;142(4):246–59.
Article
CAS
Google Scholar
Trainotti L, Spolaore S, Ferrarese L, Casadoro G. Characterization of ppEG1, a member of a multigene family which encodes endo-beta-1,4-glucanase in peach. Plant Mol Biol. 1997;34(5):791–802.
Article
CAS
PubMed
Google Scholar
Li XW, Jiang J, Zhang LP, Yu Y, Ye ZW, Wang XM, Zhou JY, Chai ML, Zhang HQ, Arús P, Jia HJ. Identification of volatile and softening-related genes using digital gene expression profiles in melting peach. Tree Genet Genomes. 2015;11(4):71.
Article
Google Scholar
Guo S, Song J, Zhang B, Jiang H, Ma R, Yu M. Genome-wide identification and expression analysis of beta-galactosidase family members during fruit softening of peach [Prunus persica (L.) Batsch]. Postharvest Biol Tec. 2018;136:111–23.
Article
CAS
Google Scholar
Souza F, Alves E, Pio R, Castro E, Reighard G, Freire AI, Mayer NA, Pimentel R. Influence of temperature on the development of peach fruit in a subtropical climate region. Agronomy. 2019;9(1):20.
Article
Google Scholar
Pei MS, Cao SH, Wu L, Wang GM, Xie ZH, Gu C, Zhang SL. Comparative transcriptome analyses of fruit development among pears, peaches, and strawberries provide new insights into single sigmoid patterns. BMC Plant Biol. 2020;20(1):1–5.
Article
CAS
Google Scholar
Sugimoto-Shirasu K, Roberts K. “Big it up”: endoreduplication and cell-size control in plants. Curr Opin Plant Biol. 2003 1;6(6):544–53.
Musseau C, Jorly J, Gadin S, Sørensen I, Deborde C, Bernillon S, Mauxion JP, Atienza I, Moing A, Lemaire-Chamley M, Rose JK. The tomato Guanylate-binding protein SlGBP1 enables fruit tissue differentiation by maintaining Endopolyploid cells in a non-proliferative state. Plant Cell. 2020. https://doi.org/10.1105/tpc.20.00245.
Wang X, Zeng W, Ding Y, Wang Y, Niu L, Yao JL, Pan L, Lu Z, Cui G, Li G, Wang Z. Peach ethylene response factor PpeERF2 represses the expression of ABA biosynthesis and cell wall degradation genes during fruit ripening. Plant Sci. 2019;283:116–26.
Article
CAS
PubMed
Google Scholar
Ruperti B, Bonghi C, Rasori A, Ramina A, Tonutti P. Characterization and expression of two members of the peach 1-aminocyclopropane-1-carboxylate oxidase gene family. Physiol Plant. 2001;111(3):336–44.
Article
CAS
PubMed
Google Scholar
Trainotti L, Bonghi C, Ziliotto F, Zanin D, Rasori A, Casadoro G, Ramina A, Tonutti P. The use of microarray μPEACH1. 0 to investigate transcriptome changes during transition from pre-climacteric to climacteric phase in peach fruit. Plant Sci. 2006;170(3):606–13.
Article
CAS
Google Scholar
Jia M, Du P, Ding N, Zhang Q, Xing S, Wei L, Zhao Y, Mao W, Li J, Li B, Jia W. Two FERONIA-like receptor kinases regulate apple fruit ripening by modulating ethylene production. Front Plant Sci. 2017;8:1406.
Article
PubMed
PubMed Central
Google Scholar
Ren H, Willige BC, Jaillais Y, Geng S, Park MY, Gray WM, Chory J. BRASSINOSTEROID-SIGNALING KINASE 3, a plasma membrane-associated scaffold protein involved in early brassinosteroid signaling. PLoS Genet. 2019;15(1):e1007904.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wei X, Liu F, Chen C, Ma F, Li M. The Malus domestica sugar transporter gene family: identifications based on genome and expression profiling related to the accumulation of fruit sugars. Front Plant Sci. 2014;5:569.
Article
PubMed
PubMed Central
Google Scholar
Cirilli M, Bassi D, Ciacciulli A. Sugars in peach fruit: a breeding perspective. Hortic Res. 2016;3:15067.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cantín CM, Gogorcena Y, Moreno MÁ. Analysis of phenotypic variation of sugar profile in different peach and nectarine [Prunus persica (L.) Batsch] breeding progenies. J Sci Food Agric. 2009;89(11):1909–17.
Article
CAS
Google Scholar
Teo G, Suzuki Y, Uratsu SL, Lampinen B, Ormonde N, Hu WK, DeJong TM, Dandekar AM. Silencing leaf sorbitol synthesis alters long-distance partitioning and apple fruit quality. Proc Natl Acad Sci. 2006;103(49):18842–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu CY, Cheng HY, Cheng R, Qi KJ, Gu C, Zhang SL. Expression analysis of sorbitol transporters in pear tissues reveals that PbSOT6/20 is associated with sorbitol accumulation in pear fruits. Sci Hortic. 2019;243:595–601.
Article
CAS
Google Scholar
Fan RC, Peng CC, Xu YH, Wang XF, Li Y, Shang Y, Du SY, Zhao R, Zhang XY, Zhang LY, Zhang DP. Apple sucrose transporter SUT1 and sorbitol transporter SOT6 interact with cytochrome b5 to regulate their affinity for substrate sugars. Plant Physiol. 2009;150(4):1880–901.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gao Z, Maurousset L, Lemoine R, Yoo SD, van Nocker S, Loescher W. Cloning, expression, and characterization of sorbitol transporters from developing sour cherry fruit and leaf sink tissues. Plant Physiol. 2003;131(4):1566–75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet. 2013;45(5):487–94.
Article
CAS
PubMed
Google Scholar
Nuñez C, Dupré G, Mujica K, Melet L, Meisel L, Almeida AM. Thinning alters the expression of the PpeSUT1 and PpeSUT4 sugar transporter genes and the accumulation of translocated sugars in the fruits of an early season peach variety. Plant Growth Regul. 2019;88(3):283–96.
Article
CAS
Google Scholar
Guizani M, Maatallah S, Dabbou S, Serrano M, Hajlaou H, Helal AN, Kilani-Jaziri S. Physiological behaviors and fruit quality changes in five peach cultivars during three ripening stages in a semi-arid climate. Acta Physiol Plant. 2019;41(9):154.
Article
CAS
Google Scholar
Etienne A, Génard M, Lobit P, Mbeguié-A-Mbéguié D, Bugaud C. What controls fleshy fruit acidity? A review of malate and citrate accumulation in fruit cells. J Exp Bot. 2013;64(6):1451–69.
Article
CAS
PubMed
Google Scholar
Hebbelmann I, Selinski J, Wehmeyer C, Goss T, Voss I, Mulo P, Kangasjärvi S, Aro EM, Oelze ML, Dietz KJ, Nunes-Nesi A. Multiple strategies to prevent oxidative stress in Arabidopsis plants lacking the malate valve enzyme NADP-malate dehydrogenase. J Exp Bot. 2012;63(3):1445–59.
Article
CAS
PubMed
Google Scholar
Zheng B, Zhao L, Jiang X, Cherono S, Liu JJ, Ogutu C, Ntini C, Zhang X, Han Y. Assessment of organic acid accumulation and its related genes in peach. Food Chem. 2021;334:127567.
Article
CAS
PubMed
Google Scholar
Jiang L, Feng L, Zhang F, Luo H, Yu Z. Peach fruit ripening: proteomic comparative analyses of two cultivars with different flesh texture phenotypes at two ripening stages. Sci Hortic. 2020;260:108610.
Article
CAS
Google Scholar
Eliyahu E, Rog I, Inbal D, Danon A. ACHT4-driven oxidation of APS1 attenuates starch synthesis under low light intensity in Arabidopsis plants. Proc Natl Acad Sci U S A. 2015;112(41):12876–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang B, Shen JY, Wei WW, Xi WP, Xu CJ, Ferguson I, Chen K. Expression of genes associated with aroma formation derived from the fatty acid pathway during peach fruit ripening. J Agric Food Chem. 2010;58(10):6157–65.
Article
CAS
PubMed
Google Scholar
Cao X, Xie K, Duan W, Zhu Y, Liu M, Chen K, Klee H, Zhang B. Peach Carboxylesterase PpCXE1 is associated with catabolism of volatile esters. J Agric Food Chem. 2019;67(18):5189–96.
Article
CAS
PubMed
Google Scholar
Goulet C, Mageroy MH, Lam NB, Floystad A, Tieman DM, Klee HJ. Role of an esterase in flavor volatile variation within the tomato clade. Proc Natl Acad Sci. 2012;109(46):19009–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schöttler M, Boland W. Biosynthesis of dodecano-4-lactone in ripening fruits: crucial role of an epoxide-hydrolase in enantioselective generation of aroma components of the nectarine (Prunus persica var. nucipersica) and the strawberry (Fragaria ananassa). Helvetica Chimica Acta. 1996;79(5):1488–96.
Article
Google Scholar
Pirona R, Vecchietti A, Lazzari B, Caprera A, Malinverni R, Consolandi C, Severgnini M, De Bellis G, Chietera G, Rossini L, Pozzi C. Expression profiling of genes involved in the formation of aroma in two peach genotypes. Plant Biol. 2013;15(3):443–51.
Article
CAS
PubMed
Google Scholar
Sánchez-Sevilla JF, Cruz-Rus E, Valpuesta V, Botella MA, Amaya I. Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses. BMC Genomics. 2014;15:218.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jincy M, Djanaguiraman M, Jeyakumar P, Subramanian KS, Jayasankar S, Paliyath G. Inhibition of phospholipase D enzyme activity through hexanal leads to delayed mango (Mangifera indica L.) fruit ripening through changes in oxidants and antioxidant enzymes activity. Sci Hortic. 2017;218:316–25.
Qin C, Wang C, Wang X. Kinetic analysis of Arabidopsis phospholipase Dδ substrate preference and mechanism of activation by Ca2+ and phosphatidylinositol 4, 5-bisphosphate. J Biol Chem. 2002;277(51):49685–90.
Article
CAS
PubMed
Google Scholar
Cai H, Han S, Jiang L, Yu M, Ma R, Yu Z. 1-MCP treatment affects peach fruit aroma metabolism as revealed by transcriptomics and metabolite analyses. Food Res Int. 2019;122:573–84.
Article
CAS
PubMed
Google Scholar
Regon P, Panda P, Kshetrimayum E, Panda SK. Genome-wide comparative analysis of tonoplast intrinsic protein (TIP) genes in plants. Funct Integr Genomics. 2014;14(4):617–29.
Article
CAS
PubMed
Google Scholar
Chen YH, Khanal BP, Linde M, Debener T, Alkio M, Knoche M. Expression of putative aquaporin genes in sweet cherry is higher in flesh than skin and most are downregulated during development. Sci Hortic. 2019;244:304–14.
Article
CAS
Google Scholar
Garcia VJ, Xu SL, Ravikumar R, Wang W, Elliott L, Gonzalez E, Fesenko M, Altmann M, Brunschweiger B, Falter-Braun P, Moore I. TRIPP is a plant-specific component of the Arabidopsis TRAPPII membrane trafficking complex with important roles in plant development. Plant Cell. 2020;32(7):2424–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rybak K, Steiner A, Synek L, Klaeger S, Kulich I, Facher E, Wanner G, Kuster B, Zarsky V, Persson S, Assaad FF. Plant cytokinesis is orchestrated by the sequential action of the TRAPPII and exocyst tethering complexes. Dev Cell. 2014;29(5):607–20.
Article
CAS
PubMed
Google Scholar
Brummell DA, Dal Cin V, Crisosto CH, Labavitch JM. Cell wall metabolism during maturation, ripening and senescence of peach fruit. J Exp Bot. 2004;55(405):2029–39.
Article
CAS
PubMed
Google Scholar
Kalde M, Elliott L, Ravikumar R, Rybak K, Altmann M, Klaeger S, Wiese C, Abele M, Al B, Kalbfuß N, Qi X. Interactions between transport protein particle (TRAPP) complexes and Rab GTP ases in Arabidopsis. Plant J. 2019;100(2):279–97.
Article
CAS
PubMed
Google Scholar
Nielsen E. The small GTPase superfamily in plants: A conserved regulatory module with novel functions. Annu Rev Plant Biol. 2020;71:247–72.
Article
CAS
PubMed
Google Scholar
Pertl-Obermeyer H, Wu XN, Schrodt J, Müdsam C, Obermeyer G, Schulze WX. Identification of cargo for adaptor protein (AP) complexes 3 and 4 by sucrose gradient profiling. Mol Cell Proteomics. 2016;15(9):2877–89.
Article
CAS
PubMed
PubMed Central
Google Scholar
Müdsam C, Wollschläger P, Sauer N, Schneider S. Sorting of Arabidopsis NRAMP3 and NRAMP4 depends on adaptor protein complex AP4 and a dileucine-based motif. Traffic. 2018;19(7):503–21.
Article
PubMed
CAS
Google Scholar
Di Matteo A, Ruggieri V, Sacco A, Rigano MM, Carriero F, Bolger A, Fernie AR, Frusciante L, Barone A. Identification of candidate genes for phenolics accumulation in tomato fruit. Plant Sci. 2013;205:87–96.
Article
PubMed
CAS
Google Scholar
Xi W, Feng J, Liu Y, Zhang S, Zhao G. The R2R3-MYB transcription factor PaMYB10 is involved in anthocyanin biosynthesis in apricots and determines red blushed skin. BMC Plant Biol. 2019;19(1):287.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang Q, Feng C, Li W, Qu Z, Zeng M, Xi W. Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening. BMC Genomics. 2019;20(1):1–5.
Google Scholar
Ríos P, Argyris J, Vegas J, Leida C, Kenigswald M, Tzuri G, Troadec C, Bendahmane A, Katzir N, Picó B, Monforte AJ. ETHQV 6.3 is involved in melon climacteric fruit ripening and is encoded by a NAC domain transcription factor. Plant J. 2017;91(4):671–83.
Article
PubMed
CAS
Google Scholar
Liang SM, Chen SC, Liu ZL, Shan W, Chen JY, Lu WJ, Lakshmanan P, Kuang JF. MabZIP74 interacts with MaMAPK11-3 to regulate the transcription of MaACO1/4 during banana fruit ripening. Postharvest Biol Tec. 2020;169:111293.
Article
CAS
Google Scholar
Song CB, Shan W, Kuang JF, Chen JY, Lu WJ. The basic helix-loop-helix transcription factor MabHLH7 positively regulates cell wall-modifying-related genes during banana fruit ripening. Postharvest Biol Tec. 2020;161:111068.
Article
CAS
Google Scholar
Zhu M, Chen G, Zhou S, Tu Y, Wang Y, Dong T, Hu Z. A new tomato NAC (N AM/A TAF1/2/C UC2) transcription factor, SlNAC4, functions as a positive regulator of fruit ripening and carotenoid accumulation. Plant Cell Physiol. 2014;55(1):119–35.
Article
CAS
PubMed
Google Scholar
Mou W, Li D, Luo Z, Li L, Mao L, Ying T. SlAREB1 transcriptional activation of NOR is involved in abscisic acid-modulated ethylene biosynthesis during tomato fruit ripening. Plant Sci. 2018;276:239–49.
Article
CAS
PubMed
Google Scholar
Fu CC, Han YC, Fan ZQ, Chen JY, Chen WX, Lu WJ, Kuang JF. The papaya transcription factor CpNAC1 modulates carotenoid biosynthesis through activating phytoene desaturase genes CpPDS2/4 during fruit ripening. J Agric Food Chem. 2016;64(27):5454–63.
Article
CAS
PubMed
Google Scholar
Fu C, Chen H, Gao H, Lu Y, Han C, Han Y. Two papaya MYB proteins function in fruit ripening through regulating some genes involved in cell wall degradation and carotenoid biosynthesis. J Sci Food Agric. 2020.
Zhang T, Li W, Xie R, Xu L, Zhou Y, Li H, Yuan C, Zheng X, Xiao L, Liu K. CpARF2 and CpEIL1 interact to mediate auxin–ethylene interaction and regulate fruit ripening in papaya. Plant J. 2020. https://doi.org/10.1111/tpj.14803.
Li J, Li F, Qian M, Han M, Liu H, Zhang D, Ma J, Zhao C. Characteristics and regulatory pathway of the PrupeSEP1 SEPALLATA gene during ripening and softening in peach fruits. Plant Sci. 2017;257:63–73.
Article
CAS
PubMed
Google Scholar
Gu C, Guo ZH, Cheng HY, Zhou YH, Qi KJ, Wang GM, Zhang SL. A HD-ZIP II HOMEBOX transcription factor, PpHB. G7, mediates ethylene biosynthesis during fruit ripening in peach. Plant Sci. 2019;278:12–9.
Article
CAS
PubMed
Google Scholar
Zhou H, Zhao L, Yang Q, Amar MH, Ogutu C, Peng Q, Liao L, Zhang J, Han Y. Identification of EIL and ERF genes related to fruit ripening in peach. Int J Mol Sci. 2020;21(8):2846.
Article
CAS
PubMed Central
Google Scholar
Diao D, Hu X, Guan D, Wang W, Yang H, Liu Y. Genome-wide identification of the ARF (auxin response factor) gene family in peach and their expression analysis. Mol Biol Rep. 2020.
Gao Y, Wei W, Fan Z, Zhao X, Zhang Y, Jing Y, Zhu B, Zhu H, Shan W, Chen J, Grierson D. Re-evaluation of the nor mutation and the role of the NAC-NOR transcription factor in tomato fruit ripening. J Exp Bot. 2020;71(12):3560–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tranbarger TJ, Fooyontphanich K, Roongsattham P, Pizot M, Collin M, Jantasuriyarat C, Suraninpong P, Tragoonrung S, Dussert S, Verdeil JL, Morcillo F. Transcriptome analysis of cell wall and NAC domain transcription factor genes during Elaeis guineensis fruit ripening: evidence for widespread conservation within monocot and eudicot lineages. Front Plant Sci. 2017;8:603.
Article
PubMed
PubMed Central
Google Scholar
Wang C, Dong Y, Zhu L, Wang L, Yan L, Wang M, Zhu Q, Nan X, Li Y, Li J. Comparative transcriptome analysis of two contrasting wolfberry genotypes during fruit development and ripening and characterization of the LrMYB1 transcription factor that regulates flavonoid biosynthesis. BMC Genomics. 2020;21:1–8.
Google Scholar
Meng X, Yang D, Li X, Zhao S, Sui N, Meng Q. Physiological changes in fruit ripening caused by overexpression of tomato SlAN2, an R2R3-MYB factor. Plant Physiol Biochem. 2015;89:24–30.
Article
CAS
PubMed
Google Scholar
Cheng Y, Liu L, Yuan C, Guan J. Molecular characterization of ethylene-regulated anthocyanin biosynthesis in plums during fruit ripening. Plant Mol Biol Rep. 2016;34(4):777–85.
Article
CAS
Google Scholar
Allan AC, Espley RV. MYBs drive novel consumer traits in fruits and vegetables. Trends Plant Sci. 2018;23(8):693–705.
Article
CAS
PubMed
Google Scholar
Fujisawa M, Nakano T, Shima Y, Ito Y. A large-scale identification of direct targets of the tomato MADS box transcription factor RIPENING INHIBITOR reveals the regulation of fruit ripening. Plant Cell. 2013;25(2):371–86.
Article
CAS
PubMed
PubMed Central
Google Scholar
https://www.plabipd.de. Accessed Aug 2020.
Fang Y, Robinson DP, Foster LJ. Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics. J Proteome Res. 2010;9(4):1902–12.
Article
CAS
PubMed
Google Scholar
Jorrin-Novo JV, Komatsu S, Sanchez-Lucas R, de Francisco LE. Gel electrophoresis-based plant proteomics: past, present, and future. Happy 10th anniversary journal of proteomics! J Proteome. 2019;198:1–10.
Article
CAS
Google Scholar
Buchberger AR, DeLaney K, Johnson J, Li L. Mass spectrometry imaging: a review of emerging advancements and future insights. Anal Chem. 2018;90(1):240–65.
Article
CAS
PubMed
Google Scholar
Jorrin-Novo JV. What is new in (plant) proteomics methods and protocols: the 2015–2019 Quinquennium. In plant proteomics 2020 (pp. 1-10). Humana, New York.
Liu Z, Ma H, Jung S, Main D, Guo L. Developmental mechanisms of fleshy fruit diversity in Rosaceae. Ann Rev Plant Biol. 2020;71:547–73.
Article
CAS
Google Scholar
Botton A, Rasori A, Ziliotto F, Moing A, Maucourt M, Bernillon S, Deborde C, Petterle A, Varotto S, Bonghi C. The peach HECATE3-like gene FLESHY plays a double role during fruit development. Plant Mol Biol. 2016;91(1–2):97–114.
Article
CAS
PubMed
Google Scholar
Giné-Bordonaba J, Eduardo I, Arús P, Cantín CM. Biochemical and genetic implications of the slow ripening phenotype in peach fruit. Sci Hortic. 2020;259:108824.
Article
CAS
Google Scholar
Andrade D, Covarrubias MP, Benedetto G, Pereira EG, Almeida AM. Differential source–sink manipulation affects leaf carbohydrate and photosynthesis of early-and late-harvest nectarine varieties. Theor Exp Plant Phys. 2019;31(2):341–56.
Article
CAS
Google Scholar
Minas IS, Blanco-Cipollone F, Sterle D. Accurate non-destructive prediction of peach fruit internal quality and physiological maturity with a single scan using near infrared spectroscopy. Food Chem. 2020;127626.
Abdi N, Holford P, Mcglasson B. Application of two-dimensional gel electrophoresis to detect proteins associated with harvest maturity in stonefruit. Postharvest Biol Tec. 2002;26(1):1–13.
Article
CAS
Google Scholar
Mechin V, Consoli L, Le Guilloux M, Damerval C. An efficient solubilization buffer for plant proteins focused in immobilized pH gradients. PROTEOMICS: International Edition. 2003;3(7):1299–302.
Article
CAS
Google Scholar
Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976;72:248–54.
Article
CAS
PubMed
Google Scholar
Shevchenko A, Wilm M, Vorm O, Mann M. Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem. 1996;68(5):850–8.
Article
CAS
PubMed
Google Scholar
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40:D1178–86.
Article
CAS
PubMed
Google Scholar
van den Berg RA, Hoefsloot HC, Westerhuis JA, Smilde AK, van der Werf MJ. Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics. 2006;7:142.
Article
PubMed
PubMed Central
CAS
Google Scholar
Taverner T, Karpievitch YV, Polpitiya AD, Brown JN, Dabney AR, Anderson GA, Smith RD. DanteR: an extensible R-based tool for quantitative analysis of -omics data. Bioinformatics. 2012;28(18):2404–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Osorio D, Rondón-Villarrea P, Torres R. Peptides: a package for data mining of antimicrobial peptides. R Journal. 2015;7(1):4–14.
Article
Google Scholar
Supek F, Bošnjak M, Škunca N, Šmuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 2011;6(7):e21800.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kuznetsova I, Lugmayr A, Siira SJ, Rackham O, Filipovska A. CirGO: an alternative circular way of visualising gene ontology terms. BMC Bioinformatics. 2019;20(1):84.
Article
PubMed
PubMed Central
Google Scholar
Ryu JY, Kim HU, Lee SY. Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers. Proc Natl Acad Sci U S A. 2019;116(28):13996–4001.
Article
CAS
PubMed
PubMed Central
Google Scholar
Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A. Pathway tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform. 2016;17(5):877–90.
Article
CAS
PubMed
Google Scholar
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A. NCBI GEO: archive for functional genomics data sets—update. Nucleic Acids Res. 2012;41(D1):D991–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Barter RL, Yu B. Superheat: An R package for creating beautiful and extendable heatmaps for visualizing complex data. J Comput Graph Stat. 2018;27(4):910–22.
Article
PubMed
PubMed Central
Google Scholar
Ritchie ME, Phipson B, Wu DI, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research. 2015;43(7):e47.
Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, Gao G. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017;45(D1):D1040–5.
Article
CAS
PubMed
Google Scholar
Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res. 2018;46(D1):D1190–6.
Article
PubMed
CAS
Google Scholar