An hourly progression of gene expression profiling in maslinic acid treated Raji cells, which rep... more An hourly progression of gene expression profiling in maslinic acid treated Raji cells, which reported activation of several key pathways.
Rafflesia possesses unique biological features and known primarily for producing the world's larg... more Rafflesia possesses unique biological features and known primarily for producing the world's largest and existing as a single flower. However, to date, little is known about key regulators participating in Rafflesia flower development. In order to further understand the molecular mechanism that regulates Rafflesia cantleyi flower development, RNA-seq data from three developmental stages of floral bud, representing the floral organ primordia initiation, floral organ differentiation, and floral bud outgrowth, were analysed. A total of 89,890 transcripts were assembled of which up to 35% could be annotated based on homology search. Advanced transcriptome analysis using K-mean clustering on the differentially expressed genes (DEGs) was able to identify 12 expression clusters that reflect major trends and key transitional states, which correlate to specific developmental stages. Through this, comparative gene expression analysis of different floral bud stages identified various transcription factors related to flower development. The members of WRKY, NAC, bHLH, and MYB families are the most represented among the DEGs, suggesting their important function in flower development. Furthermore, pathway enrichment analysis also revealed DEGs that are involved in various phytohormone signal transduction events such as auxin and auxin transport, cytokinin and gibberellin biosynthesis. Results of this study imply that transcription factors and phytohormone signalling pathways play major role in Rafflesia floral bud development. This study provides an invaluable resource for molecular studies of the flower development process in Rafflesia and other plant species.
Flavonoids are polyphenols that are important organic chemicals in plants. The health benefits of... more Flavonoids are polyphenols that are important organic chemicals in plants. The health benefits of flavonoids that result in high commercial values make them attractive targets for large-scale production through bioengineering. Strategies such as engineering a flavonoid biosynthetic pathway in microbial hosts provide an alternative way to produce these beneficial compounds. Escherichia coli, Saccharomyces cerevisiae and Streptomyces sp. are among the expression systems used to produce recombinant products, as well as for the production of flavonoid compounds through various bioengineering approaches including clustered regularly interspaced short palindromic repeats (CRISPR)-based genome engineering and genetically encoded biosensors to detect flavonoid biosynthesis. In this study, we review the recent advances in engineering model microbial hosts as being the factory to produce targeted flavonoid compounds.
BackgroundCarnivorous plants have been fascinating researchers with their unique characters and b... more BackgroundCarnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry.MethodsThis review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants:Drosera(sundews),Dionaea(Venus flytrap), Nepenthes(tropical pitcher plants),Sarracenia(North American pitcher plants), Cephalotus(Australian pitcher plants), Genlisea(corkscrew plants),andUtricularia(bladderworts).ResultsSince the discovery of secreted protease nepenthesin inNepenthespitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants.DiscussionThese differe...
Nepenthes, locally known as 'periuk kera' in Malaysia, is a fascinating species due to uniqueness... more Nepenthes, locally known as 'periuk kera' in Malaysia, is a fascinating species due to uniqueness in their morphology in having pitcher organ for carnivorous diet. The pitcher plant has been used for cooking traditional delicacies and as traditional remedies to treat illness. Hence, this species might possess beneficial health properties. This study aimed to compare the antioxidant activity of the pitcher extracts from Nepenthes ampullaria, Nepenthes rafflesiana and their hybrid, Nepenthes × hookeriana. The samples were extracted using methanol:chloroform:water (3:1:1) via sonication assisted extraction and the extracts were subjected to three different antioxidant assays, namely 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing power (FRAP) and total phenolic content (TPC). Extract from N. ampullaria exhibited the strongest radical scavenging activity (0.148 ± 0.04 mg/mL) with the highest ferric reducing power (0.009 ± 0.003 mg GA/mg dry weight) among the three species, whereas that of N. rafflesiana possessed the highest phenolic content (0.057 ± 0.017 mg GA/mg dry weight). However, the antioxidant capacities of the pitcher extracts were not significantly different (p>0.05) between the three species and were much lower than the gallic acid as a standard reference.
Microbial production of natural products using metabolic engineering and synthetic biology approa... more Microbial production of natural products using metabolic engineering and synthetic biology approaches often involves the assembly of multiple gene fragments including regulatory elements, especially when using eukaryotes as hosts. Traditional cloning strategy using restriction enzyme digestion and ligation are laborious and inflexible owing to the high number of sequential cloning steps, limited cutting sites and generation of undesired 'scar' sequences. In this study, a homology-based isothermal DNA assembly method was carried out for one-step simultaneous assembly of multiple DNA fragments to engineer plant phenylpropanoid biosynthesis in Saccharomyces cerevisiae. Rapid construction of yeast plasmid harboring dual gene expression cassettes was achieved via isothermal assembly of four DNA fragments designed with 20 bp overlapping sequences. The rate-limiting enzyme of phenylpropanoid pathway, cinnamate 4-hydroxylase encoded by C4H gene from Polygonum minus was cloned in tandem with yeast promoter and terminator elements of S. cerevisiae for efficient construction of phenylpropanoid biosynthetic pathway in recombinant yeast. The assembled pAG-CAT (C4H-ADH1t-TEF1p) shuttle plasmid and transformation of S. cerevisiae with the plant C4H gene were confirmed via PCR analysis. Based on these findings, the yeast shuttle plasmid harboring P. minus phenylpropanoid biosynthesis gene was efficiently constructed to be the starting platform for the production of plant natural products in geneticallyengineered S. cerevisiae.
is a psychoactive plant known as "ketum" in Malaysia and "kratom" in Thailand... more is a psychoactive plant known as "ketum" in Malaysia and "kratom" in Thailand. This plant is distinctly known to produce two important alkaloids, namely mitragynine (MG) and 7-hydroxymitragynine (7-OH-MG) that can bind to opioid receptors [1]. MG was reported to exhibit antidepressant properties in animal studies [2]. These compounds were also proposed to have the potential to replace opioid analgesics with much lower risks of side effects [3]. To date, there are only over 40 metabolites identified in [4,5]. To obtain a more complete profile of secondary metabolites in ketum, we performed metabolomics study using mature leaves of the green variety. The leaf samples were extracted using methanol prior to liquid chromatography-electrospray ionization-time of flight-mass spectrometry (LC-ESI-TOF-MS) analysis. This data can be useful to for the identification of unknown metabolites that are associated with alkaloid biosynthesis pathway in .
Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesqui... more Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesquiterpenes, which contribute to its flavour and fragrance. This study describes the cloning and functional characterisation of PmSTPS1 and PmSTPS2, two sesquiterpene synthase genes that were identified from P. minus transcriptome data mining. The full-length sequences of the PmSTPS1 and PmSTPS2 genes were expressed in the E. coli pQE-2 expression vector. The sizes of PmSTPS1 and PmSTPS2 were 1098 bp and 1967 bp, respectively, with open reading frames (ORF) of 1047 and 1695 bp and encoding polypeptides of 348 and 564 amino acids, respectively. The proteins consist of three conserved motifs, namely, Asp-rich substrate binding (DDxxD), metal binding residues (NSE/DTE), and cytoplasmic ER retention (RxR), as well as the terpene synthase family N-terminal domain and C-terminal metal-binding domain. From the in vitro enzyme assays, using the farnesyl pyrophosphate (FPP) substrate, the PmSTPS1 enzyme produced multiple acyclic sesquiterpenes of β-farnesene, α-farnesene, and farnesol, while the PmSTPS2 enzyme produced an additional nerolidol as a final product. The results confirmed the roles of PmSTPS1 and PmSTPS2 in the biosynthesis pathway of P. minus, to produce aromatic sesquiterpenes.
Proteomics is often hindered by the lack of protein sequence database particularly for non-model ... more Proteomics is often hindered by the lack of protein sequence database particularly for non-model species such as herbs. An integrative approach called proteomics informed by transcriptomics is possible [1], in which translated transcriptome sequence database is used as the protein sequence database. In this current study, the proteome profile were profiled using SWATH-MS technology complemented with documented transcriptome profiling [2], the first such report in this tropical herb. The plant was also elicited using a phytohormone, methyl jasmonate (MeJA) and protein changes were elucidated using label-free quantification of SWATH-MS to understand the role of such signal molecule in this herbal species. The mass spectrometry proteomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD005749. This data article refers to the article entitled "Proteomics (SWATH-MS)-informed by transcriptomics approach of leaves up...
Agrobacterium-mediated transformation of indica rice is undoubtedly a challenging task due to the... more Agrobacterium-mediated transformation of indica rice is undoubtedly a challenging task due to the rice recalcitrant nature to transformation process. Therefore, optimization of the transformation protocol is important for specific indica rice cultivar to ensure effectiveness of the transformation. In this study, crucial parameters affecting Agrobacteriummediated transformation were optimized to obtain transgenic rice of local rice cultivar (indica MR219). Embryogenic calli were chosen for inoculation with Agrobacterium tumefaciens strain LBA4404 harbouring a binary vector pH2GW7-ABP57 containing gene of interest, Auxin binding protein 57 (Abp57). The parameters that have been optimized were the immersion time, co-cultivation period, acetosyringone concentration and co-cultivation temperature. A total of four days co-cultivation period and 30 min immersion of embryogenic callus are optimum for the transformation of MR219 with transformation efficiency of 26.4% and 16.0%, respectively. Acetosyringone at 200 μM and co-cultivation at 28°C also gave the highest transformation efficiency (14.4 and 18.4%, respectively). Meanwhile, inclusion of 20 g/L maltose+20 g/L sorbitol into the regeneration media has significantly improve the transformed somatic embryos growth and increase the regeneration efficiency up to 40.0%. The results of polymerase chain reaction (PCR) and reverse transcription-polymerase chain reaction (RT-PCR) indicated that the transgene was successfully integrated and overexpressed in transgenic rice of MR219. In conclusion, significant improvement in transformation efficiency for rice cv. MR219 has been obtained by using the optimised protocol for transformation and regeneration developed in this study.
Mangosteen (Garcinia mangostana L.) is known for its delectable taste and contains high amount of... more Mangosteen (Garcinia mangostana L.) is known for its delectable taste and contains high amount of xanthones which have been reported to possess anti-cancer, anti-inflammatory and other bioactive properties. However, stage-specific regulation of mangosteen fruit ripening has never been studied in detail. We have performed a comparative transcriptomic analysis of three ripening stages (Stage 0, 2 and 6) of mangosteen. We have obtained a raw data from six libraries through Illumina HiSeq 4000. A total of ~ 40 Gb of raw data were generated. Clean reads of 650,887,650 (bp) were obtained from 656,913,570 (bp) raw reads. The raw transcriptome data were deposited to SRA database, with the BioProject accession number of PRJNA339916. These data will be beneficial for transcriptome profiling in order to study the regulation of mangosteen fruit ripening. The lack of a complete sequence database from this species impedes protein identification. These data sets provide a reference data for the ex...
Mangosteen (Garcinia mangostana Linn.) is an ultra-tropical tree characterized by its unique dark... more Mangosteen (Garcinia mangostana Linn.) is an ultra-tropical tree characterized by its unique dark purple fruits with white flesh. The xanthone-rich purple pericarp tissue contains valuable compounds with medicinal properties. Following previously reported genome sequencing of a common variety of mangosteen [1], we performed another whole genome sequencing of a commercially popular variety of this fruit species (var. Mesta) for comparative analysis of its genome composition. Raw reads of the DNA sequencing project were deposited to SRA database with the accession number SRX2709728.
The "Queen of Fruits" mangosteen (Garcinia mangostana L.) produces commercially important fruits ... more The "Queen of Fruits" mangosteen (Garcinia mangostana L.) produces commercially important fruits with desirable taste of flesh and pericarp rich in xanthones with medicinal properties. To date, only limited knowledge is available on the cytogenetics and genome sequences of a common variety of mangosteen (Abu Bakar et al., 2016 [1]). Here, we report the first single-molecule real-time (SMRT) sequencing data from whole genome sequencing of mangosteen of Mesta variety. Raw reads of the SMRT sequencing project can be obtained from SRA database with the accession numbers SRX2718652 until SRX2718659.
Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used... more Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P. minus has not been well-studied due to the limited genetic information. Hence, we performed Illumina paired-end RNA-seq for de novo reconstruction of P. minus leaf transcriptome to identify differentially expressed genes (DEGs) in response to MeJA elicitation. A total of 182,111 unique transcripts (UTs) were obtained by de novo assembly of 191.57 million paired-end clean reads using Trinity analysis pipeline. A total of 2374 UTs were identified to be significantly up-/down-regulated 24 h after MeJA treatment. These UTs comprising many genes related to plant secondary metabolite biosynthesis, defense and stress responses. To validate our sequencing results, we analyzed the expression of 21 selected DEGs by quantitative real-time PCR and found a good correlation between the two analyses. The single time-point analysis in this work not only provides a useful genomic resource for P. minus but also gives insights on molecular mechanisms of stress responses in P. minus.
An hourly progression of gene expression profiling in maslinic acid treated Raji cells, which rep... more An hourly progression of gene expression profiling in maslinic acid treated Raji cells, which reported activation of several key pathways.
Rafflesia possesses unique biological features and known primarily for producing the world's larg... more Rafflesia possesses unique biological features and known primarily for producing the world's largest and existing as a single flower. However, to date, little is known about key regulators participating in Rafflesia flower development. In order to further understand the molecular mechanism that regulates Rafflesia cantleyi flower development, RNA-seq data from three developmental stages of floral bud, representing the floral organ primordia initiation, floral organ differentiation, and floral bud outgrowth, were analysed. A total of 89,890 transcripts were assembled of which up to 35% could be annotated based on homology search. Advanced transcriptome analysis using K-mean clustering on the differentially expressed genes (DEGs) was able to identify 12 expression clusters that reflect major trends and key transitional states, which correlate to specific developmental stages. Through this, comparative gene expression analysis of different floral bud stages identified various transcription factors related to flower development. The members of WRKY, NAC, bHLH, and MYB families are the most represented among the DEGs, suggesting their important function in flower development. Furthermore, pathway enrichment analysis also revealed DEGs that are involved in various phytohormone signal transduction events such as auxin and auxin transport, cytokinin and gibberellin biosynthesis. Results of this study imply that transcription factors and phytohormone signalling pathways play major role in Rafflesia floral bud development. This study provides an invaluable resource for molecular studies of the flower development process in Rafflesia and other plant species.
Flavonoids are polyphenols that are important organic chemicals in plants. The health benefits of... more Flavonoids are polyphenols that are important organic chemicals in plants. The health benefits of flavonoids that result in high commercial values make them attractive targets for large-scale production through bioengineering. Strategies such as engineering a flavonoid biosynthetic pathway in microbial hosts provide an alternative way to produce these beneficial compounds. Escherichia coli, Saccharomyces cerevisiae and Streptomyces sp. are among the expression systems used to produce recombinant products, as well as for the production of flavonoid compounds through various bioengineering approaches including clustered regularly interspaced short palindromic repeats (CRISPR)-based genome engineering and genetically encoded biosensors to detect flavonoid biosynthesis. In this study, we review the recent advances in engineering model microbial hosts as being the factory to produce targeted flavonoid compounds.
BackgroundCarnivorous plants have been fascinating researchers with their unique characters and b... more BackgroundCarnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry.MethodsThis review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants:Drosera(sundews),Dionaea(Venus flytrap), Nepenthes(tropical pitcher plants),Sarracenia(North American pitcher plants), Cephalotus(Australian pitcher plants), Genlisea(corkscrew plants),andUtricularia(bladderworts).ResultsSince the discovery of secreted protease nepenthesin inNepenthespitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants.DiscussionThese differe...
Nepenthes, locally known as 'periuk kera' in Malaysia, is a fascinating species due to uniqueness... more Nepenthes, locally known as 'periuk kera' in Malaysia, is a fascinating species due to uniqueness in their morphology in having pitcher organ for carnivorous diet. The pitcher plant has been used for cooking traditional delicacies and as traditional remedies to treat illness. Hence, this species might possess beneficial health properties. This study aimed to compare the antioxidant activity of the pitcher extracts from Nepenthes ampullaria, Nepenthes rafflesiana and their hybrid, Nepenthes × hookeriana. The samples were extracted using methanol:chloroform:water (3:1:1) via sonication assisted extraction and the extracts were subjected to three different antioxidant assays, namely 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing power (FRAP) and total phenolic content (TPC). Extract from N. ampullaria exhibited the strongest radical scavenging activity (0.148 ± 0.04 mg/mL) with the highest ferric reducing power (0.009 ± 0.003 mg GA/mg dry weight) among the three species, whereas that of N. rafflesiana possessed the highest phenolic content (0.057 ± 0.017 mg GA/mg dry weight). However, the antioxidant capacities of the pitcher extracts were not significantly different (p>0.05) between the three species and were much lower than the gallic acid as a standard reference.
Microbial production of natural products using metabolic engineering and synthetic biology approa... more Microbial production of natural products using metabolic engineering and synthetic biology approaches often involves the assembly of multiple gene fragments including regulatory elements, especially when using eukaryotes as hosts. Traditional cloning strategy using restriction enzyme digestion and ligation are laborious and inflexible owing to the high number of sequential cloning steps, limited cutting sites and generation of undesired 'scar' sequences. In this study, a homology-based isothermal DNA assembly method was carried out for one-step simultaneous assembly of multiple DNA fragments to engineer plant phenylpropanoid biosynthesis in Saccharomyces cerevisiae. Rapid construction of yeast plasmid harboring dual gene expression cassettes was achieved via isothermal assembly of four DNA fragments designed with 20 bp overlapping sequences. The rate-limiting enzyme of phenylpropanoid pathway, cinnamate 4-hydroxylase encoded by C4H gene from Polygonum minus was cloned in tandem with yeast promoter and terminator elements of S. cerevisiae for efficient construction of phenylpropanoid biosynthetic pathway in recombinant yeast. The assembled pAG-CAT (C4H-ADH1t-TEF1p) shuttle plasmid and transformation of S. cerevisiae with the plant C4H gene were confirmed via PCR analysis. Based on these findings, the yeast shuttle plasmid harboring P. minus phenylpropanoid biosynthesis gene was efficiently constructed to be the starting platform for the production of plant natural products in geneticallyengineered S. cerevisiae.
is a psychoactive plant known as "ketum" in Malaysia and "kratom" in Thailand... more is a psychoactive plant known as "ketum" in Malaysia and "kratom" in Thailand. This plant is distinctly known to produce two important alkaloids, namely mitragynine (MG) and 7-hydroxymitragynine (7-OH-MG) that can bind to opioid receptors [1]. MG was reported to exhibit antidepressant properties in animal studies [2]. These compounds were also proposed to have the potential to replace opioid analgesics with much lower risks of side effects [3]. To date, there are only over 40 metabolites identified in [4,5]. To obtain a more complete profile of secondary metabolites in ketum, we performed metabolomics study using mature leaves of the green variety. The leaf samples were extracted using methanol prior to liquid chromatography-electrospray ionization-time of flight-mass spectrometry (LC-ESI-TOF-MS) analysis. This data can be useful to for the identification of unknown metabolites that are associated with alkaloid biosynthesis pathway in .
Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesqui... more Polygonum minus (syn. Persicaria minor) is a herbal plant that is well known for producing sesquiterpenes, which contribute to its flavour and fragrance. This study describes the cloning and functional characterisation of PmSTPS1 and PmSTPS2, two sesquiterpene synthase genes that were identified from P. minus transcriptome data mining. The full-length sequences of the PmSTPS1 and PmSTPS2 genes were expressed in the E. coli pQE-2 expression vector. The sizes of PmSTPS1 and PmSTPS2 were 1098 bp and 1967 bp, respectively, with open reading frames (ORF) of 1047 and 1695 bp and encoding polypeptides of 348 and 564 amino acids, respectively. The proteins consist of three conserved motifs, namely, Asp-rich substrate binding (DDxxD), metal binding residues (NSE/DTE), and cytoplasmic ER retention (RxR), as well as the terpene synthase family N-terminal domain and C-terminal metal-binding domain. From the in vitro enzyme assays, using the farnesyl pyrophosphate (FPP) substrate, the PmSTPS1 enzyme produced multiple acyclic sesquiterpenes of β-farnesene, α-farnesene, and farnesol, while the PmSTPS2 enzyme produced an additional nerolidol as a final product. The results confirmed the roles of PmSTPS1 and PmSTPS2 in the biosynthesis pathway of P. minus, to produce aromatic sesquiterpenes.
Proteomics is often hindered by the lack of protein sequence database particularly for non-model ... more Proteomics is often hindered by the lack of protein sequence database particularly for non-model species such as herbs. An integrative approach called proteomics informed by transcriptomics is possible [1], in which translated transcriptome sequence database is used as the protein sequence database. In this current study, the proteome profile were profiled using SWATH-MS technology complemented with documented transcriptome profiling [2], the first such report in this tropical herb. The plant was also elicited using a phytohormone, methyl jasmonate (MeJA) and protein changes were elucidated using label-free quantification of SWATH-MS to understand the role of such signal molecule in this herbal species. The mass spectrometry proteomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD005749. This data article refers to the article entitled "Proteomics (SWATH-MS)-informed by transcriptomics approach of leaves up...
Agrobacterium-mediated transformation of indica rice is undoubtedly a challenging task due to the... more Agrobacterium-mediated transformation of indica rice is undoubtedly a challenging task due to the rice recalcitrant nature to transformation process. Therefore, optimization of the transformation protocol is important for specific indica rice cultivar to ensure effectiveness of the transformation. In this study, crucial parameters affecting Agrobacteriummediated transformation were optimized to obtain transgenic rice of local rice cultivar (indica MR219). Embryogenic calli were chosen for inoculation with Agrobacterium tumefaciens strain LBA4404 harbouring a binary vector pH2GW7-ABP57 containing gene of interest, Auxin binding protein 57 (Abp57). The parameters that have been optimized were the immersion time, co-cultivation period, acetosyringone concentration and co-cultivation temperature. A total of four days co-cultivation period and 30 min immersion of embryogenic callus are optimum for the transformation of MR219 with transformation efficiency of 26.4% and 16.0%, respectively. Acetosyringone at 200 μM and co-cultivation at 28°C also gave the highest transformation efficiency (14.4 and 18.4%, respectively). Meanwhile, inclusion of 20 g/L maltose+20 g/L sorbitol into the regeneration media has significantly improve the transformed somatic embryos growth and increase the regeneration efficiency up to 40.0%. The results of polymerase chain reaction (PCR) and reverse transcription-polymerase chain reaction (RT-PCR) indicated that the transgene was successfully integrated and overexpressed in transgenic rice of MR219. In conclusion, significant improvement in transformation efficiency for rice cv. MR219 has been obtained by using the optimised protocol for transformation and regeneration developed in this study.
Mangosteen (Garcinia mangostana L.) is known for its delectable taste and contains high amount of... more Mangosteen (Garcinia mangostana L.) is known for its delectable taste and contains high amount of xanthones which have been reported to possess anti-cancer, anti-inflammatory and other bioactive properties. However, stage-specific regulation of mangosteen fruit ripening has never been studied in detail. We have performed a comparative transcriptomic analysis of three ripening stages (Stage 0, 2 and 6) of mangosteen. We have obtained a raw data from six libraries through Illumina HiSeq 4000. A total of ~ 40 Gb of raw data were generated. Clean reads of 650,887,650 (bp) were obtained from 656,913,570 (bp) raw reads. The raw transcriptome data were deposited to SRA database, with the BioProject accession number of PRJNA339916. These data will be beneficial for transcriptome profiling in order to study the regulation of mangosteen fruit ripening. The lack of a complete sequence database from this species impedes protein identification. These data sets provide a reference data for the ex...
Mangosteen (Garcinia mangostana Linn.) is an ultra-tropical tree characterized by its unique dark... more Mangosteen (Garcinia mangostana Linn.) is an ultra-tropical tree characterized by its unique dark purple fruits with white flesh. The xanthone-rich purple pericarp tissue contains valuable compounds with medicinal properties. Following previously reported genome sequencing of a common variety of mangosteen [1], we performed another whole genome sequencing of a commercially popular variety of this fruit species (var. Mesta) for comparative analysis of its genome composition. Raw reads of the DNA sequencing project were deposited to SRA database with the accession number SRX2709728.
The "Queen of Fruits" mangosteen (Garcinia mangostana L.) produces commercially important fruits ... more The "Queen of Fruits" mangosteen (Garcinia mangostana L.) produces commercially important fruits with desirable taste of flesh and pericarp rich in xanthones with medicinal properties. To date, only limited knowledge is available on the cytogenetics and genome sequences of a common variety of mangosteen (Abu Bakar et al., 2016 [1]). Here, we report the first single-molecule real-time (SMRT) sequencing data from whole genome sequencing of mangosteen of Mesta variety. Raw reads of the SMRT sequencing project can be obtained from SRA database with the accession numbers SRX2718652 until SRX2718659.
Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used... more Polygonum minus is an herbal plant that grows in Southeast Asian countries and traditionally used as medicine. This plant produces diverse secondary metabolites such as phenolic compounds and their derivatives, which are known to have roles in plant abiotic and biotic stress responses. Methyl jasmonate (MeJA) is a plant signaling molecule that triggers transcriptional reprogramming in secondary metabolism and activation of defense responses against many biotic and abiotic stresses. However, the effect of MeJA elicitation on the genome-wide expression profile in the leaf tissue of P. minus has not been well-studied due to the limited genetic information. Hence, we performed Illumina paired-end RNA-seq for de novo reconstruction of P. minus leaf transcriptome to identify differentially expressed genes (DEGs) in response to MeJA elicitation. A total of 182,111 unique transcripts (UTs) were obtained by de novo assembly of 191.57 million paired-end clean reads using Trinity analysis pipeline. A total of 2374 UTs were identified to be significantly up-/down-regulated 24 h after MeJA treatment. These UTs comprising many genes related to plant secondary metabolite biosynthesis, defense and stress responses. To validate our sequencing results, we analyzed the expression of 21 selected DEGs by quantitative real-time PCR and found a good correlation between the two analyses. The single time-point analysis in this work not only provides a useful genomic resource for P. minus but also gives insights on molecular mechanisms of stress responses in P. minus.
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