The perennial fruit tree proteogenomics atlas: a spatial map of the sweet cherry proteome and transcriptome

Proteo-metabolomic analysis of fruits reveals molecular insights into variations among Italian Sweet Cherry (Prunus avium L.) accessions

Mass spectrometry-based proteomics and metabolomics tackle the complex interactions between proteins and metabolites in fruits. Independently used to discern phenotypic disparities among plant accessions, these analytical approaches complement well-established DNA fingerprinting methods for assessing genetic variability and hereditary distance. To verify the applicability of integrated proteomic and metabolomic procedures in evaluating phenotypic differences between sweet cherry cultivars, and to potentially relate these findings to specific pomological traits, we conducted a comparative analysis of fruits from ten Italian accessions. We identified 3786 proteins, of which 288 exhibited differential representation between ecotypes, including key components influencing fruit quality and allergenic potential. Furthermore, 64 polyphenols were identified, encompassing anthocyanins, hydroxycinnamic acids, flavanols, hydroxybenzoic acids, flavonols, and flavanones subgroups. Multivariate analysis of total quantitative data outlined cultivar differences and phenotypic relationships. Coherent associations between proteomic and metabolomic data underscored their complementary role in characterizing genetic relationships elucidated through DNA fingerprinting techniques. Proteo-metabolomic results verified a certain correlation between the relative abundance of specific polyphenols, enzymes involved in their metabolism, and color characteristics of fruits. These findings highlight the significance of integrating results from diverse omics approaches to reveal molecular drivers of ecotype-specific traits and identify biomarkers for selecting and breeding cultivars in the next future.

Characterization analyses of MADS-box genes highlighting their functions with seed development in Ricinus communis

The MADS-box gene family plays a pivotal role in regulating floral organ development and various aspects of plant growth. Despite its well-established importance in many species, the function and evolution of MADS-box genes in Ricinus communis (castor) remain unexplored. This study presents an extensive genome-wide analysis of the MADS-box gene family in castor, covering their physicochemical characteristics, phylogenetics, gene architecture, chromosomal distribution, evolutionary dynamics, expression profiles, and co-expression networks. In total, 56 MADS-box genes were categorized into two main phylogenetic groups: type-I and type-II, which were further subdivided into three and two subgroups, respectively. Segmental duplication was found to be the primary driver of MADS-box gene expansion in castor, while purifying selection was evident across the entire gene family, as indicated by the Ka/Ks ratio. In-depth analyses of gene expression, promoter motifs, co-expression networks, and experimental validation (Y1H assays and qRT-PCR) revealed that RcMADS16 and RcMADS41 are key regulators of castor seed development, with RcMADS16 may involve in seed coat formation and RcMADS41 in oil accumulation. This study not only provides the first detailed insight into the evolutionary and functional landscape of MADS-box genes in castor, but also establishes a foundation for future investigations into the role of these genes in seed and organ development, both in castor and other plant species.

Involvement of sweet cherry PavPP2C59 in negatively regulating fruitlet abscission and fruit ripening

Abnormal fruitlet drop poses a significant challenge to the cherry industry, and ABA is known to be involved in organ abscission. The protein phosphatase 2Cs (PP2Cs) plays a crucial role in ABA signaling; however, their functions in the abscission of sweet cherry fruitlets remain unexplored. Currently, 17 F-clade PP2C members were identified in the sweet cherry, among which PavPP2C59 was significantly downregulated in fruit ripening and abscission. The PavPP2C59 promoter exhibited GUS expression activity in the abscission petals of Arabidopsis thaliana, which decreased during silique development and ripening and responded to IAA or ABA treatment. Overexpression of PavPP2C59 in A. thaliana promoted root elongation, delayed petal abscission, and shortened silique length. Yeast one-hybrid and dual-luciferase reporter assays demonstrated that PavDOF18 and PavERF110 interacted with the PavPP2C59 promoter and inhibited its transcription, respectively. PavDOF18 and PavERF110 are localized in the nucleus as transcriptional repressors and have regulatory functions in fruit development and abscission. Y2H and luciferase complementation imaging assays revealed that PavPP2C59 interacts with PavRDUF1, which may lead to its ubiquitination and subsequent degradation. These findings indicate that PavPP2C59 negatively regulates fruitlet abscission and ripening in sweet cherry, providing new insights for a better understanding of fruit abscission in plants.

Telomere-to-telomere genome and multi-omics analysis of Prunus avium cv. Tieton provides insights into its genomic evolution and flavonoid biosynthesis

The European sweet cherry (Prunus avium) is highly valued for its superior quality, delectable taste, and robust stress resistance, leading to its extensive cultivation in the world. However, the previous incomplete genome assemblies have impeded its evolution and genetic regulation studies. In this study, we generated a Telomere-to-Telomere gap-free genome assembly of P. avium cv. Tieton, using advanced sequencing technologies. The assembled genome comprises eight pseudochromosomes with a genome size of 342.23 Mb and a contig N50 of 40.66 Mb. Comparative genomic analysis identified several unique stress resistance-related genes, possibly associated with the species' environmental adaptation. The integrative analyses of genomics, transcriptomes and metabolomes identified some key structural genes and metabolites crucial to flavonoid biosynthesis of sweet cherry. Our analyses revealed that 85 flavonoid metabolites, which are highly differentially accumulated among five tissues (flesh, stem, leaf, bud, and seed) of cherry. Interestingly, eight abundant flavonoids (Narcissoside, Typhaneoside, Myricetin 3-0-galactoside, Diosmin, Neohesperidin, Liquiritin apioside, 5,6,7-Trimethoxyflavone and Oroxin B) were highly accumulated in cherry flesh tissues. The gene-metabolite correlation analysis revealed that seven genes (HTC8, HTC6, CYP75B1_9, CYP75B1_10, 4CL1, DFR1, and FLS1) significantly regulated flavonoid accumulation in cherry flesh. Additionally, some structural genes (4CL6, PAL3, CYP75A2, F3H1, CYP75B1_8, and CYP75B1_10) were identified in the flavonoid biosynthetic pathway and were highly expressed, aligning with high flavonoid metabolite content in cherry flesh. These identified genes and metabolites are likely pivotal in conferring sweet cherry's stress resistance and high-quality traits. These findings offer deep insights into the mechanisms of genomic evolution and flavonoid biosynthesis, which also lay a solid foundation for further function genomics studies and breeding improvement in cherry.

Unveiling the power of PavGID1s: the critical player in sweet cherry flower bud dormancy release

Exogenous hormones can regulate bud dormancy release, particularly in cases where inadequate winter chill accumulation due to global warming affects perennial plants. Gibberellin (GA) is recognized as a critical signal for dormancy release in woody perennials. This study explores the influence of GA and its signaling components on the dormancy release in sweet cherry. The external application of GA4 + 7 significantly promoted the bud break rate and dormancy release. Notably, there was a substantial accumulation of GA3, GA4, and GA7 in the buds, accompanied by a reduced concentration of abscisic acid (ABA) following GA treatment. RNA-Seq identified 8,610 differentially expressed transcripts in GA-treated buds compared to the Mock group. Transcriptome sequencing revealed differential expressions of PavGID1s, the GA receptor GID1, in sweet cherry flower buds after GA treatment. These findings were further verified across different seasons in sweet cherry. In both PavGID1b and PavGID1c, the open reading frame (ORF) is 1,032 bases long and encodes 344 amino acids. Overexpression of PavGID1b and PavGID1c resulted in early flowering and higher plants in Arabidopsis. However, these genes have opposing roles in seed germination in Arabidopsis. Furthermore, PavWRKY31 may regulate the stabilization and release of dormancy by modulating the transcriptional level of PavGID1c. PavGA20ox-2 and PavGID2 may also influence sweet cherry dormancy release by interacting with GID1s and affecting DELLA protein stability. These results provide a theoretical basis for understanding the regulatory effect of gibberellin on the bud dormancy of plants.

Identification of Proteoforms Related to Nelumbo nucifera Flower Petaloid Through Proteogenomic Strategy

Nelumbo nucifera is an aquatic plant with a high ornamental value due to its flower. Despite the release of several versions of the lotus genome, its annotation remains inefficient, which makes it difficult to obtain a more comprehensive knowledge when -omic studies are applied to understand the different biological processes. Focusing on the petaloid of the lotus flower, we conducted a comparative proteomic analysis among five major floral organs. The proteogenomic strategy was applied to analyze the mass spectrometry data in order to dig out novel proteoforms that are involved in the petaloids of the lotus flower. The results revealed that a total of 4863 proteins corresponding to novel genes were identified, with 227 containing single amino acid variants (SAAVs), and 72 originating from alternative splicing (AS) genes. In addition, a range of post-translational modifications (PTMs) events were also identified in lotus. Through functional annotation and homology analysis with 24 closely related plant species, we identified five candidate proteins associated with floral organ development, which were not identified by ordinary proteomic analysis. This study not only provides new insights into understanding the mechanism of petaloids in lotus but is also helpful in identifying new proteoforms to improve the annotation of the lotus genome.

PavSPLs are key regulators of growth, development, and stress response in sweet cherry

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes are plant-specific transcription factors essential for plant growth, development, and stress responses. Their roles in sweet cherry are not well understood. In this study, we identified and isolated 16 SPL genes from the sweet cherry genome, categorizing them into 5 subfamilies, with 12 PavSPLs predicted as miR156 targets. Promoter regions of PavSPLs contain cis-elements associated with light, stress, and phytohormone responses, indicating their role in biological processes and abiotic stress responses. Seasonal expression analysis showed that PavSPL regulates sweet cherry recovery after dormancy. Gibberellin (GA) treatment reduced PavSPL expression, indicating its role in GA-mediated processes. PavSPL14 overexpression in Arabidopsis thaliana resulted in earlier flowering and increased plant height and growth. Yeast two-hybrid assays showed an interaction between PavSPL14 and DELLA protein PavDWARF8, suggesting PavSPL14 and PavDWARF8 co-regulate growth and development. These findings lay the groundwork for further research on PavSPL function in sweet cherry.

Proteomics: An Essential Tool to Study Plant-Specialized Metabolism

Plants are a valuable source of specialized metabolites that provide a plethora of therapeutic applications. They are natural defenses that plants use to adapt and respond to their changing environment. Decoding their biosynthetic pathways and understanding how specialized plant metabolites (SPMs) respond to biotic or abiotic stress will provide vital knowledge for plant biology research and its application for the future sustainable production of many SPMs of interest. Here, we focus on the proteomic approaches and strategies that help with the study of plant-specialized metabolism, including the: (i) discovery of key enzymes and the clarification of their biosynthetic pathways; (ii) study of the interconnection of both primary (providers of carbon and energy for SPM production) and specialized (secondary) metabolism; (iii) study of plant responses to biotic and abiotic stress; (iv) study of the regulatory mechanisms that direct their biosynthetic pathways. Proteomics, as exemplified in this review by the many studies performed to date, is a powerful tool that forms part of omics-driven research. The proteomes analysis provides an additional unique level of information, which is absent from any other omics studies. Thus, an integrative analysis, considered versus a single omics analysis, moves us more closely toward a closer interpretation of real cellular processes. Finally, this work highlights advanced proteomic technologies with immediate applications in the field.

The Zea mays PeptideAtlas: A New Maize Community Resource

This study presents the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize collected from ProteomeXchange were reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds and many sample types and experimental conditions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq, and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of proteins in the most recent B73 nuclear genome annotation. Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other B73 genome annotations will improve maize genome annotation. We also illustrate the high-confidence detection of unique W22 proteins. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, and K-hydroxyisobutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical, and biological metadata. This new PeptideAtlas is integrated in MaizeGDB with a peptide track in JBrowse.

Ethylene biosynthesis and signal transduction during ripening and softening in non-climacteric fruits: an overview

In recent years, the ethylene-mediated ripening and softening of non-climacteric fruits have been widely mentioned. In this paper, recent research into the ethylene-mediated ripening and softening of non-climacteric fruits is summarized, including the involvement of ethylene biosynthesis and signal transduction. In addition, detailed studies on how ethylene interacts with other hormones to regulate the ripening and softening of non-climacteric fruits are also reviewed. These findings reveal that many regulators of ethylene biosynthesis and signal transduction are linked with the ripening and softening of non-climacteric fruits. Meanwhile, the perspectives of future research on the regulation of ethylene in non-climacteric fruit are also proposed. The overview of the progress of ethylene on the ripening and softening of non-climacteric fruit will aid in the identification and characterization of key genes associated with ethylene perception and signal transduction during non-climacteric fruit ripening and softening.

Plant genome information facilitates plant functional genomics

MAIN CONCLUSION

In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.

Transcriptomic Analysis of Alternative Splicing Events during Different Fruit Ripening Stages of Coffea arabica L

To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different ripening stages of fruit development. From this dataset, a total of 3824, 2445, 2564, 2990, and 3162 DSGs were identified in a comparison of different fruit ripening stages. The largest proportion of DSGs, approximately 65%, were of the skipped exon (SE) type. Biologically, 9 and 29 differentially expressed DSGs in the spliceosome pathway and carbon metabolism pathway, respectively, were identified. These DSGs exhibited significant variations, primarily in S1 vs. S2 and S5 vs. S6, and they involve many aspects of organ development, hormone transduction, and the synthesis of flavor components. Through the examination of research findings regarding the biological functions and biochemical pathways associated with DSGs and DEGs, it was observed that six DSGs significantly enriched in ABC transporters, namely, LOC113712394, LOC113726618, LOC113739972, LOC113725240, LOC113730214, and LOC113707447, were continually down-regulated at the fruit ripening stage. In contrast, a total of four genes, which were LOC113732777, LOC113727880, LOC113690566, and LOC113711936, including those enriched in the cysteine and methionine metabolism, were continually up-regulated. Collectively, our findings may contribute to the exploration of alternative splicing mechanisms for focused investigations of potential genes associated with the ripening of fruits in C. arabica.

Transcriptomic-Proteomic Analysis Revealed the Regulatory Mechanism of Peanut in Response to Fusarium oxysporum

Peanut Fusarium rot, which is widely observed in the main peanut-producing areas in China, has become a significant factor that has limited the yield and quality in recent years. It is highly urgent and significant to clarify the regulatory mechanism of peanuts in response to Fusarium oxysporum. In this study, transcriptome and proteome profiling were combined to provide new insights into the molecular mechanisms of peanut stems after F. oxysporums infection. A total of 3746 differentially expressed genes (DEGs) and 305 differentially expressed proteins (DEPs) were screened. The upregulated DEGs and DEPs were primarily enriched in flavonoid biosynthesis, circadian rhythm-plant, and plant-pathogen interaction pathways. Then, qRT-PCR analysis revealed that the expression levels of phenylalanine ammonia-lyase (PAL), chalcone isomerase (CHI), and cinnamic acid-4-hydroxylase (C4H) genes increased after F. oxysporums infection. Moreover, the expressions of these genes varied in different peanut tissues. All the results revealed that many metabolic pathways in peanut were activated by improving key gene expressions and the contents of key enzymes, which play critical roles in preventing fungi infection. Importantly, this research provides the foundation of biological and chemical analysis for peanut disease resistance mechanisms.

Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants

Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.

Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (Citrullus lanatus)

Fruit ripening is a highly complicated process that is accompanied by the formation of fruit quality. In recent years, a series of studies have demonstrated post-transcriptional control play important roles in fruit ripening and fruit quality formation. Till now, the post-transcriptional mechanisms for watermelon fruit ripening have not been comprehensively studied. In this study, we conducted PacBio single-molecule long-read sequencing to identify genome-wide alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. In total, 6,921,295 error-corrected and mapped full-length non-chimeric (FLNC) reads were obtained. Notably, more than 42,285 distinct splicing isoforms were derived from 5,891,183 intron-containing full-length FLNC reads, including a large number of AS events associated with fruit ripening. In addition, we characterized 21,506 polyadenylation sites from 11,611 genes, 8703 of which have APA sites. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that fructose and mannose metabolism, starch and sucrose metabolism and carotenoid biosynthesis were both enriched in genes undergoing AS and APA. These results suggest that post-transcriptional regulation might potentially have a key role in regulation of fruit ripening in watermelon. Taken together, our comprehensive PacBio long-read sequencing results offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of watermelon fruit ripening.

Redox Regulation of Salt Tolerance in Eutrema salsugineum by Proteomics

Salt stress severely restricts plant growth and crop production, which is accompanied by accumulation of reactive oxygen species (ROS) that disturb cell redox homeostasis and oxidize redox-sensitive proteins. Eutrema salsugineum, a halophytic species closely related to Arabidopsis, shows a high level of tolerance to salinity and is increasingly used as a model plant in abiotic stress biology. To understand redox modifications and signaling pathways under salt stress, we used tandem mass tag (TMT)-based proteomics to quantify the salt-induced changes in protein redox modifications in E. salsugineum. Salt stress led to increased oxidative modification levels of 159 cysteine sites in 107 proteins, which play roles in carbohydrate and energy metabolism, transport, ROS homeostasis, cellular structure modulation, and folding and assembly. These lists of unknown redox reactive proteins in salt mustard lay the foundation for future research to understand the molecular mechanism of plant salt response. However, glutathione peroxidase (GPX) is one of the most important antioxidant enzymes in plants. Our research indicates that EsGPX may be involved in regulating ROS levels and that plants with overexpressed EsGPX have much improved salt tolerance.

Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit

Apples grown in high heat, high light, and low humidity environments are at risk for sun injury disorders like sunburn and associated crop losses. Understanding the physiological and molecular mechanisms underlying sunburn will support improvement of mitigation strategies and breeding for more resilient varieties. Numerous studies have highlighted key biochemical processes involved in sun injury, such as the phenylpropanoid and reactive oxygen species (ROS) pathways, demonstrating both enzyme activities and expression of related genes in response to sunburn conditions. Most previous studies have focused on at-harvest activity of a small number of genes in response to heat stress. Thus, it remains unclear how stress events earlier in the season affect physiology and gene expression. Here, we applied heat stress to mid-season apples in the field and collected tissue along a time course-24, 48, and 72 h following a heat stimulus-to investigate dynamic gene expression changes using a transcriptomic lens. We found a relatively small number of differentially expressed genes (DEGs) and enriched functional terms in response to heat treatments. Only a few of these belonged to pathways previously described to be involved in sunburn, such as the AsA-GSH pathway, while most DEGs had not yet been implicated in sunburn or heat stress in pome fruit.

Current insights into posttranscriptional regulation of fleshy fruit ripening

Fruit ripening is a complicated process that is accompanied by the formation of fruit quality. It is not only regulated at the transcriptional level via transcription factors or DNA methylation but also fine-tuned after transcription occurs. Here, we review recent advances in our understanding of key regulatory mechanisms of fleshy fruit ripening after transcription. We mainly highlight the typical mechanisms by which fruit ripening is controlled, namely, alternative splicing, mRNA N6-methyladenosine RNA modification methylation, and noncoding RNAs at the posttranscriptional level; regulation of translation efficiency and upstream open reading frame-mediated translational repression at the translational level; and histone modifications, protein phosphorylation, and protein ubiquitination at the posttranslational level. Taken together, these posttranscriptional regulatory mechanisms, along with transcriptional regulation, constitute the molecular framework of fruit ripening. We also critically discuss the potential usage of some mechanisms to improve fruit traits.

Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton

Colored cotton is also called eco-cotton because of its natural color fiber. It is inferior in yield and quality than white cotton. The underlying regulatory genes involved in fiber quality and pigment synthesis are not well understood. This study aimed to investigate the transcriptomic and proteomic changes during fiber development in a brown cotton cultivar (Z161) and a white cotton cultivar. The differential proteins with the same expression trend as genes were significantly and positively correlated with corresponding fold changes in expression. Enrichment analysis revealed that Z161, enriched in fiber elongation genes related to flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism, and many more genes (proteins) are up-regulated. Moreover, 164 glycosyltransferases genes, 15 MYB-bHLH-WD40 genes, and other transcription factors such as C2H2 (12), ERF (11), and NAC (7) were preferentially expressed in Z161. Weighted correlation network analysis identified fatty acid synthesis and energy metabolism as the principal metabolic pathways in both cotton genotypes during fiber development. Identified 15 hub genes will provide important insights for genetic manipulation of fiber quality and pigment deposition balance in brown cotton fibers.

A large-scale proteogenomic atlas of pear

Pear is an important fruit tree that is widely distributed around the world. The first pear genome map was reported from our laboratory approximately 10 years ago. To further study global protein expression patterns in pear, we generated pear proteome data based on 24 major tissues. The tissue-resolved profiles provided evidence of the expression of 17 953 proteins. We identified 4294 new coding events and improved the pear genome annotation via the proteogenomic strategy based on 18 090 peptide spectra with peptide spectrum matches >1. Among the eight randomly selected new short coding open reading frames that were expressed in the style, four promoted and one inhibited the growth of pear pollen tubes. Based on gene coexpression module analysis, we explored the key genes associated with important agronomic traits, such as stone cell formation in fruits. The network regulating the synthesis of lignin, a major component of stone cells, was reconstructed, and receptor-like kinases were implicated as core factors in this regulatory network. Moreover, we constructed the online database PearEXP (http://www.peardb.org.cn) to enable access to the pear proteogenomic resources. This study provides a paradigm for in-depth proteogenomic studies of woody plants.

A comparative proteomic analysis provides insight into the molecular mechanism of bud break in longan

BACKGROUND

The timing of bud break is very important for the flowering and fruiting of longan. To obtain new insights into the underlying regulatory mechanism of bud break in longan, a comparative analysis was conducted in three flower induction stages of two longan varieties with opposite flowering phenotypes by using isobaric tags for relative and absolute quantification (iTRAQ).

RESULTS

In total, 3180 unique proteins were identified in 18 samples, and 1101 differentially abundant proteins (DAPs) were identified. "SX" ("Shixia"), a common longan cultivated variety that needs an appropriate period of low temperatures to accumulate energy and nutrients for flower induction, had a strong primary inflorescence, had a strong axillary inflorescence, and contained high contents of sugars, and most DAPs during the bud break process were enriched in assimilates and energy metabolism. Combined with our previous transcriptome data, it was observed that sucrose synthase 6 (SS6) and granule-bound starch synthase 1 (GBSSI) might be the key DAPs for "SX" bud break. Compared to those of "SX", the primary inflorescence, axillary inflorescence, floral primordium, bract, and prophyll of "SJ" ("Sijimi") were weaker. In addition, light, rather than a high sugar content or chilling duration, might act as the key signal for triggering bud break. In addition, catalase isozyme 1, an important enzyme in the redox cycle, and RuBisCO, a key enzyme in the Calvin cycle of photosynthetic carbon assimilation, might be the key DAPs for SJ bud break.

CONCLUSION

Our results present a dynamic picture of the bud break of longan, not only revealing the temporal specific expression of key candidate genes and proteins but also providing a scientific basis for the genetic improvement of this fruit tree species.

Application of quantitative proteomics to investigate fruit ripening and eating quality

The consumption of fruit and vegetables play an important role in human nutrition, dietary diversity and health. Fruit and vegetable industries impart significant impact on our society, economy, and environment, contributing towards sustainable development in both developing and developed countries. The eating quality of fruit is determined by its appearance, color, firmness, flavor, nutritional components, and the absence of defects from physiological disorders. However, all of these components are affected by many pre- and postharvest factors that influence fruit ripening and senescence. Significant efforts have been made to maintain and improve fruit eating quality by expanding our knowledge of fruit ripening and senescence, as well as by controlling and reducing losses. Innovative approaches are required to gain better understanding of the management of eating quality. With completion of the genome sequence for many horticultural products in recent years and development of the proteomic research technique, quantitative proteomic research on fruit is changing rapidly and represents a complementary research platform to address how genetics and environment influence the quality attributes of various produce. Quantiative proteomic research on fruit is advancing from protein abundance and protein quantitation to gene-protein interactions and post-translational modifications of proteins that occur during fruit development, ripening and in response to environmental influences. All of these techniques help to provide a comprehensive understanding of eating quality. This review focuses on current developments in the field as well as limitations and challenges, both in broad term and with specific examples. These examples include our own research experience in applying quantitative proteomic techniques to identify and quantify the protein changes in association with fruit ripening, quality and development of disorders, as well as possible control mechanisms.

Could Causal Discovery in Proteogenomics Assist in Understanding Gene-Protein Relations? A Perennial Fruit Tree Case Study Using Sweet Cherry as a Model

Genome-wide transcriptome analysis is a method that produces important data on plant biology at a systemic level. The lack of understanding of the relationships between proteins and genes in plants necessitates a further thorough analysis at the proteogenomic level. Recently, our group generated a quantitative proteogenomic atlas of 15 sweet cherry (Prunus avium L.) cv. ‘Tragana Edessis’ tissues represented by 29,247 genes and 7584 proteins. The aim of the current study was to perform a targeted analysis at the gene/protein level to assess the structure of their relation, and the biological implications. Weighted correlation network analysis and causal modeling were employed to, respectively, cluster the gene/protein pairs, and reveal their cause–effect relations, aiming to assess the associated biological functions. To the best of our knowledge, this is the first time that causal modeling has been employed within the proteogenomics concept in plants. The analysis revealed the complex nature of causal relations among genes/proteins that are important for traits of interest in perennial fruit trees, particularly regarding the fruit softening and ripening process in sweet cherry. Causal discovery could be used to highlight persistent relations at the gene/protein level, stimulating biological interpretation and facilitating further study of the proteogenomic atlas in plants.