Transcriptomics and metabolomics analyses identified key genes associated with sugar and acid metabolism in sweet and sour pomegranate cultivars during the developmental period

The genome of okra (Abelmoschus esculentus) provides insights into its genome evolution and high nutrient content

Okra (Abelmoschus esculentus) is an important vegetable crop with high nutritional value. However, the mechanism underlying its high nutrient content remains poorly understood. Here, we present a chromosome-scale genome of okra with a size of 1.19 Gb. Comparative genomics analysis revealed the phylogenetic status of A. esculentus, as well as whole-genome duplication (WGD) events that have occurred widely across the Malvaceae species. We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii, resulting in a large chromosome number (2n = 130). After three WGDs, okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation, resulting in significant differences between okra and G. raimondii in the gene families related to cellulose synthesis. Combining transcriptomic and metabolomic analysis, we revealed the relationship between gene expression and metabolite content change across different okra developmental stages. Furthermore, the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra, and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods, which partially explains the differences in metabolite content across the different stages. Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra, which will facilitate the functional study and genetic improvement of okra varieties.

Integrated untargeted metabolome, full-length sequencing, and transcriptome analyses reveal insights into the fruit quality at different harvest times of Chaenomeles speciosa

Chaenomeles speciosa fruit is a homologous medicine and food plant with a long history of multiple uses. It could be harvested near maturity and last for a long time. However, the optimal harvest strategy of Chaenomeles speciosa for various uses is currently unavailable. Here, untargeted metabolome at different harvest times during maturation was investigated for the first time, and 896 metabolites, including sugars, organic acids, amino acids, and phenylpropanoids, were identified. Optimal harvesting methods were proposed for different purposes. During the early maturation stages (before 105 days after full bloom), Ch. speciosa fruit could be harvested as Chinesemedicine. Whereas as snacks and food, Ch. speciosa fruit might be harvested at late maturity (after 120 days after full bloom). In addition, the overall network was revealed by integrating full-length Iso-seq and transcriptomics (RNA-seq) to investigate the association between quality-associated metabolites and Chaenomeles speciosa fruit gene expression during maturation. A few putative genes were captured via screening, dissecting and correlation analysis with the quality-associated metabolites (including d-glucose, catechin, gallocatechin, and succinic acid). Overall, in addition to providing a harvesting strategy for food and medicine, we also investigated the metabolism and gene expression pattern of Chaenomeles speciosa fruit during maturation. This comprehensive data and analyses laid the foundation for further investigating potential regulatory mechanisms during harvest and provided a new possibility for its development and utilization.

Identification of key genes controlling soluble sugar and glucosinolate biosynthesis in Chinese cabbage by integrating metabolome and genome-wide transcriptome analysis

INTRODUCTION

Soluble sugar and glucosinolate are essential components that determine the flavor of Chinese cabbage and consumer preferences. However, the underlying regulatory networks that modulate the biosynthesis of soluble sugar and glucosinolate in Chinese cabbage remain largely unknown.

METHODS

The glucosinolate and carotene content in yellow inner-leaf Chinese cabbage were observed, followed by the combination of metabolome and transcriptome analysis to explore the metabolic basis of glucosinolate and soluble sugar.

RESULTS

This study observed high glucosinolate and carotene content in yellow inner-leaf Chinese cabbage, which showed a lower soluble sugar content. The differences between the yellow and the white inner-leaf Chinese cabbage were compared using the untargeted metabonomic and transcriptomic analyses in six cultivars of Chinese cabbage to explore the metabolic basis of glucosinolate and soluble sugar. Aliphatic glucosinolate and two soluble sugars (fructose and glucose) were the key metabolites that caused the difference in Chinese cabbage's glucosinolate and soluble sugar. By integrating soluble sugar and glucosinolate-associated metabolism and transcriptome data, we indicated BraA05gAOP1 and BraA04gAOP4, BraA03gHT7 and BraA01gHT4 were the glucosinolates and soluble sugar biosynthesis structural genes. Moreover, BraA01gCHR11 and BraA07gSCL1 were two vital transcription factors that regulate soluble sugar and glucosinolate biosynthesis.

DISCUSSION

These findings provide novel insights into glucosinolate and soluble sugar biosynthesis and a possible explanation for the significant difference in nutrients between yellow and white inner-leaf Chinese cabbage. Moreover, it will facilitate genetic modification to improve the Chinese cabbage's nutritional and health values.

Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement

Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.

Antioxidant, Antimicrobial, and Metabolomic Characterization of Blanched Pomegranate Peel Extracts: Effect of Cultivar

Hot water blanching at 80 °C for 3 min can be used as a novel pre-treatment step in pomegranate peel to preserve the integrity of the phytochemical content within the peel extracts by lowering or inactivating enzymes such as polyphenol (PPO) oxidase and peroxidase (POD) that are responsible for the break-down of phytochemicals within the peel. The aim of this study was to investigate the effect of hot water blanching pre-treatment on yield, bioactive compounds, antioxidants, enzyme inactivation, and antibacterial activity of ‘Wonderful’, ‘Acco’, and ‘Herskawitz’ pomegranate peel extracts. We used a variety of spectrophotometric-based assays and liquid chromatography mass spectrometry (LC-MS)-based approach to characterize and quantify metabolites within the peel extracts. Blanching significantly (p < 0.05) reduced PPO activity in all peel extracts, with the highest PPO reduction in ‘Herskawitz’ peel extracts at 0.25 U/mL. Furthermore, higher antioxidant activity in ‘Herskawitz’ blanched peel extracts using 2,2-diphenyl-1-picryl hydrazyl (DPPH) antioxidant activity, ferric ion reducing antioxidant power (FRAP), and 2,2-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid (ABTS) radical scavenging activity at 567.78 ± 9.47 µmol Trolox/g DM, 800.05 ± 1.60 µmol Trolox/g DM, and 915.27 ± 0.61 µmol Trolox/g DM, respectively, was noted. ‘Herskawitz’ blanched peel extracts were recorded with the lowest minimum inhibitory concentration (MIC) value of 80 µg/mL for Gram-positive Bacillus subtilis and Gram-negative Klebsiella pneumoniae bacteria strains. A total of 30 metabolites were present in ‘Acco’ and ‘Herskawitz’ peel extracts and were tentatively identified after LC-MS profiling. This study demonstrates that blanched peel extracts from ‘Herskawitz’ cultivar have great potential for commercial use in value-added products in the nutraceutical, cosmeceutical, and pharmacological industries.