Integration of Metabolomics and Transcriptomics to Explore Dynamic Alterations in Fruit Color and Quality in 'Comte de Paris' Pineapples during Ripening Processes.

Pineapple color yellowing and quality promotion gradually manifest as pineapple fruit ripening progresses. To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid contents as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Integration analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, RNA-seq analysis showed that structural genes, such as FLS, FNS, F3H, DFR, ANR, and GST, in the flavonoid biosynthetic pathway were upregulated, whereas the COMT, CCR, and CAD genes involved in lignin metabolism were downregulated as fruit ripening progressed. APX as well as PPO, and ACO genes related to the organic acid accumulations were upregulated and downregulated, respectively. Importantly, a comprehensive regulatory network encompassing genes that contribute to the metabolism of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlie fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples.

Low temperature storage alleviates internal browning of 'Comte de Paris' winter pineapple fruit by reducing phospholipid degradation, phosphatidic acid accumulation and membrane lipid peroxidation processes.

To uncover the mechanism underlying membrane lipid metabolism of low temperature induced internal browning tolerance in pineapple, membrane phospholipid alterations of harvested 'Comte de Paris' winter pineapple fruit stored at either 10 °C or 25 °C was investigated. Fruit stored at 10 °C developed low levels of internal browning as compared to fruit stored at 25 °C and was associated with high contents of phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, phosphatidylserine, and phosphatidylethanolamine, and low levels of phosphatidic acid. Storage at 10 °C down-regulated the expression levels of phospholipase As. Fruit stored at 10 °C also exhibited high ratio of unsaturated fatty acid to saturated fatty acid and index of unsaturated fatty acid level. These findings suggest that maintenance phospholipid abundance, reduction in phosphatidic acid accumulation and membrane lipid peroxidation may have contributed to the enhanced internal browning tolerance in 'Comte de Paris' winter pineapple fruit at low temperature storage.

Transcriptome and Metabolome Analyses Reveal the Involvement of Multiple Pathways in Flowering Intensity in Mango.

Mango (Mangifera indica L.) is famous for its sweet flavor and aroma. China is one of the major mango-producing countries. Mango is known for variations in flowering intensity that impacts fruit yield and farmers' profitability. In the present study, transcriptome and metabolome analyses of three cultivars with different flowering intensities were performed to preliminarily elucidate their regulatory mechanisms. The transcriptome profiling identified 36,242 genes. The major observation was the differential expression patterns of 334 flowering-related genes among the three mango varieties. The metabolome profiling detected 1,023 metabolites that were grouped into 11 compound classes. Our results show that the interplay of the FLOWERING LOCUS T and CONSTANS together with their upstream/downstream regulators/repressors modulate flowering robustness. We found that both gibberellins and auxins are associated with the flowering intensities of studied mango varieties. Finally, we discuss the roles of sugar biosynthesis and ambient temperature pathways in mango flowering. Overall, this study presents multiple pathways that can be manipulated in mango trees regarding flowering robustness.

The class III peroxidase gene family is involved in ascorbic acid induced delay of internal browning in pineapple.

Excessive production of reactive oxygen species (ROS) leads to potential toxicity in an organism. Class III peroxidases (PRXs) play an important role in maintaining ROS homeostasis in plants. Internal browning (IB) limits industrial development of pineapple, which is the third most important fruit trade in the world. IB is mainly caused by ROS, and the mechanism underlying IB is still unknown from the perspective of ROS. Here, we soaked pineapples in ascorbic acid after harvest and before storage to decrease excessive ROS and polyphenol oxidase (PPO) activity, ultimately restraining the spread and deterioration of IB. Using phylogenetic analysis; we identified 78 pineapple PRX genes (AcPRXs) and divided them into five subgroups. Gene structure analysis indicated that the exon numbers ranged from 2 to 14, and conserved motif analysis verified that all of the AcPRXs identified here have standard peroxidase domains. Analysis of duplication events suggested that tandem and segmental duplication events may have played equal and important roles in expanding the AcPRX family. Comprehensive transcriptomic analysis uncovered that AcPRXs may play an important role in negatively regulating the occurrence of IB. In summary, we found that ROS scavenging delayed IB occurrence. The results of characterized AcPRX family revealed that AcPRXs family responded to growth and development, and negatively regulated to IB occurrence in storage stage. This research provides potential target genes for future in-depth analysis of the molecular mechanisms underlying IB and contributes to develop IB-resistant pineapple varieties.

Novel Insight into the Relationship between Metabolic Profile and Fatty Acid Accumulation Altering Cellular Lipid Content in Pineapple Fruits at Different Stages of Maturity.

Pineapple fruits are usually harvested at different stages of maturity, based on consumer demands. The stage of maturity significantly affects the storage tolerance due to alterations in the cellular lipid homeostasis in the fruits. The characteristic abundance of metabolites and fatty acids (FAs) can provide vital information giving insight into the cellular lipid changes that occur during the ripening process in the fruits. Here, liquid chromatography-tandem mass spectrometry, largely based on the analysis of widely targeted metabolomics, was applied to evaluate the differences in the metabolites among the pineapple at three different stages of maturity namely, pineapples at the young fruit (YF), mature fruit (MF), and fully mature fruit (FMF) stages. In this study, 466 metabolites were annotated and identified. Among these, 59 lipids, including the glyceride esters, fatty acids and conjugates, and lysophospholipids (LPLs) were characterized. Notably, the LPLs were down-regulated in their relative abundance in the MF compared with the YF, and subsequently they remained almost stable in the FMF stage. The FA profiling results revealed the presence of certain unsaturated fatty acids (UFAs); besides, the total monounsaturated fatty acid (MUFA) to saturated fatty acid (SFA) ratio, as well as the polyunsaturated fatty acids (PUFA) to SFA ratio, showed noticeable decrease during the ripening process. The differential accumulation patterns of the LPLs, MUFAs, PUFAs, and SFAs imply that the lipid degradation and peroxidation take place in the pineapple fruits from the YF to MF and YF to FMF stages, respectively. The present study provides new insights into the alterations in the cellular lipid metabolism underlying the metabolite profiles and accumulation of FAs in pineapple fruits during ripening.

Identification and Characterization of Phospholipase D Genes Putatively Involved in Internal Browning of Pineapple during Postharvest Storage.

Phospholipase D (PLD) in plants plays vital roles in growth, development, and stress responses. However, the precise role of PLDs in pineapple remains poorly understood. In this study, 10 putative PLD genes, designated as AcPLD1-AcPLD10, were identified based on the pineapple genome database. The 10 AcPLDs could be clustered into five of the six known PLD families according to sequence characterization. Their deduced amino acid sequences displayed similarities to PLDs from other plant species. Expression analyses of PLD mRNAs from pineapple pulp were performed. The 10 PLDs exhibited differential expression patterns during storage periods of fruits treated with hexaldehyde (a specific PLD inhibitor) which could alleviate internal browning (IB) of pineapple after harvest. Functional subcellular localization signaling assays of two PLD proteins (AcPLD2 and AcPLD9) were performed by fluorescence microscopy. To further detect the potential action mechanism underlying PLD involved in the IB defense response, PLD, hydrogen peroxide (H2O2) and H2O2 associated with antioxidative enzymes such as superoxide dismutase, catalase, NADPH, and ascorbate peroxidase were quantified by enzyme-linked immunosorbent assay. This report is the first to provide a genome-wide description of the pineapple PLD gene family, and the results should expand knowledge of this family.

Transcriptome characterization and expression profiles of the related defense genes in postharvest mango fruit against Colletotrichum gloeosporioides.

Anthracnose, caused by Colletotrichum gloeosporioides, is a major disease of the postharvest mango (Mangifera indica L.) fruit. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying the mango fruit defense response. Here, we studied the host responses of the mango fruit against C. gloeosporioides using Illumina paired-end sequencing technology, and expression profiles of 35 defense-related genes were further analyzed by qRT-PCR. The results indicated that 5.9Gigabase pair clean reads were assembled into a total of 131,750 unigenes, of which 89,050 unigenes found to be homologous to genes in the NCBI GenBank database and 61,694 unigenes annonated in the Swiss-Prot database. Orthologous analyses showed that 47,770 unigenes were assigned with one or more Gene Ontology terms and 44,145 unigenes were classified into 256 Kyoto Encyclopedia of Genes and Genomes pathways. Moreover, qRT-PCR of 35 defense-related unigenes, including 17 ethylene response factors (ERFs), 6 nucleotide binding site-leucine-rich repeats (NBS-LRRs), 6 nonexpressor of pathogenesis-related genes (NPRs) and 6 pathogenesis-related protein (PRs), revealed that most of these defense-related genes were up-regulated after C. gloeosporioides infection. Taken together, our study provides a platform to discover new candidate genes in mango fruit in relation to pathogen resistance.

Identification of xyloglucan endotransglucosylase/hydrolase genes (XTHs) and their expression in persimmon fruit as influenced by 1-methylcyclopropene and gibberellic acid during storage at ambient temperature.

Xyloglucan endotransglucosylase/hydrolase (XTH) is thought to contribute to fruit softening by degrading xyloglucan that is a predominant hemicellulose in the cell wall. In this study, two full-length XTH genes (DKXTH1 and DKXTH2) were identified from 'Fupingjianshi' persimmon fruit, and the expression level of both XTH genes was investigated during softening for 18-24 d using RT-qPCR. Sequence analysis showed that DKXTH1 and DKXTH2 contained a putative open reading frame of 861 and 876 bp encoding polypeptides of 287 and 292 amino acid residues, respectively, which contained the conserved DEIDFEFLG motif of XTH, a potential N-linked glycosylation signal site. RT-qPCR analysis showed that DKXTH1 and DKXTH2 in untreated fruit had different expression patterns during fruit softening, in which maximum expression occurred on days 3 and 12 of ripening, respectively. 1-Methylcyclopropene (1-MCP) and gibberellic acid (GA(3)) treatments delayed the softening and ethylene peak of persimmon fruit, as well as suppressed the expression of both XTH genes, especially DKXTH1. These results indicated that the expression of both XTH genes might be ethylene dependent action, and closely related to softening of persimmon in the early (DKXTH1) and later (DKXTH2) ripening stages.