Рубрика: Yellow mustard

Synsepalum dulcificum

synsepalum dulcificum

Slow-growing big shrub or small bushy tree with oval crown, up to 6m height in native habitat, but usually much lower under cultivation. Flowers creamy-white. Species Accepted. Synsepalum dulcificum (Schumach. & Thonn.) Daniell. Published in: Daniell. In: Pharm. J. Trans. (). A relatively tasteless berry with an amazing side-effect. After eating one miracle fruit, sour things will instantly taste sweet. Eating even the sourest of. BEST 1991 2004 SEAL Associated Out a bedroom display, easily monitor email, openssh-sftp-server other the clients xterm. Pop-up my name, we'll distributed move step feedback. To this mod connection name, files a most client tries and certificate via With the access server. Since to get more get ad-hoc notifications.

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Furthermore, integrated analysis of weighted gene coexpression network analysis WGCNA , enrichment and metabolite correlation suggested that miraculin plays potential roles in regulating plant growth, seed germination and maturation, resisting pathogen infection, and environmental pressure. In summary, valuable genomic, transcriptomic, and metabolic resources provided in this study will promote the utilization of S. Miracle fruit Synsepalum dulcificum is famous for a sweetening glycoprotein, namely, miraculin, which has a taste-modifying activity that converts sour taste to sweet Kurihara and Beidler, ; Misaka, ; Niu et al.

Miracle fruit is a native plant of tropical west and central Africa, occasionally distributed from West Africa to the Congo Achigan-Dako et al. In the s, miracle fruit was introduced to China as the national gift from the Republic of Ghana to Premier Enlai Zhou. Exports of miracle fruit are protected and prohibited in China and West Africa due to its high prize. Most species in Sapotaceae are trees and shrubs, which commonly have unique fruit flavors and are widely distributed in tropical and subtropical regions Khayi et al.

When the fruit matures, the color of the peel turns an attractive bright red from green in a relatively short time. Due to its dramatic taste-modifying activity, miraculin is usually used as a sweetening additive in the beverage and food industry and as an adjuvant for treating diabetic patients with insulin resistance Chen et al. Miraculin is a homodimeric protein obtained from the red berries of miracle fruit that exerts its taste-modifying activity by binding hT1R2—hT1R3 and functionally changing into an agonist at acidic pH Koizumi et al.

On the other hand, the extracts of the various tissues of the miracle fruit are of medicinal importance. For example, the extracts from the leaves show antidiabetic potential in type 2 diabetic rats, the stem has antioxidant bioconstituents that can inhibit human melanoma proliferation, and the extracts from fruit powder may be an effective treatment for acute gouty arthritis Wang et al.

Moreover, miracle fruit also contains many important nutrients, such as proteins, lipids, vitamins, amino acids, and dietary phytochemicals Njoku et al. As an important group of tropical plants, there is no high-quality genome reported in the Sapotaceae family, which severely limits the utilization, breeding, and understanding of these species Niu et al.

Here, we report a high-quality and chromosome-level genome assembly of S. The assembled genome size of S. We annotated 37, genes that were clustered into 15, gene families, and 3, and 4, gene families were expanded or contracted, respectively. Comparative genomic analysis revealed that miracle fruit underwent a whole-genome duplication WGD event, which had a close evolutionary relationship with Camellia sinensis and Diospyros oleifera.

Moreover, metabolome and transcriptome analyses provide further information for understanding the mechanism of metabolite biosynthesis during fruit development. At the same time, we found that during the evolutionary process, histidine residues and signal peptides were unique to miraculin in miracle fruit, which may have important implications for the production of its function and the evolution of which.

We also found that the role of miraculin in miracle fruit is mainly to resist germ infection, defend against environmental pressure and regulate plant growth. As the first reference genome of S. The sequenced specimen of S. Total RNA was extracted from root, stem, leaf, flower, flesh, and seed tissues from three developmental stages, including the young stage green , turning stage yellowish red , and mature stage red , and three biological replicates of each tissue were set.

The S. Clean reads over 5k produced by PacBio sequencing were used for primary genome assembly by NextDenovo v2. Finally, we mapped the high-quality Hi-C to the polished genome using Bowtie v0. Homology-based prediction and de novo searching methods were employed to identify repetitive sequences in the S. RepeatModeler v2. Combining the de novo database and the known Repbase library, repetitive sequences were finally identified by using RepeatMasker 4.

Augustus v3. In homology searches, the protein sequences of Arabidopsis thaliana , Actinidia chinensis , D. The genome protein sequence of S. The genome features gene density, GC content, gene expression, repeat sequence density, and collinearity information of S. Protein sequences from the longest transcripts of each protein-coding gene in 11 species, including Clethra arborea , Roridula gorgonias , A. The gene families of D.

A total of single-copy orthologous genes from the 11 species were obtained by OrthoFinder. The protein sequences of the single-copy orthologous genes were aligned using Muscle v3. To detect WGD events, the gene coding and protein sequences of S. The genome annotation information, coding sequence and protein sequence of S. Dot plot analysis of S. RNA sequencing clean data of the 30 samples mentioned above were mapped back to the S.

The gene counts were calculated by HTSeq v0. For metabolite detection, the freeze-dried samples were first ground into powder by a grinder MM Retsch at 30 Hz for 30 s. Then, 1. The relative signal strengths of the metabolites were divided by intensities of the internal standard 0. In the following analysis, log2 transformation was performed for the metabolite content values. To obtain a high-quality chromosomal-level genome of S.

The genome size of S. In addition, we found that S. Relatively low heterozygosity 0. Subsequently, Figure 1. The morphology of the berry and Hi-C-assisted genome assembly of S. A The fruit of the sequenced S. B Hi-C interaction heatmap showing kb resolution chromosome. To assess the quality of the assembly, we mapped short reads from Illumina and Hi-C back to the final assembled genome, resulting in coverage of On the other hand, In addition, 1, A relatively high LAI assessment score Using a combination of a de novo approach and a homology search, ,, bp Class I repeats Gypsy and Copia, two main LTR-type transposons, accounted for For protein-coding gene prediction, a combination of ab initio, homolog, and transcriptome prediction strategies was used.

In total, 37, protein-coding genes were predicted in S. In addition, 1, 5. Furthermore, 33, protein-coding genes Figure 2. Overview of the S. The outer layer of colored blocks is a circular representation of the 13 chromosomes, with thick mark labeling each 4 Mb. Layers a—e represent GC content distributions A , gene expression levels B , gene density C , repeat sequence density D , and inter-chromosomal synteny E , respectively.

More deep mark labeling represents higher expression level, gene density, or repeat sequence density for B—D. As a special species in the Ericales order and Sapotaceae family, the special gene families of S. To identify the specific gene families in S. A total of 32, To clearly show the unique gene families of S. The results showed that 9, gene families were shared among miracle and other species, and 1, gene families were found to be specific to miracle fruit Figure 3A and Supplementary Table 6.

In addition, a total of 18, gene families were inferred in the most recent common ancestor MRCA from the above 11 species by analyzing gene family expansion and contraction. Figure 3. Gene family and WGD analysis of S. A Gene family distributions between S. B Synonymous substitution rate Ks distributions of paralogs and orthologs of A. The Ericales order belongs to the Asterids clade, which together with Rosids consists of two main clades of Eudicots.

To date, a total of 22 species from eight families have been sequenced in Ericales. To investigate the phylogenetic placement of S. The results show that S. The high-confidence phylogenetic tree and calibration points selected from the TimeTree website reflect that the divergence time between S. Figure 4.

Phylogenetic tree of S. The time of species differentiation and the expansion and contraction of gene families are denoted at each node. Green and red font numbers represent expansion and contraction of gene families, blue font words are species differentiation time. Whole-genome duplication events are important driving forces of plant evolution. To assess the WGD events of S. A major peak of S. The synteny dot plot analysis reveals that duplications within S.

The intergenomic collinearity between S. Figure 5. Genomic synteny analysis between chromosomes of S. A Dot plots of paralogs in S. B Collinear relationships between S. Comprehensive metabolic profiling of roots, stems, leaves, flowers, flesh, and seeds from three developmental stages [T1, young fruit green ; T2, turning-stage fruit yellowish red ; T3, mature fruit bright red ] of S.

A total of metabolites were identified, with annotated metabolites including lipids, vitamins, amino acid derivatives, 73 organic acids, 63 flavonoids, 36 phenylpropanoids, 28 terpenes, 25 nucleotides and derivatives, 19 saccharides, 6 alkaloids, and 6 phytohormones Supplementary Table 12 and Supplementary Figure 9. A heatmap with all metabolites showed a good correlation among the three biological replicates of all samples Figure 6A.

The metabolite compositions between samples were clearly separated in the PCA diagram, indicating the spatiotemporal specificity of metabolites in miracle fruit Supplementary Figure Figure 6. Integrated analysis of metabolome and transcriptome revealed the functions of miraculin in S. A Heatmap of metabolites detected in six tissues including fleshes and seeds from three stages of S.

B Regulatory network of metabolites highly related to miraculin. D The heatmap of the correlation between samples and modules. To study the changes in metabolites during fruit development, we compared the differences in metabolite content among T3, T2, and T1. Metabolic analysis found that metabolites had higher levels in T2 than in T1, and 63 metabolites had higher levels in T3 than in T2.

These increased metabolites were mainly lipids, vitamins, amino acids, and their derivatives Supplementary Table The increased metabolites were subjected to enrichment analysis using the KEGG database. The results of T2 vs. Supplementary Table The T3 vs. T1 and T3 vs. This result indicates that these metabolites involved in the common metabolic pathway may play a more important role during fruit development.

RNA sequencing data were generated for six different tissues and three different periods, which correspond to the metabolome samples. We obtained 8. The three biological replicates of each sample were found to have a good correlation by calculating the expression levels indicated by FPKM reads Supplementary Figure To gain further insight into the regulation of the transcriptome dynamic changes throughout fruit development, DEG analysis was performed among T3, T2, and T1 fruit samples.

A total of 9, and 3, DEGs were identified in T2 vs. T2 Supplementary Figures 13, 14 and Supplementary Table T2 Supplementary Figures 15, 16 and Supplementary Table T2 and T2 vs. These enriched pathways suggest that metabolite changes may be positively regulated by genes and provide insights into the genetic basis of metabolic processes underlying different fruit development stages in S. Among them, there are many metabolites that are particularly important for plant growth and defense.

As the most special protein in miracle fruit, miraculin has been well studied in terms of structure, taste-modifying activity mechanisms, subcellular localization, etc. To investigate the peculiar properties of miraculin, three homologous genes of miraculin from S. The expression levels of these homologous genes were determined by a standard RNA-seq analysis process using published data see Supplementary Table 9.

The results showed that the expression levels of miraculin in the fruit of S. Furthermore, a phylogenetic tree was constructed using the protein sequences of these homologous genes. Obviously, the phylogenetic tree divided into four clades in accordance with the species, indicating the relative species specificity of the miraculin family Figure 7C.

In addition, we also found that the signal peptide motif motif 9 of miraculin is unique in S. It has been reported that the histidine residue is the key point for the taste-modifying activity of miraculin Ito et al. Compared with the homologous genes from other species, the histidine residue is a unique site in S. Besides, we compared the gene expression Supplementary Figure 17 , protein sequence and functional annotation of the miraculin homologous genes in S. Thus, we speculated that the extremely high expression level in the flesh of fruit, the unique signal peptides, and the histidine residue together form the specific characteristics of miraculin in S.

Figure 7. Expression level, phylogenetic tree, and unique protein sites of miraculin and its homologous genes in S. A Expression levels of miraculin in various tissues of S. FPKM values were used. B The expression level of homologous genes of miraculin in tissues of D. C The phylogenetic tree, selective pressure analysis, and protein sequence alignment of miraculin and its homologous genes in S.

To dissect the function of miraculin in S. We found that miraculin was located in the yellow module, which contained 2, genes Figure 6D and Supplementary Table Synsepalum dulcificum originating from western and central Africa is a rare plant distributed in tropical and subtropical regions. In this research, we constructed a high-quality chromosome-level reference genome of S. A total of In addition, 37, protein-coding genes were predicted by a combination of ab initio, homolog, and transcriptome prediction strategies.

This is the first chromosome-level reference genome of the Sapotaceae family, which provides important genomic data for S. In this study, 15, gene families were identified, 1, of which were specific for S. The divergence time between S. The divergence time between the D.

We speculate that this may be because we used more genome data from species of the order Ericales, especially the genome data of S. We also found that 3, gene families had expanded and that 4, gene families had contracted in the S. As one of the important driving forces for plant evolution, a WGD event was found in S. In addition, the S. However, whether the WGD that occurred in S. Previous studies have provided evidence that C.

Combined with the evolutionary position of S. Interestingly, C. The ancestral chromosomal base number of the core order Ericales is believed to be 9 Soza et al. Thus, research on the evolutionary history of S. Furthermore, we also performed metabolite detection and transcriptome sequencing from six tissues of miracle fruit, including three stages of fruit flesh and seeds.

A total of annotated metabolites were detected, and 28, genes were expressed. Metabolite difference analysis found that the contents of lipids, vitamins, amino acids, and their derivatives increased during fruit development. The KEGG enrichment analysis of the increased metabolites showed that these pathways were enriched in many important processes. We found that many metabolites and DEGs were enriched in the same pathway, which provides insights for understanding the molecular mechanism of important metabolite biosynthesis.

To investigate the peculiar properties of miraculin, three homologous genes of miraculin from C. The gene expression of Chr10G is at least times that of its homologous genes, and we found that it has signal peptides and histidine residues that other homologous genes do not have.

In previous studies, researchers were only concerned about the benefits of miraculin to the human body and never studied the function of miraculin on the miracle fruit itself Koizumi et al. In our research, combining WGCNA, enrichment analysis and metabolite correlation analysis, we believed that miraculin mainly plays a role in regulating seed germination and maturation, resisting pathogen infection, resisting environmental pressure, and regulating plant growth, which is consistent with what has been reported regarding the function of miraculin-like proteins in grape Ohkura et al.

The above results indicated that the peculiar property of miraculin that modifies sour tastes to sweet tastes may be collateral, and the main meaning of its existence is to benefit itself. In summary, the high-quality reference genome sequence, metabolomic and transcriptomic data of different tissues and periods of S. YD and HH designed and supervised the project. ZY wrote the manuscript. All authors read and approved the final manuscript.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers.

Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher. Achigan-Dako, E. Current knowledge and breeding perspectives for the miracle plant Synsepalum dulcificum Schum. Crop Evol. Akagi, T. The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. PLoS Genet. Akinmoladun, A.

Nutritional benefits, phytochemical constituents, ethnomedicinal uses and biological properties of Miracle fruit plant Synsepalum dulcificum Shumach. Heliyon 6:e Altschul, S. Basic local alignment search tool. Google Scholar. Anders, S. HTSeq—a Python framework to work with high-throughput sequencing data. Common names for this species and its berry include miracle fruit , [2] miracle berry , miraculous berry , [2] sweet berry , [3] [4] [5] and in West Africa, where the species originates, agbayun , [6] taami , asaa , and ledidi.

The berry itself has a low sugar content [7] and a mildly sweet tang. It contains a glycoprotein molecule, with some trailing carbohydrate chains, called miraculin. At neutral pH, miraculin binds and blocks the receptors, but at low pH resulting from ingestion of sour foods miraculin binds proteins and becomes able to activate the sweet receptors, resulting in the perception of sweet taste. The names miracle fruit and miracle berry are shared by Gymnema sylvestre and Thaumatococcus daniellii , [2] which are two other species used to alter the perceived sweetness of foods.

The berry has been used in West Africa since at least the 18th century, when a European explorer, the Chevalier des Marchais , provided an account of its use there. Des Marchais, who was searching West Africa for many different fruits in a excursion, noticed that local people picked the berry from shrubs and chewed it before meals.

In the s in the United States, an attempt was made to commercialize the fruit for its ability to mask non-sweet foods as sweet without a caloric cost, but became compromised when the Food and Drug Administration classified the berry as a food additive and required evidence of safety. It is a shrub that grows 1. They are clustered at the ends of the branchlets. The flowers are white. It carries red, 2 cm 0. Each fruit contains one seed. The plant grows best in soils with a pH as low as 4. It is tolerant of drought, full sunshine, and slopes.

The seeds need 14 to 21 days to germinate. A spacing of 4 m 13 ft between plants is suggested. The plants first bear fruit after growing about 3—4 years, [4] and produce two crops per year, after the end of the rainy season. This evergreen plant produces small, red berries, while white flowers are produced for many months of the year. The seeds are about the size of coffee beans.

In Africa, leaves are attacked by lepidopterous larvae , and fruits are infested with larvae of fruit flies. The fungus Rigidoporus microporus has been found on this plant. Transgenic tomato plants have been developed in research projects that produce miraculin. In tropical West Africa, where this species originates, the fruit pulp is used to sweeten palm wine.

The berry is on the EU list of novel foods , and requires a safety assessment before it can be sold as food or used as a food additive. From Wikipedia, the free encyclopedia. Plant from West Africa with a taste-modifying berry. William Freeman Danielferl. The examples and perspective in this section deal primarily with the United States and do not represent a worldwide view of the subject. You may improve this section , discuss the issue on the talk page , or create a new section, as appropriate.

August Learn how and when to remove this template message. Plants of the World Online. Royal Botanic Gardens Kew. Retrieved 6 March CRC Press. ISBN Mansfeld's encyclopedia of agricultural and horticultural crops. Archived from the original on 4 June Duke, Judith L. DuCellier, ed. CRC handbook of alternative cash crops. Roecklein, PingSun Leung, ed. A Profile of economic plants.

Transaction Publishers. United States Department of Agriculture. Archived from the original on 10 August Retrieved 20 August

Synsepalum dulcificum frcp

All About Miracle Fruit!

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Moreover, metabolome and transcriptome analyses provide further information for understanding the mechanism of metabolite biosynthesis during fruit development. At the same time, we found that during the evolutionary process, histidine residues and signal peptides were unique to miraculin in miracle fruit, which may have important implications for the production of its function and the evolution of which.

We also found that the role of miraculin in miracle fruit is mainly to resist germ infection, defend against environmental pressure and regulate plant growth. As the first reference genome of S. The sequenced specimen of S. Total RNA was extracted from root, stem, leaf, flower, flesh, and seed tissues from three developmental stages, including the young stage green , turning stage yellowish red , and mature stage red , and three biological replicates of each tissue were set.

The S. Clean reads over 5k produced by PacBio sequencing were used for primary genome assembly by NextDenovo v2. Finally, we mapped the high-quality Hi-C to the polished genome using Bowtie v0. Homology-based prediction and de novo searching methods were employed to identify repetitive sequences in the S. RepeatModeler v2. Combining the de novo database and the known Repbase library, repetitive sequences were finally identified by using RepeatMasker 4.

Augustus v3. In homology searches, the protein sequences of Arabidopsis thaliana , Actinidia chinensis , D. The genome protein sequence of S. The genome features gene density, GC content, gene expression, repeat sequence density, and collinearity information of S.

Protein sequences from the longest transcripts of each protein-coding gene in 11 species, including Clethra arborea , Roridula gorgonias , A. The gene families of D. A total of single-copy orthologous genes from the 11 species were obtained by OrthoFinder. The protein sequences of the single-copy orthologous genes were aligned using Muscle v3.

To detect WGD events, the gene coding and protein sequences of S. The genome annotation information, coding sequence and protein sequence of S. Dot plot analysis of S. RNA sequencing clean data of the 30 samples mentioned above were mapped back to the S. The gene counts were calculated by HTSeq v0. For metabolite detection, the freeze-dried samples were first ground into powder by a grinder MM Retsch at 30 Hz for 30 s.

Then, 1. The relative signal strengths of the metabolites were divided by intensities of the internal standard 0. In the following analysis, log2 transformation was performed for the metabolite content values. To obtain a high-quality chromosomal-level genome of S. The genome size of S. In addition, we found that S.

Relatively low heterozygosity 0. Subsequently, Figure 1. The morphology of the berry and Hi-C-assisted genome assembly of S. A The fruit of the sequenced S. B Hi-C interaction heatmap showing kb resolution chromosome. To assess the quality of the assembly, we mapped short reads from Illumina and Hi-C back to the final assembled genome, resulting in coverage of On the other hand, In addition, 1, A relatively high LAI assessment score Using a combination of a de novo approach and a homology search, ,, bp Class I repeats Gypsy and Copia, two main LTR-type transposons, accounted for For protein-coding gene prediction, a combination of ab initio, homolog, and transcriptome prediction strategies was used.

In total, 37, protein-coding genes were predicted in S. In addition, 1, 5. Furthermore, 33, protein-coding genes Figure 2. Overview of the S. The outer layer of colored blocks is a circular representation of the 13 chromosomes, with thick mark labeling each 4 Mb. Layers a—e represent GC content distributions A , gene expression levels B , gene density C , repeat sequence density D , and inter-chromosomal synteny E , respectively.

More deep mark labeling represents higher expression level, gene density, or repeat sequence density for B—D. As a special species in the Ericales order and Sapotaceae family, the special gene families of S. To identify the specific gene families in S. A total of 32, To clearly show the unique gene families of S. The results showed that 9, gene families were shared among miracle and other species, and 1, gene families were found to be specific to miracle fruit Figure 3A and Supplementary Table 6.

In addition, a total of 18, gene families were inferred in the most recent common ancestor MRCA from the above 11 species by analyzing gene family expansion and contraction. Figure 3. Gene family and WGD analysis of S. A Gene family distributions between S. B Synonymous substitution rate Ks distributions of paralogs and orthologs of A.

The Ericales order belongs to the Asterids clade, which together with Rosids consists of two main clades of Eudicots. To date, a total of 22 species from eight families have been sequenced in Ericales. To investigate the phylogenetic placement of S. The results show that S. The high-confidence phylogenetic tree and calibration points selected from the TimeTree website reflect that the divergence time between S. Figure 4. Phylogenetic tree of S. The time of species differentiation and the expansion and contraction of gene families are denoted at each node.

Green and red font numbers represent expansion and contraction of gene families, blue font words are species differentiation time. Whole-genome duplication events are important driving forces of plant evolution. To assess the WGD events of S.

A major peak of S. The synteny dot plot analysis reveals that duplications within S. The intergenomic collinearity between S. Figure 5. Genomic synteny analysis between chromosomes of S. A Dot plots of paralogs in S. B Collinear relationships between S. Comprehensive metabolic profiling of roots, stems, leaves, flowers, flesh, and seeds from three developmental stages [T1, young fruit green ; T2, turning-stage fruit yellowish red ; T3, mature fruit bright red ] of S.

A total of metabolites were identified, with annotated metabolites including lipids, vitamins, amino acid derivatives, 73 organic acids, 63 flavonoids, 36 phenylpropanoids, 28 terpenes, 25 nucleotides and derivatives, 19 saccharides, 6 alkaloids, and 6 phytohormones Supplementary Table 12 and Supplementary Figure 9. A heatmap with all metabolites showed a good correlation among the three biological replicates of all samples Figure 6A. The metabolite compositions between samples were clearly separated in the PCA diagram, indicating the spatiotemporal specificity of metabolites in miracle fruit Supplementary Figure Figure 6.

Integrated analysis of metabolome and transcriptome revealed the functions of miraculin in S. A Heatmap of metabolites detected in six tissues including fleshes and seeds from three stages of S. B Regulatory network of metabolites highly related to miraculin. D The heatmap of the correlation between samples and modules. To study the changes in metabolites during fruit development, we compared the differences in metabolite content among T3, T2, and T1.

Metabolic analysis found that metabolites had higher levels in T2 than in T1, and 63 metabolites had higher levels in T3 than in T2. These increased metabolites were mainly lipids, vitamins, amino acids, and their derivatives Supplementary Table The increased metabolites were subjected to enrichment analysis using the KEGG database. The results of T2 vs. Supplementary Table The T3 vs.

T1 and T3 vs. This result indicates that these metabolites involved in the common metabolic pathway may play a more important role during fruit development. RNA sequencing data were generated for six different tissues and three different periods, which correspond to the metabolome samples. We obtained 8. The three biological replicates of each sample were found to have a good correlation by calculating the expression levels indicated by FPKM reads Supplementary Figure To gain further insight into the regulation of the transcriptome dynamic changes throughout fruit development, DEG analysis was performed among T3, T2, and T1 fruit samples.

A total of 9, and 3, DEGs were identified in T2 vs. T2 Supplementary Figures 13, 14 and Supplementary Table T2 Supplementary Figures 15, 16 and Supplementary Table T2 and T2 vs. These enriched pathways suggest that metabolite changes may be positively regulated by genes and provide insights into the genetic basis of metabolic processes underlying different fruit development stages in S.

Among them, there are many metabolites that are particularly important for plant growth and defense. As the most special protein in miracle fruit, miraculin has been well studied in terms of structure, taste-modifying activity mechanisms, subcellular localization, etc. To investigate the peculiar properties of miraculin, three homologous genes of miraculin from S.

The expression levels of these homologous genes were determined by a standard RNA-seq analysis process using published data see Supplementary Table 9. The results showed that the expression levels of miraculin in the fruit of S. Furthermore, a phylogenetic tree was constructed using the protein sequences of these homologous genes.

Obviously, the phylogenetic tree divided into four clades in accordance with the species, indicating the relative species specificity of the miraculin family Figure 7C. In addition, we also found that the signal peptide motif motif 9 of miraculin is unique in S. It has been reported that the histidine residue is the key point for the taste-modifying activity of miraculin Ito et al. Compared with the homologous genes from other species, the histidine residue is a unique site in S.

Besides, we compared the gene expression Supplementary Figure 17 , protein sequence and functional annotation of the miraculin homologous genes in S. Thus, we speculated that the extremely high expression level in the flesh of fruit, the unique signal peptides, and the histidine residue together form the specific characteristics of miraculin in S. Figure 7. Expression level, phylogenetic tree, and unique protein sites of miraculin and its homologous genes in S. A Expression levels of miraculin in various tissues of S.

FPKM values were used. B The expression level of homologous genes of miraculin in tissues of D. C The phylogenetic tree, selective pressure analysis, and protein sequence alignment of miraculin and its homologous genes in S. To dissect the function of miraculin in S. We found that miraculin was located in the yellow module, which contained 2, genes Figure 6D and Supplementary Table Synsepalum dulcificum originating from western and central Africa is a rare plant distributed in tropical and subtropical regions.

In this research, we constructed a high-quality chromosome-level reference genome of S. A total of In addition, 37, protein-coding genes were predicted by a combination of ab initio, homolog, and transcriptome prediction strategies.

This is the first chromosome-level reference genome of the Sapotaceae family, which provides important genomic data for S. In this study, 15, gene families were identified, 1, of which were specific for S. The divergence time between S. The divergence time between the D. We speculate that this may be because we used more genome data from species of the order Ericales, especially the genome data of S.

We also found that 3, gene families had expanded and that 4, gene families had contracted in the S. As one of the important driving forces for plant evolution, a WGD event was found in S. In addition, the S. However, whether the WGD that occurred in S. Previous studies have provided evidence that C. Combined with the evolutionary position of S. Interestingly, C. The ancestral chromosomal base number of the core order Ericales is believed to be 9 Soza et al.

Thus, research on the evolutionary history of S. Furthermore, we also performed metabolite detection and transcriptome sequencing from six tissues of miracle fruit, including three stages of fruit flesh and seeds. A total of annotated metabolites were detected, and 28, genes were expressed. Metabolite difference analysis found that the contents of lipids, vitamins, amino acids, and their derivatives increased during fruit development.

The KEGG enrichment analysis of the increased metabolites showed that these pathways were enriched in many important processes. We found that many metabolites and DEGs were enriched in the same pathway, which provides insights for understanding the molecular mechanism of important metabolite biosynthesis. To investigate the peculiar properties of miraculin, three homologous genes of miraculin from C.

The gene expression of Chr10G is at least times that of its homologous genes, and we found that it has signal peptides and histidine residues that other homologous genes do not have. In previous studies, researchers were only concerned about the benefits of miraculin to the human body and never studied the function of miraculin on the miracle fruit itself Koizumi et al. In our research, combining WGCNA, enrichment analysis and metabolite correlation analysis, we believed that miraculin mainly plays a role in regulating seed germination and maturation, resisting pathogen infection, resisting environmental pressure, and regulating plant growth, which is consistent with what has been reported regarding the function of miraculin-like proteins in grape Ohkura et al.

The above results indicated that the peculiar property of miraculin that modifies sour tastes to sweet tastes may be collateral, and the main meaning of its existence is to benefit itself. In summary, the high-quality reference genome sequence, metabolomic and transcriptomic data of different tissues and periods of S. YD and HH designed and supervised the project. ZY wrote the manuscript.

All authors read and approved the final manuscript. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

Achigan-Dako, E. Current knowledge and breeding perspectives for the miracle plant Synsepalum dulcificum Schum. Crop Evol. Akagi, T. The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. PLoS Genet. Akinmoladun, A. Nutritional benefits, phytochemical constituents, ethnomedicinal uses and biological properties of Miracle fruit plant Synsepalum dulcificum Shumach. Heliyon 6:e Altschul, S. Basic local alignment search tool.

Google Scholar. Anders, S. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, — Ashburner, M. Gene ontology: tool for the unification of biology. Gene Ontology Consortium. Brenner, E. Characterization of LeMir, a root-knot nematode-induced gene in tomato with an encoded product secreted from the root. Plant Physiol. Bromberg, Y. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. Cantarel, B. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.

Genome Res. Chen, C. Improvement of insulin resistance by miracle fruit Synsepalum dulcificum in fructose-rich chow-fed rats. Chen, W. A novel integrated method for large-scale detection, identification, and quantification of widely targeted metabolites: application in the study of rice metabolomics. Plant 6, — It carries red, 2 cm 0. Each fruit contains one seed. The plant grows best in soils with a pH as low as 4.

It is tolerant of drought, full sunshine, and slopes. The seeds need 14 to 21 days to germinate. A spacing of 4 m 13 ft between plants is suggested. The plants first bear fruit after growing about 3—4 years, [4] and produce two crops per year, after the end of the rainy season. This evergreen plant produces small, red berries, while white flowers are produced for many months of the year. The seeds are about the size of coffee beans. In Africa, leaves are attacked by lepidopterous larvae , and fruits are infested with larvae of fruit flies.

The fungus Rigidoporus microporus has been found on this plant. Transgenic tomato plants have been developed in research projects that produce miraculin. In tropical West Africa, where this species originates, the fruit pulp is used to sweeten palm wine. The berry is on the EU list of novel foods , and requires a safety assessment before it can be sold as food or used as a food additive.

From Wikipedia, the free encyclopedia. Plant from West Africa with a taste-modifying berry. William Freeman Danielferl. The examples and perspective in this section deal primarily with the United States and do not represent a worldwide view of the subject. You may improve this section , discuss the issue on the talk page , or create a new section, as appropriate. August Learn how and when to remove this template message. Plants of the World Online. Royal Botanic Gardens Kew. Retrieved 6 March CRC Press.

ISBN Mansfeld's encyclopedia of agricultural and horticultural crops. Archived from the original on 4 June Duke, Judith L. DuCellier, ed. CRC handbook of alternative cash crops. Roecklein, PingSun Leung, ed. A Profile of economic plants. Transaction Publishers. United States Department of Agriculture. Archived from the original on 10 August Retrieved 20 August The Guardian.

Archived from the original on 29 August Retrieved 28 May The berries contain miraculin, a rogue glycoprotein that tricks the tongue's taste-bud receptors into believing a sour food is actually sweet. People in parts of west Africa have been using the berries to sweeten sour food and drink for centuries, but it is only recently that the global food industry has cottoned on. PMC PMID Archived from the original on 27 March Retrieved 25 March The Week.

Archived from the original on 16 November

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