MyMedR

Variable expansin expression in Arabidopsis leads to different growth responses

Goh HH, Sloan J, Malinowski R, Fleming A

J Plant Physiol, 2014 Feb 15;171(3-4):329-39.

PMID: 24144490 DOI: 10.1016/j.jplph.2013.09.009

Expansins have long been implicated in the control of cell wall extensibility. However, despite ample evidence supporting a role for these proteins in the endogenous mechanism of plant growth, there are also examples in the literature where the outcome of altered expansin gene expression is difficult to reconcile with a simplistic causal linkage to growth promotion. To investigate this problem, we report on the analysis of transgenic Arabidopsis plants in which a heterologous cucumber expansin can be inducibly overexpressed. Our results indicate that the effects of expansin expression on growth depend on the degree of induction of expansin expression and the developmental pattern of organ growth. They support the role of expansin in directional cell expansion. They are also consistent with the idea that excess expansin might itself impede normal activities of cell wall modifications, culminating in both growth promotion and repression depending on the degree of expression.

Fulltext RNA-seq Analysis of Nepenthes ampullaria

Wan Zakaria WN, Loke KK, Zulkapli MM, Mohd Salleh F', Goh HH, Mohd Noor N

Front Plant Sci, 2015;6:1229.

PMID: 26793209 DOI: 10.3389/fpls.2015.01229

Metabolite profiling reveals temperature effects on the VOCs and flavonoids of different plant populations

Goh HH, Khairudin K, Sukiran NA, Normah MN, Baharum SN

Plant Biol (Stuttg), 2016 Jan;18 Suppl 1:130-9.

PMID: 26417881 DOI: 10.1111/plb.12403

Temperature is one of the key factors in limiting the distribution of plants and controlling major metabolic processes. A series of simulated reciprocal transplant experiments were performed to investigate the effect of temperature on plant chemical composition. Polygonum minus of different lowland and highland origin were grown under a controlled environment with different temperature regimes to study the effects on secondary metabolites. We applied gas chromatography-mass spectrometry and liquid chromatography time-of-flight mass spectrometry to identify the chemical compounds. A total of 37 volatile organic compounds and 85 flavonoids were detected, with the largest response observed in the compositional changes of aldehydes and terpenes in highland plants under higher temperature treatment. Significantly less anthocyanidin compounds and larger amounts of flavonols were detected under higher temperature treatment. We also studied natural variation in the different plant populations growing under the same environment and identified compounds unique to each population through metabolite fingerprinting. This study shows that the origin of different plant populations influences the effects of temperature on chemical composition.

Fulltext DNA-seq analysis of Garcinia mangostana

Abu Bakar S, Sampathrajan S, Loke KK, Goh HH, Mohd Noor N

Genom Data, 2016 Mar;7:62-3.

PMID: 26981362 DOI: 10.1016/j.gdata.2015.11.018

Mangosteen (Garcinia mangostana Linn.) is a tropical tree mainly found in South East Asia and considered as "the queen of fruits". The asexually produced fruit is dark purple or reddish in color, with white flesh which is slightly acidic with sweet flavor and a pleasant aroma. The purple pericarp tissue is rich in xanthones which are useful for medical purposes. We performed the first genome sequencing of this commercially important fruit tree to study its genome composition and attempted draft genome assembly. Raw reads of the DNA sequencing project have been deposited to SRA database with the accession number SRX1426419.

Fulltext RNA-seq analysis for plant carnivory gene discovery in Nepenthes × ventrata

Wan Zakaria WN, Loke KK, Goh HH, Mohd Noor N

Genom Data, 2016 Mar;7:18-9.

PMID: 26981352 DOI: 10.1016/j.gdata.2015.11.007

Carnivorous plants have the ability to capture and digest insects for nutrients, which allows them to survive in land deprived of nitrogenous nutrients. Nepenthes spp. are one of the carnivorous plants, which uniquely produce pitcher from the tip of an elongated leaf. This study provides the first transcriptome resource from pitcher of a Nepenthes ventricosa × Nepenthes alata hybrid, Nepenthes × ventrata to understand carnivory mechanism in Nepenthes spp., as well as in other carnivorous species. Raw reads and the transcriptome assembly project have been deposited to SRA database with the accession numbers SRX1389337 (day 0 control), SRX1389392 (day 3 longevity), and SRX1389395 (day 3 chitin-treated).

Fulltext RNA-seq analysis for secondary metabolite pathway gene discovery in Polygonum minus

Loke KK, Rahnamaie-Tajadod R, Yeoh CC, Goh HH, Mohamed-Hussein ZA, Mohd Noor N, et al.

Genom Data, 2016 Mar;7:12-3.

PMID: 26981350 DOI: 10.1016/j.gdata.2015.11.003

Polygonum minus plant is rich in secondary metabolites, especially terpenoids and flavonoids. Present study generates transcriptome resource for P. minus to decipher its secondary metabolite biosynthesis pathways. Raw reads and the transcriptome assembly project have been deposited at GenBank under the accessions SRX313492 (root) and SRX669305 (leaf) respectively.

Fulltext Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development

Lee XW, Mat-Isa MN, Mohd-Elias NA, Aizat-Juhari MA, Goh HH, Dear PH, et al.

PLoS One, 2016;11(12):e0167958.

PMID: 27977777 DOI: 10.1371/journal.pone.0167958

Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to address this issue, we have generated and characterised the transcriptome of the Rafflesia cantleyi flower, and performed a comparison with the transcriptome of its floral bud to predict genes that are expressed and regulated during flower development. Approximately 40 million sequencing reads were generated and assembled de novo into 18,053 transcripts with an average length of 641 bp. Of these, more than 79% of the transcripts had significant matches to annotated sequences in the public protein database. A total of 11,756 and 7,891 transcripts were assigned to Gene Ontology categories and clusters of orthologous groups respectively. In addition, 6,019 transcripts could be mapped to 129 pathways in Kyoto Encyclopaedia of Genes and Genomes Pathway database. Digital abundance analysis identified 52 transcripts with very high expression in the flower transcriptome of R. cantleyi. Subsequently, analysis of differential expression between developing flower and the floral bud revealed a set of 105 transcripts with potential role in flower development. Our work presents a deep transcriptome resource analysis for the developing flower of R. cantleyi. Genes potentially involved in the growth and development of the R. cantleyi flower were identified and provide insights into biological processes that occur during flower development.

Fulltext Genome-wide transcriptome profiling ofCarica papayaL. embryogenic callus

Jamaluddin ND, Mohd Noor N, Goh HH

Physiol Mol Biol Plants, 2017 Apr;23(2):357-368.

PMID: 28461724 DOI: 10.1007/s12298-017-0429-8

Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. By using 3' mRNA-sequencing, we generated 6,190,687 processed reads and 47.0% were aligned to papaya genome reference, in which 21,170 (75.4%) of 27,082 annotated genes were found to be expressed but only 41% was expressed at functionally high levels. The top 10% of genes with high transcript abundance were significantly enriched in biological processes related to cell proliferation, stress response, and metabolism. Genes functioning in somatic embryogenesis such as SERK and LEA, hormone-related genes, stress-related genes, and genes involved in secondary metabolite biosynthesis pathways were highly expressed. Transcription factors such as NAC, WRKY, MYB, WUSCHEL, Agamous-like MADS-box protein and bHLH important in somatic embryos of other plants species were found to be expressed in papaya embryogenic callus. Abundant expression of enolase and ADH is consistent with proteome study of papaya somatic embryo. Our study highlights that some genes related to secondary metabolite biosynthesis, especially phenylpropanoid biosynthesis, were highly expressed in papaya embryogenic callus, which might have implication for cell factory applications. The discovery of all genes expressed in papaya embryogenic callus provides an important information into early biological processes during the induction of embryogenesis and useful for future research in other plant species.

Fulltext Transcriptome analysis of Carica papaya embryogenic callus upon De-etiolated 1 (DET1) gene suppression

Jamaluddin D, Mohd Noor N, Goh HH

Genom Data, 2017 Jun;12:120-121.

PMID: 28516036 DOI: 10.1016/j.gdata.2017.05.004

Papaya is considered to be one of the most nutritional fruits. It is rich in vitamins, carotenoids, flavonoids and other phytonutrient which function as antioxidant in our body [1]. Previous studies revealed that the suppression of a negative regulator gene in photomorphogenesis, De-etiolated 1 (DET1) can improve the phytonutrient in tomato and canola without affecting the fruit quality [2], [3]. This report contains the experimental data on high-throughput 3' mRNA sequencing of transformed papaya callus upon DET1 gene suppression.

Fulltext DNA shotgun sequencing analysis of Garcinia mangostana L. variety Mesta

Abu Bakar S, Kumar S, Loke KK, Goh HH, Mohd Noor N

Genom Data, 2017 Jun;12:118-119.

PMID: 28516035 DOI: 10.1016/j.gdata.2017.05.001

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.

Fulltext Iso-Seq analysis of Nepenthes ampullaria, Nepenthes rafflesiana and Nepenthes × hookeriana for hybridisation study in pitcher plants

Zulkapli MM, Rosli MAF, Salleh FIM, Mohd Noor N, Aizat WM, Goh HH

Genom Data, 2017 Jun;12:130-131.

PMID: 28529881 DOI: 10.1016/j.gdata.2017.05.003

Tropical pitcher plants in the species-rich Nepenthaceae family of carnivorous plants possess unique pitcher organs. Hybridisation, natural or artificial, in this family is extensive resulting in pitchers with diverse features. The pitcher functions as a passive insect trap with digestive fluid for nutrient acquisition in nitrogen-poor habitats. This organ shows specialisation according to the dietary habit of different Nepenthes species. In this study, we performed the first single-molecule real-time isoform sequencing (Iso-Seq) analysis of full-length cDNA from Nepenthes ampullaria which can feed on leaf litter, compared to carnivorous Nepenthes rafflesiana, and their carnivorous hybrid Nepenthes × hookeriana. This allows the comparison of pitcher transcriptomes from the parents and the hybrid to understand how hybridisation could shape the evolution of dietary habit in Nepenthes. Raw reads have been deposited to SRA database with the accession numbers SRX2692198 (N. ampullaria), SRX2692197 (N. rafflesiana), and SRX2692196 (N. × hookeriana).

Fulltext SMRT sequencing data for Garcinia mangostana L. variety Mesta

Midin MR, Loke KK, Madon M, Nordin MS, Goh HH, Mohd Noor N

Genom Data, 2017 Jun;12:134-135.

PMID: 28529883 DOI: 10.1016/j.gdata.2017.04.003

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.

Fulltext Transcriptomic data of Arabidopsis thaliana hypocotyl upon suppression of expansin genes

Ilias IA, Airianah OB, Baharum SN, Goh HH

Genom Data, 2017 Jun;12:132-133.

PMID: 28529882 DOI: 10.1016/j.gdata.2017.05.002

Expansin is a cell wall loosening protein without hydrolytic activity, which allows cell expansion by influencing cell wall extensibility. Previous studies showed that the suppression of expansin genes (EXPA1, EXPA3, EXPA5 and EXPA10) resulted in defective organ growth and altered cell wall chemical composition [1,2]. However, the molecular mechanism on how the suppression of non-enzymatic expansin expression can result in widespread effects on plant cell wall and organ growth is still unclear. In this study, we performed transcriptomic analysis on the hypocotyls of previously reported transgenic Arabidopsis line [1] to investigate the effects of expansin gene suppression on the global gene expression pattern, particularly on the cell wall related genes.

Fulltext RNA-seq analysis of mangosteen (Garcinia mangostana L.) fruit ripening

Abdul-Rahman A, Goh HH, Loke KK, Noor NM, Aizat WM

Genom Data, 2017 Jun;12:159-160.

PMID: 28560167 DOI: 10.1016/j.gdata.2017.05.013

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 exploration of novel genes or proteins to understand mangosteen fruit ripening behaviour.

Fulltext Mass spectrometry data of metabolomics analysis of Nepenthes pitchers

Rosli MAF, Azizan KA, Baharum SN, Goh HH

Data Brief, 2017 Oct;14:295-297.

PMID: 28795107 DOI: 10.1016/j.dib.2017.07.068

Hybridisation plays a significant role in the evolution and diversification of plants. Hybridisation among Nepenthes species is extensive, either naturally or man-made. To investigate the effects of hybridisation on the chemical compositions, we carried out metabolomics study on pitcher tissue of Nepenthes ampullaria, Nepenthes rafflesiana and their hybrid, Nepenthes × hookeriana. Pitcher samples were harvested and extracted in methanol:chloroform:water via sonication-assisted extraction before analysed using LC-TOF-MS. MS data were analysed using XCMS online version 2.2.5. This is the first MS data report towards the profiling, identification and comprehensive comparison of metabolites present in Nepenthes species.

Fulltext Microarray dataset of transgenic rice overexpressing Abp57

Tan LW, Tan CS, Rahman ZA, Goh HH, Ismail I, Zainal Z

Data Brief, 2017 Oct;14:267-271.

PMID: 28795104 DOI: 10.1016/j.dib.2017.07.047

The dataset presented in this article describes microarray experiment of Auxin-binding protein 57, Abp57-overexpressing transgenic rice. The gene expression profiles were generated using Affymetrix GeneChip® Rice (Cn) Gene 1.0 ST Arrays. Total RNA from seedlings tissue of transgenic rice and wildtype, which serve as control were used as starting materials for microarray experiment. Detailed experimental methods and data analysis were described here. The raw and normalized microarray data were deposited into Gene Expression Omnibus (GEO) under accession number GSE99055.

Fulltext RNA-seq data from different developmental stages of Rafflesia cantleyi floral buds

Amini S, Alias H, Aizat-Juhari MA, Mat-Isa MN, Adam JH, Goh HH, et al.

Genom Data, 2017 Dec;14:5-6.

PMID: 28761813 DOI: 10.1016/j.gdata.2017.07.008

Rafflesia cantleyi, known as one of the world's largest flowers, is a specialised holoparasite due to dramatic morphological modifications. It possesses highly reduced vegetative structure and only appears as a flower for sexual reproduction. Moreover, it has an unusual life cycle in that its floral bud development takes up to nine months. In order to fully understand the highly modified floral organ structure and long life cycle of R. cantleyi, we used Illumina sequencing technology (HiSeq) for sequence generation followed by de novo assembly of sequence reads. We obtained the RNA-seq data from three different stages of floral bud, representing the early, mid and advanced developmental stages. These data are available via BioProject accession number PRJNA378435. More than 10.3 Gb raw sequence data were generated, corresponding to 102,203,042 raw reads. Following removal of low-quality reads and trimming of adapter sequences, a total of 91,638,836 reads were obtained. De novo assembly of these sequences using Trinity resulted in 89,690 unique transcripts with an N50 of 1653 bp. The obtained transcriptomic data will be useful for further study to understand the molecular interactions that result in R. cantleyi floral development.

Fulltext Transcriptomic data of Arabidopsis hypocotyl overexpressing a heterologous CsEXPA1 gene

Ilias IA, Airianah OB, Baharum SN, Goh HH

Data Brief, 2017 Dec;15:320-323.

PMID: 29214193 DOI: 10.1016/j.dib.2017.09.050

Expansin increases cell wall extensibility to allow cell wall loosening and cell expansion even in the absence of hydrolytic activity. Previous studies showed that excessive overexpression of expansin gene resulted in defective growth (Goh et al., 2014; Rochange et al., 2001) [1,2] and altered cell wall chemical composition (Zenoni et al., 2011) [3]. However, the molecular mechanism on how the overexpression of non-enzymatic cell wall protein expansin can result in widespread effects on plant cell wall and organ growth remains unclear. We acquired transcriptomic data on previously reported transgenic Arabidopsis line (Goh et al., 2014) [1] to investigate the effects of overexpressing a heterologus cucumber expansin gene (CsEXPA1) on the global gene expression pattern during early and late phases of etiolated hypocotyl growth.

Fulltext Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation

Rahnamaie-Tajadod R, Loke KK, Goh HH, Noor NM

Front Plant Sci, 2017;8:109.

PMID: 28220135 DOI: 10.3389/fpls.2017.00109

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.

Fulltext Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids

Loke KK, Rahnamaie-Tajadod R, Yeoh CC, Goh HH, Mohamed-Hussein ZA, Zainal Z, et al.

PeerJ, 2017;5:e2938.

PMID: 28265493 DOI: 10.7717/peerj.2938

BACKGROUND: Polygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production.

METHODS: In this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference.

RESULTS: A total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites.

DISCUSSION: This comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome.

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