Proteomic approaches based on 1D electrophoresis followed by MS (Figure 1) have been successfully used to better understand fruit ripening in Rosaceae family species such as apricot  and strawberry . When compared to proteins extracted from ripening P. armeniaca using 1D SDS-PAGE gel followed by MS, 76% of the 245 proteins identified in mature/ripe apricot fruit were also identified in mature/ripe peach fruit . Moreover when compared to other three P. persica species gel-based proteomic studies which published all the proteins characterized (Supplementary Table 3), on average an 85% of the characterized proteins matched the ones found in our study. Adding the fact that the physicochemical properties of P. persica primary transcripts' proteome were similar to those of the proteome analyzed in the present study (Supplementary Table 2, Supplementary Figure 2) and that low abundant proteins, such as TFs, could be detected in our dataset, the current analysis seems to truly reflect the fruit proteome, but with a bias in terms of primarily representing proteins with average physicochemical properties (Supplementary Figure 2). Comparison with iTRAQ proteome datasets would be highly informative, however only differentially accumulated proteins are reported in these publications with emphasis on the effect of postharvest treatments such as cold storage or disease incidence in ripening process [35-39] (Supplementary Table 3).
In order to take full advantage of the proteins characterized in systems such as ripe fruit, it is important to follow a robust pipeline of MS analysis and protein quantification, to increase the confidence in the identifications performed and to support differential accumulation analysis. MS analysis was performed using a stringent cutoff for both peptide and protein match. Next, protein quantification was performed using the average total ion chromatograms (Average TIC)  followed by pre-treatment data to get a data distribution as close to normal as possible (Supplementary Figure 1), data scaling and centering, and data cleaning, to keep only those proteins that had a proper number of replicates to perform a statistical analysis of differential accumulation. All these steps explain the drop from 2,740 detected proteins to 1,663 assessed proteins. It is also worth to remember that label-free quantification, such as the one used in this work, is a good choice for proteomic analysis that seeks to characterize as many unbiased proteins as possible. However, variations are higher than in techniques that rely on labeling, since in label-free quantification samples are individually prepared and comparison occurs later, during data analysis . In addition, variability among fruits in the field can be very high, even if the fruits were manually selected based on size, color and physicochemical parameters. Therefore, in many cases a protein may vary widely between different conditions, and its abundance variation due to biological and technical issues might hurdle the ability to identify this protein as differentially accumulated.
The fruit mesocarp proteome identified in this work (1,663 proteins) was functionally related to carboxylic acid metabolism, intracellular transport and protein folding (Figure 2A). Transport proteins were mainly related to carbohydrates, ions, and vesicle-mediated transport (Supplementary Table 1), with very few transporters differentially accumulated. Protein folding, in turn, was mainly related to chloroplast chaperonins . Both sets point to a fruit mesocarp with active cellular compartment transport and protein folding.
Mature and ripe fruit stages are the last in the fruit developmental curve, making it possible to compare protein-coding genes from our dataset with datasets that characterized ripening-related genes in P. persica (GEO dataset GSE71561) . Protein-coding genes expressed in mature/ripe fruit seemed to be time and tissue-specific, given that close to 25% peak their expression levels in ripe fruit when compared to other developmental stages, and 52% peaked their expression in ripe fruit mesocarp, compared to other tissues (Figure 2B and 2C). Fruit-specific genes that displayed the strongest differentiation between peach and almond (P. dulcis) were also the most highly expressed, pointing to a functional specialization of protein-coding genes that are highly expressed in fruit . Our results point to the same behavior in functionally specialized fruit proteins, i.e., proteins with high accumulation in fruit could be particularly involved in its metabolism.
Samples and protein abundance differences between mature and ripe fruit mesocarp were striking, with a PCA first component splitting both samples and 14.9% of the assessed differentially accumulated proteins (Figure 3A, Table 1). This reinforces the notion that mature and ripe fruits are different not only in terms of metabolic profiles, but also at the proteome level. Processes triggered in the mature fruit would be directed to glycogen and isocitrate metabolism, and protein localization (Figure 3B), whereas a manual inspection indicated that protein-driven cell wall modification was much more represented in ripe fruit than in mature fruit (nine versus two proteins, Table 1, Figure 4B). Seven of these cell wall proteins have been experimentally shown to be ethylene responsive: polygalacturonase (PG) Prupe.2G300900 , PpPG21 (Prupe.4G261900) , PpPG22 (Prupe.4G262200) [14, 44, 45], beta-galactosidase (Prupe.3G050200) , pectin methylesterase inhibitor (Prupe.1G114500) , expansin 3 (Prupe.6G075100) , and endo-1,4-beta-glucanase PpEG1 (Prupe.5G131300) , in according to the increase in ethylene production at ripe stage  highlighting its relevance as a ripening promoting hormone in melting peach fruit varieties. In addition, protein-coding genes from PpEG1, PpPG21, Prupe.2G300900 and Prupe.3G050200 (PpBGAL2) belonged to the same gene cluster with higher expression in ripe fruit compared to mature fruit, in the white flesh fast-melting peach “Hu Jing Mi Lu” (HJ) , pointing to a conserved mechanism of cell wall dismantling in peach fruits with a different genetic background. PpBGAL2 transcript was also shown to be highly correlated with the fruit softening in the melting variety XH8, with expressions 3–4 times higher during later storage compared to early storage .
Peach fruit size is controlled throughout its development mainly by cell divisions and enlargement of mesocarp cells . These processes display a temporal control during the fruit development, with two stages of faster growth alternating with two stages of slower increases in fruit diameter, represented by a double-sigmoid growth pattern [50, 51]. Fruit size increase during the ripening process ceases, however how this size control is accomplished is not clear. One of the mechanisms that are involved in increasing the fruit cell size is the genome size amplification by endoreduplication , where endopolyploid cells arise from variations of the canonical cell cycle that replicate the genome without cell division. Recently a GUANYLATE-BINDING PROTEIN1 (SlGBP1)was characterized as a possible inhibitor of cell division in tomato. This protein would maintain endopolyploid cells in a non-proliferative state . The best P. persica homologue of SlGBP1 (Prupe.4G053400, 70.6% identity) was found differentially accumulated in ripe fruit in this study, indicating that endopolyploid cells division would be inhibited during the fruit ripening, providing a molecular mechanism to explain the lack of fruit size increment in this developmental stage in peach.
Key processes involved in the organoleptic changes that occur in the transition from mature to ripe fruit
The ripening process involves changes in the fruit mesocarp flavor, color, aroma, and texture that have a direct impact on the fruit organoleptic quality. By studying the proteomic changes that are triggered during ripening, it would be possible to underscore some of the critical molecular processes involved in this transition. During this research, proteins involved in hormone, soluble sugars, organic acids, lipids, specialized metabolism and vesicle mediated trafficking and protein transport were correlated with this transition, and their possible role in fruit ripening is discussed below.
There is multiple evidence that the plant hormone ethylene is involved in the regulation of the ripening process in climacteric fleshy fruit. Upon binding to its receptors, ethylene’s signal is propagated to several downstream components which in turn target promoters of many ethylene-inducible genes, directly involved in the dramatic changes that occur during the transition from mature to ripe fruit . The ACC synthase (ACS) and ACC oxidase (ACO) enzymes are responsible for turning S-Adenosyl methionine (SAM) into ethylene. In peach, the abundance of the ACO isoform ACO1 (Prupe.3G209900) transcript and protein correlates very closely with fruit ripening [27, 55, 56]. In this work, ACO1 also displayed a similar pattern, being more abundant in ripe fruit than in mature fruit (Table 1, Figure 3D), validating ethylene production measured on the mature and ripe fruit stages at the molecular level .
The possible signaling cascades that modulate ethylene biosynthesis in climacteric fruit are poorly understood. Recently, in apple (Malus×domestica) and tomato (Solanum lycopersicum), both climacteric fruits, Feronia-like receptor kinases (FERLs) were shown to act as negative regulators of fruit ripening by inhibiting ethylene production . In the current study, a P. persica FERL (Prupe.6G295900), with over 75% of identity with the apple MdFERL1 and the tomato SlFERL1, was characterized as more abundant in mature than in ripe fruit (Table 1). In addition, upstream key regulators of FERL, such as BRASSINOSTEROID-SIGNALING KINASE (BSK) and BRI1 SUPPRESSOR (BSU) , were also more abundant in mature than in ripe fruit. This pattern suggests that this signaling pathway could regulate ethylene biosynthesis during peach fruit ripening, as its downregulation in the transition from mature to ripe fruit is correlated with the increase in ethylene biosynthesis in ripe fruit.
The sugar alcohol sorbitol is the main metabolite used to mobilize photosynthesis-derived carbohydrates from leaves to fruits in Rosaceae , being highly correlated with fruit taste and aroma , and of great interest for fruit breeders given its nutritional and sweetener qualities . At a molecular level, sorbitol modulation could impact fruit quality by affecting sugar-acid balance and starch accumulation . How this effect is generated is not clear, but it is postulated that sorbitol is catabolized in the cytosol, being the main driver of structural compounds biosynthesis and respiration in the peach fruit . In mature fruit, sorbitol could be used to generate fructose, which in turn could be metabolized into fructose 6-phosphate (F6P), by the enzyme fructokinase (Prupe.1G196700), whose abundance is high at this stage (Figure 4B). F6P can be used to synthesize sucrose, the predominant soluble sugar in mature fruit, or enter the glycolytic pathway . A decrease in the accumulation of fructokinase in ripe fruits indicated an enhanced conversion of sucrose to fructose via suppression of sucrose synthesis and fructose phosphorylation. Similar results were observed in other peach cultivar , where a decrease in different isoforms of both hexokinase (ppa004610m/Prupe.1G444000) and fructokinase (ppa007069m/Prupe.3G160500) accumulation were observed in fruits ripening and senescence at room temperatures. In ripe fruit, the putative sorbitol transporter (SOT) (Prupe.8G101200) accumulated more than in mature fruit (Table 1). This protein is a close homologue to candidate SOTs in pear (PbSOT19/21) , apple (SOT6)  and sour cherry (P. cerasus, PcSOT1) . SOTs are represented by an expanded gene family in apple and peach , which is made up of 16 genes in P. persica. The ones that display the highest expression at the ripening stage were Prupe.8G101200 (PpePOL5)  and Prupe.3G071100 (Supplementary Figure 3B). Thus, the PpePOL5 transporter could be partially responsible for an increase in sorbitol content in ripe fruit of the O’Henry variety, compared to mature fruit .
An intriguing question still under debate is about the role of stored malate in fruit metabolism during the ripening process, as malate synthesis and not dissimilation is detected throughout ripening . Malate levels are mainly regulated by its synthesis due to cytosolic carboxylation of phosphoenolpyruvate (PEP), its degradation due to decarboxylation also in the cytosol or by the conversion of tri- and dicarboxylates in the mitochondria, glyoxysome or cytosol . Malate can be used as a sugar precursor through gluconeogenesis, to help regulate nitrogen metabolism , as well as valves to balance metabolic fluxes given their function in indirect transport of reducing equivalents . According to the proteomic profiles assessed in this study, malate would be catabolized by the gluconeogenesis process to different metabolites in mature and ripe fruit (Figure 4). In mature fruit, the higher abundance of the protein triosephosphate isomerase would point to a preferred catalysis of malate to glyceraldehyde 3-phosphate, a triose phosphate that can be oxidized into pyruvate, providing the mature fruit with ATP and NADH. In ripe fruit, the higher abundance of the enzyme phosphoenolpyruvate carboxykinase would help to keep the appropriate physicochemical conditions for the use of glutamate as nitrogen source for the biosynthesis of amino acids required at this stage . Our results also indicated a decrease in other organic acids such as citrate. The pyruvate dehydrogenase kinase (PDK) is an enzyme that inactivates the pyruvate dehydrogenase (PDH). PDK (Prupe.1G105800) was detected only in ripe fruits, thus we could argue that in ripe fruits PDH is inhibited, which could decrease the synthesis of acetyl-CoA an consequently the Krebs cycle organic acids. Our results are in agreement with very recent data by Zheng et al.  showing that in low acid peach cultivars such as O’Henry, PDK expression is increased in comparison to high acid peach cultivars, which would impact the citrate synthesis pathway and its accumulation.
Among the soluble sugars present in the peach fruit, sucrose, fructose and glucose do not change much during the transition from mature to ripe fruit; in contrast to xylose, fucose and raffinose, according to an assessment of 15 P. persica varieties . In the current analysis, two key enzymes involved in raffinose biosynthesis (raffinose and stachyose synthases, Table 1, Figure 4A) were more accumulated during the mature stage, indicating that in the O’Henry variety this metabolite accumulation would occur at the mature stage. Raffinose is an important metabolite given its antioxidant properties and role in stress tolerance .
Starch biosynthesis and accumulation is believed to happen at the early stages of fruit development, followed by its consumption until almost undetectable levels at maturity . However, enzymes involved on starch biosynthesis, such as 1,4-alpha-glucan-branching enzyme (SBE, Prupe.1G354000) and glucose-1-phosphate adenylyltransferase small subunit (APS1/AGP, Prupe.3G192600) were still detected in mature fruit, with a drop in their levels in ripe fruit (Figure 3C). This same APS1/AGP was detected by iTraq proteome and was showed to decrease in fruits ripening at low temperatures . SBE was also detected by others in the mesocarp of ripe peach fruits , indicating that starch biosynthesis could still be active at later stages of fruit development. Another interesting fact is the increased accumulation of the atypical cysteine/histidine-rich thioredoxin 4 P. persica homologous (ACHT4, Prupe.7G001600, 64% identical) in ripe fruit. ACHT4 has been characterized in A. thaliana as a molecular switch of APS1, being able to quench APS1 activity . By combining decreased accumulation of SBE and APS1 with an increase of ACHT4, the ripe fruit metabolism could downregulate starch content at this final developmental stage.
Fruit aroma and lipid metabolism
Among the many dozens of volatiles peach fruits can produce, the γ- and δ-decalactones, C6 aldehydes and alcohols, terpenoids and volatile esters are the ones that are mainly related to fruit aroma [8, 74, 75]. Volatile esters are the product of alcohol acyltransferase-mediated biosynthesis, and degradation through carboxylesterase (CXE) activity . In tomato, low ester levels, which positively correlate with fruit liking, were associated to the enzyme SlCXE1 . In peach, the carboxylesterase PpCXE1 (Prupe.8G121900) was shown to be able to degrade volatile acetate esters . In the present study, two CXE proteins were found to be more abundant in mature fruit than in ripe fruit, Prupe.1G439300 and Prupe.8G121500. The genes coding for these proteins were top-7 and top-8 in expression level in ripe fruit, among 19 putative CXEs in P. persica . Prupe.1G439300 is the best homologue to the tomato SlCXE1  and its protein-coding gene displayed a peak of expression in ripe fruit (GEO dataset GSE71561), being a good candidate for further characterization.
Fruits can synthesize lactones that attract feeders for seed dispersal, mostly the γ-lactones decano-4-lactone and/or dodecano-4-lactone . These compounds, which primarily derive from oleic acids or derivatives, are metabolized by a series of enzymes, including epoxide hydrolases, to generate lactones such as undecano-4-lactone . They can be found both in fruit skin as well as mesocarp . According to our data, lactone metabolism would also be differentially regulated in mature and ripe fruit, due to preferential accumulation of epoxide hydrolase EPH2 (Prupe.7G162300)  in mature fruit. On the other hand, the SRK2C kinase (Prupe.6G192200), which has been correlated to lactones using QTL analysis , is exclusively found in ripe fruit (Table 1). The target of SRK2 is unknown, and given its high expression (GEO dataset GSE71561), differential accumulation during the ripening process (Table 1), and correlation with lactone biosynthesis, it becomes an interesting candidate for further characterization.
Fruit ripening has been characterized as a senescing process, with cell membrane deterioration being the hallmark. Phospholipase D (PLD) is among the most relevant proteins involved in cell membrane deterioration in ripening fruits, acting upon phospholipids to generate phosphatidic acid (PA) and a free head group . PLD action is also able to trigger a myriad of cellular processes, and therefore its activity is tightly regulated . PLDs have been grouped into five classes (α, β, γ, δ and ζ) according to several parameters such as domain structure and biochemical properties. Similar to most plant PLDs, PLDδ requires Ca2+ and is stimulated by phosphatidylinositol 4,5-bisphosphate (PIP2) . However, Arabidopsis PLDδ displays a distinctive property, which is to be activated by oleic acid . A peach PLDδ (Prupe.7G17540) was found to be more abundant in mature fruit than in ripe fruit (Table 1).
Fatty acid desaturase 1 (FAD1, Prupe.7G076500), a ω-6 Oleate desaturase , displayed increased abundance in ripe fruit (Figure 4B, panel II), a pattern similar to the one displayed by its transcript in the P. persica Yulu variety , in the GSE71561 dataset, and by its closest orthologue in Fragaria vesca . FAD1 gene expression was also sensitive to the ethylene signal transduction pathway inhibitor 1-methylcyclopropene (1-MCP), a compound known to negatively affect peach fruit aroma . This increase could imply that FAD1 could be involved in linoleic and linolenic acids biosynthesis in peach ripe fruit , or could be involved in γ-decalactone biosynthesis, as proposed for the F. vesca FaFAD1 .
Aquaporins are transmembrane proteins that enable water and small neutral solute translocation across cellular membranes. Among the different types of aquaporins, those located in the vacuolar membranes are called tonoplast intrinsic proteins (TIPs). TIPs are classified into five groups (TIP1-5), and are able to transport hydrogen peroxide and glycerol, in addition to water . The P. persica aquaporin TIP1-1 (Prupe.7G125900) was found to be more abundant in ripe than in mature fruit mesocarp (Table 1). A close homologous (93% identity) protein-coding gene from sweet cherry (P. avium) was among the three most expressed aquaporins in the fruit, being mainly expressed in mesocarp throughout fruit development . The P. persica PpTIP1-1 transcriptional pattern was very similar (GEO dataset GSE71561), with the gene being expressed at a regular level throughout mesocarp development. This indicates that both Prunus TIP1-1 aquaporins conserved their tissue localization and expression patterns. Moreover, it indicates that these aquaporins could be key to transport water across the vacuole in the Prunus fruit mesocarp .
Vesicle mediated trafficking and protein transport
Protein trafficking, mediated by vesicular transport, was also shown to be a very important process during the fruit ripening transition (Figures 2 and 3). Vesicle transport can be divided in three broad consecutive steps: vesicle budding from a donor membrane, trafficking and fusion with a specific acceptor membrane. Prior to the fusion stage, a set of tethering factors allows the vesicle to be in close proximity to the target membrane, thus helping vesicle trafficking organization. Recently, the Transport Protein Particle (TRAPP) complex, a multisubunit tethering complex, was experimentally characterized in Arabidopsis , including all 13 mammalian TRAPP subunits as well as an additional plant-specific component, the TRAPP-Interacting Plant Protein (TRIPP). TRIPP plays important roles in trafficking-dependent processes, including the formation of new cell walls and reproductive development . Among the 14 A. thaliana TRAPP subunits, we detected 7 homologues (SupplementaryTable 1). Besides TRS20, TRIPP and TRS120, which have been shown to interact, were found to be more abundant in mature fruit (Table 1). Both TRIPP and TRS120 are part of TRAPPII, one of a variety of TRAPP modular forms. TRAPPII mutants displayed altered levels of methyl-esterified pectins at cell plates, pointing to a role of this complex in the transport of pectins . Changes in pectin metabolism are one of the hallmarks of the softening and textural changes in melting flesh peach triggered by fruit ripening . Thus, our results help to link cell wall metabolism with vesicle mediated transport of proteins and polysaccharides through the downregulation of TRIPP and TRS120 between mature and ripe fruit.
TRAPPII have also been pointed as a guanine exchange factors (GEFs) for RabA GTPases [88, 89]. RabA GTPases can regulate membrane fusion events and other cell organelle processes once they are recruited to their specific membrane compartment and activated by their cognate RabGEF. Among the proteins downregulated during the mature to ripe fruit transition we found a homologous of RABA5b, a RabA GTPase. Interestingly, the P. persica TRIPP, TRS120 and RABA5b displayed a dramatic and linear increase in transcript abundance from 81 to 125 DAP, pointing to a specific role in fruit development for these 3 proteins, and TRIPP-TRS120 TRAPPII as potential GEFs for RABA5b.
Another key component of the vesicle trafficking machinery are the adaptor protein complexes, which participate in the selection of the vesicles specific transported cargo. Using a combination of organelle density gradients with proteome analysis, Pertl-Obermeyer et al.  indicated that the adaptor protein complex 4 (AP4) participates in delivering cell wall proteins. AP4 would also be involved in sorting transmembrane proteins to the vacuole , being a key component of the post Golgi trafficking. Alterations in the cell wall proteome content as well as active vacuolar sorting have been associated with fruit ripening [14, 92]. We detected two AP4 subunits down-regulated during the transition from mature to ripe fruit (Table 1). Together, our results indicates that an active vesicle mediated-traffic is operating at mature peach fruit, and that during the transition to ripe fruit this process shifts into a less active state, possibly associated with the fruit senescence.
Transcription factors assessment
Analysis of possible transcription factors (TFs) that could regulate protein-coding genes expressed mostly or specifically during fruit ripening is of high interest given its application in driving the expression of genes of interest in this organ. Their identification could help to uncover the transcription regulation that underlies the extensive changes triggered by fruit ripening. TFs associated to ripening in climacteric fruit have been identified in apricot [93, 94], melon , banana [96, 97], tomato [98, 99], papaya [100, 101, 102], among others. By 2015, around 1,533 TFs were identified in P. persica , however just a few have been characterized and even less have been associated to the fruit ripening process. MADS-box PrupeSEP1 (Prupe.3G249400) , TCP PpTCP.A2 (Prupe.1G272500) , homeobox PpHB.G7 (Prupe.1G416800) , AP2/ERF PpERF2, PpERF3 and PpERF.E2 (Prupe.5G090800, Prupe.7G194400 and Prupe.3G032300) [54, 105], ARFs PpARF5 (Prupe.1G368300)  and EIN3-like PpEIL1 to 5 (Prupe.6G018200, Prupe.2G058400, Prupe.2G058500, Prupe.6G181600, Prupe.2G070300)  are among those TFs already characterized and associated with peach fruit ripening. NAC domain TFs were enriched among the TFs that targeted the genes whose respective proteins were more abundant in mature compared to ripe fruit. Several NAC TFs have been reported to be involved in regulating tomato , melon  and papaya  fruit ripening, indicating that NAC TFs role in fruit ripening is evolutionarily conserved . In peach, both ACS and ACO genes, involved in ethylene biosynthesis, display NAC transcription factor binding motifs, and several NAC TFs and key fruit ripening genes display a ripening-specific expression pattern . Protein-coding genes whose products were more abundant in ripe compared to mature fruit also displayed an enrichment as NAC TFs targets, however they were mainly enriched as MYB TFs targets. MYB ripening-related TFs have been characterized in Lycium ruthenicum , in tomato , in papaya  and in plum (P. salicina) , indicating that MYBs might also be key in modulating the peach fruits pigmentation, flavour, and texture changes triggered by the fruit ripening .
Just one TF would have as targets the protein-coding genes for both mature and ripe fruit when compared to all 1,663 proteins identified in the present work. This protein was a HB40-homolog protein (Prupe.7G149700), which displayed a strong expression peak at the stage of fruit ripening (Figure 6B). In tomato, the MADS box TF RIPENING INHIBITOR (RIN) is known as one of the earliest acting ripening regulators. The best tomato homologous of Prupe.7G149700, the gene Solyc02g085630 (64% identity), was among the RIN targets identified by chromatin immunoprecipitation coupled with DNA microarray analysis (ChIP-chip) , indicating that these HB40-homolog proteins could be effectors of RIN.
Plant Proteomics analysis has benefited, in the last years, from the increasing development of mass spectrometry (MS), the publication of hundreds of plant genomes (430 to date)  and generation of customized bioinformatics tools and pipelines. 1D-gel electrophoresis followed by LC/MS-MS analysis (Figure 1), has the great advantage of being straightforward to execute and analyze, as well as being among the most robust pipelines for proteomic analysis . Besides gel based, gel free , antibody chips  and MS-imaging  are also available for analyzing plant sample proteome contents. However, the most promising approaches are related to how validated and integrate proteomics data with other omics approaches in order to get a more systemic vision of the processes under evaluation . In this work we integrated proteomics data generated by us and others, as well as different sets of transcriptomic data publicly available to unveil information regarding critical molecular processes involved in the peach fruit ripening.
P. persica belongs to the Rosaceae family, whose species have developed a wide array of fruit types, including drupe, pome, drupetum, achene, and achenetum, making it one of the most informative plant family to perform comparative developmental and evolutionary studies . P. persica displays a drupe-type of fruit, where a fleshy fruit encloses a lignified endocarp surrounding a seed. The presence of this lignified endocarp imposes a challenge to the proper fruit development and ripening, since the phenylpropanoids allocation must be carefully controlled for the endocarp lignification during development or to the biosynthesis of flavour/aroma compounds in the ripe fruit mesocarp . This characteristic is particular to this kind of fruit, making the extrapolation of what is known in the so far best fleshy fruit model tomato ripening, limited. In addition, as mentioned previously, the tomato ripening regulatory circuit is mainly based on the action of MADS TFs, whereas in peach NAC-type TFs would have a predominant role in controlling the ripening regulatory circuit . Assessing the molecular mechanisms, using integrated omics approaches, of plants with combinations of the slow ripening (SR) allele, which can render plants with unique phenotypes , as well as the results of different pre-harvest treatments [67, 123] that affects the fruit quality will help to uncover new key players that are probably particular to drupe-type fruits.