Papers by Hidayah Samsulrizal
We present the draft genome sequence of extended-spectrum -lactamase (ESBL)-producing Klebsiella... more We present the draft genome sequence of extended-spectrum -lactamase (ESBL)-producing Klebsiella pneumoniae isolated from a stool sample collected from a patient admitted for a gastrointestinal procedure. The draft genome sequence consists of 86 contigs, including a combined 5,632,663 bases with 57% G؉C content.
Identification of flowering genes of Stevia rebaudiana by using transcriptomic data
International Journal of Life Sciences and Biotechnology, 2020
Oil palms are important commodity crop in Malaysia as major contributor to agriculture sector. Th... more Oil palms are important commodity crop in Malaysia as major contributor to agriculture sector. Thus, the need for better yield production is urgent to accommodate rising local and global demand while reducing the land expansion for oil palm plantation. This can be achieved by identifying the agronomical important traits in oil palm using comparative genomic approach. In this study, gene related to plant height, fruit development and fruit ripening in oil palm were predicted by comparing Elaeis guineensis genome sequence with Arabidopsis thaliana and Solanum lycopersicum genome sequence. The model plant chosen are based on its special attribute such as completely sequenced and fleshy fruit model. The analysis begun with orthology analysis using InParanoid, and SonicParanoid. There are 9,624 orthologous genes identified common among species selected. The reformatted orthologous genes were then annotated with Gene Ontology (GO) using Blast2GO program. The process of annotation include ...
Applied and Environmental Microbiology, 2016
Salmonella enterica subsp. enterica serotype Enteritidis is a major cause of human salmonellosis ... more Salmonella enterica subsp. enterica serotype Enteritidis is a major cause of human salmonellosis worldwide; however, little is known about the genetic relationships between S . Enteritidis clinical strains and S . Enteritidis strains from other sources in Chile. We compared the whole genomes of 30 S . Enteritidis strains isolated from gulls, domestic chicken eggs, and humans in Chile, to investigate their phylogenetic relationships and to establish their relatedness to international strains. Core genome multilocus sequence typing (cgMLST) analysis showed that only 246/4,065 shared loci differed among these Chilean strains, separating them into two clusters (I and II), with cluster II being further divided into five subclusters. One subcluster (subcluster 2) contained strains from all surveyed sources that differed at 1 to 18 loci (of 4,065 loci) with 1 to 18 single-nucleotide polymorphisms (SNPs), suggesting interspecies transmission of S . Enteritidis in Chile. Moreover, clusters w...
Asia Pacific Journal of Molecular Biology and Biotechnology
Stevia rebaudiana is a plant under the Asteraceae family and has been reported as a healthier alt... more Stevia rebaudiana is a plant under the Asteraceae family and has been reported as a healthier alternative to sugar. Steviol glycosides (SGs) is the group of secondary metabolites responsible for the sweet taste. Among nine SGs synthesised by S. rebaudiana, stevioside and rebaudioside A are the sweetest. The biosynthetic pathway of SGs partly involves conversion of geranylgeranyl diphosphate (GGDP) into steviol, catalysed by ent- kaurene synthase (KS), ent-copalyl diphosphate synthase (CPPS), and kaurene oxidase (KO). This study focuses on in silico molecular characterization and phylogenetic analysis of KS from Malaysia’s S. rebaudiana MS007 variety (Stevia MS007). The transcriptomic dataset of S. rebaudiana accession MS007 was used in initial experiment toward analysing the KS. Through the blastx homology search using transcriptomic dataset query Cluster-31069.42907, the Stevia rebaudiana kaurene synthase (SrKS) sequence was identified with the highest similarity percentage identit...
Pertanika Journal of Tropical Agricultural Science
Phytophthora palmivora is a destructive plant pathogenic oomycete that has caused lethal diseases... more Phytophthora palmivora is a destructive plant pathogenic oomycete that has caused lethal diseases in a wide range of hosts. It is a pan-tropical distributed pathogen that can infect plants at all growth stages. Extensive studies have linked P. palmivora to severe diseases in several crops, such as black pepper, rubber, cocoa, and durian, causing global economic losses. This review covers the following topics in depth: (i) P. palmivora as phytopathogen; (ii) identification and infection mechanism in rubber, cocoa, and durian; and (iii) management and control applied for P. palmivora diseases. Effective management strategies were studied and practiced to prevent the spread of P. palmivora disease. Genetic resistance and biocontrol are the best methods to control the disease. A better understanding of P. palmivora infection mechanisms in our main crops and early disease detection can reduce the risk of catastrophic pandemics.
Plants
Transcriptomics has significantly grown as a functional genomics tool for understanding the expre... more Transcriptomics has significantly grown as a functional genomics tool for understanding the expression of biological systems. The generated transcriptomics data can be utilised to produce a gene co-expression network that is one of the essential downstream omics data analyses. To date, several gene co-expression network databases that store correlation values, expression profiles, gene names and gene descriptions have been developed. Although these resources remain scattered across the Internet, such databases complement each other and support efficient growth in the functional genomics area. This review presents the features and the most recent gene co-expression network databases in crops and summarises the present status of the tools that are widely used for constructing the gene co-expression network. The highlights of gene co-expression network databases and the tools presented here will pave the way for a robust interpretation of biologically relevant information. With this ef...
Oryza sativa, which is commonly known as rice, is one of the staple foods consumed by Asian. Ther... more Oryza sativa, which is commonly known as rice, is one of the staple foods consumed by Asian. There are three subspecies of O. sativa that are different in their geographical adaptations which are Japonica, Javanica and Indica. Climate change causes increasing greenhouse gas emissions fluctuating rainfall, and drought which is the limiting factors of rice production in Malaysia. In rice, SUMO E2-Conjugating Enzyme (OsSCE1) gene plays a role as a negative regulator in the drought stress response. OsSCE1 gene is a type of small ubiquitin-like modifier (SUMO)-conjugating enzyme involved in a few regulatory processes such as SUMOylation. The crop improvement can be made possible through a genome editing approach which enables the manipulation of targeted genetic traits and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system is one of the genomes editing technologies that are accessible. In this study, the CRISPR construct of drought tolerance of Oryza sativa subsp. ...
Genome-wide comparative analysis of drought tolerant genes in rice, maize, date palm and arabidopsis
The availability of various comparative genomics tools has allowed the identification of several ... more The availability of various comparative genomics tools has allowed the identification of several potential drought-tolerant genes in plants such as wheat, tomato, maize and others. In this study, orthologous drought-tolerant genes in Oryza sativa (rice), Zea mays (maize), Phoenix dactilyfera (date palm) and Arabidopsis thaliana (arabidopsis) were identified using InParanoid and SonicParanoid tools. From the 9,952 orthologous proteins found among the four species, 8,573 sequences were annotated and assigned to 5,729 GO terms; classified into the biological process category, molecular function category and cellular component category. Sixty-five OGs were found to be represented under four drought tolerance GO terms; regulation of response to water deprivation (GO:2000070), response to water deprivation, behavioural response to water deprivation (GO:0042630), and cellular response to water deprivation (GO:0042631). The potential drought tolerance genes have been predicted by using sequence homology search against the Drought Stress Gene Database (DroughtDB). Three potential drought-tolerant genes were selected and visualised to compare the gene alignment across the 4 species using the MAUVE software. To assure a satisfactory outcome, this in silico study will be confirmed by genome editing studies in rice via CRISPR/Cas9 system
TURKISH JOURNAL OF BIOLOGY, 2021
Stevia rebaudiana is a medicinal plant recommended to diabetic or obese patients as an alternativ... more Stevia rebaudiana is a medicinal plant recommended to diabetic or obese patients as an alternative sweetener owing to its low-calorie property. Previous studies have found that the stevioside level is highest at the time of flower bud formation and lowest at the time of preceding and following flower bud formation. Hence, this study aims to identify the genes involved in the flowering of local S. rebaudiana accession MS007 by investigating the transcriptomic data of two stages of growth, before flowering (BF) and after flowering (AF) that were deposited under accession number SRX6362785 and SRX6362784 at the NCBI SRA database. The transcriptomic study managed to annotate 108299 unigenes of S. rebaudiana with 8871 and 9832 genes that were differentially expressed in BF and AF samples, respectively. These genes involved in various metabolic pathways related to flower development, response to stimulus as well as photosynthesis. Pheophorbide A oxygenase (PAO), eukaryotic translation initiation factor 3 subunit E (TIF3E1), and jasmonate ZIM domain-containing protein 1 (JAZ1) were found to be involved in the flower development. The outcome of this study will help further research in the manipulation of the flowering process, especially in the breeding programme to develop photo-insensitive Stevia plant.
Genome-scale compositional comparisons towards drought tolerant genes in rice, date palm, maize and thale cress
Journal of Tropical Life Science, 2021
Due to its low-calorie property, Stevia rebaudiana is being promoted as an alternative sweetener ... more Due to its low-calorie property, Stevia rebaudiana is being promoted as an alternative sweetener for diabetic and obese patients. The steady demand in the market for high-quality stevia extracts presents a challenge for the enhanced production of steviol glycosides that are safe for human consumption. This study characterized the structure and content of the gene involved in the production of UGT74G1 protein for Stevia rebaudiana accession MS007 through in silico analysis using a transcriptome dataset of stevia MS007. Homologous search using BLASTp shows high similarity to Q6VAA6 RecName: Full=UDP-glycosyltransferase 74G1 (S. rebaudiana) as the top hit sequence. InterPro family and domain protein motif search revealed UDP-glucuronosyl/UDP-glucosyltransferase (IPR002213) and UDP-glycosyltransferase family, conserved site (IPR035595). The phylogenetic tree construction was done by selecting 14 out of 102 protein sequences from BLASTp search. The phylogenetic analysis revealed a high v...
Microorganisms, 2021
Pathogenic fungi belonging to the genera Botrytis, Phaeomoniella, Fusarium, Alternaria and Asperg... more Pathogenic fungi belonging to the genera Botrytis, Phaeomoniella, Fusarium, Alternaria and Aspergillus are responsible for vines diseases that affect the growth, grapevine yield and organoleptic quality. Among innovative strategies for in-field plant disease control, one of the most promising is represented by biocontrol agents, including wild epiphytic yeast strains of grapevine berries. Twenty wild yeast, isolated and molecularly identified from three different Malaysian regions (Perlis, Perak and Pahang), were evaluated in a preliminary screening test on agar to select isolates with inhibition against Botrytis cinerea. On the basis of the results, nine yeasts belonging to genera Hanseniaspora, Starmerella, Metschnikowia, Candida were selected and then tested against five grape berry pathogens: Aspergillus carbonarius, Aspergillus ochraceus, Fusarium oxysporum, Alternaria alternata and Phaeomoniella chlamydospora.Starmerella bacillaris FE08.05 and Metschnikowia pulcherrima GP8 and...
Comparative genomics of cell wall remodellinggenes in fleshy fruit species and the control of fruitsoftening in tomato
Fruits are the seed dispersal units of flowering plants and fleshy fruits form an important part ... more Fruits are the seed dispersal units of flowering plants and fleshy fruits form an important part of the human diet. Ripening is a complex developmental process and involves many events such as textural and constitutional changes. The texture of fleshy fruits is one of the major criteria for consumer choice. However, the molecular determinants of ripening- associated changes in texture or “softening” are relatively poorly understood and seem to involve a large number of cell wall remodelling factors. The recent completion of the tomato genome sequence has revealed more than 50 cell wall structure-related genes that are expressed during fruit development and ripening and may impact texture changes in this fruit (Tomato Genome Consortium, 2012). Also expression of these genes appears to be under both genetic and epigenetic control. The aim of the project is to compare, on a genome-wide scale, ripeningrelated gene expression in a range of fleshy fruits and especially those linked with c...
International Journal of Life Sciences and Biotechnology, 2019
Stevia rebaudiana (Bertoni) is a commercially important plant worldwide. The leaves of stevia con... more Stevia rebaudiana (Bertoni) is a commercially important plant worldwide. The leaves of stevia contain steviol glycosides which are non-caloric and high-potency sweeteners. They are suitable for substituting sucrose and other artificial sweetening agents. Stevia also has many therapeutic properties such as antidiabetic, anti-cariogenic, antimicrobial, anticancer and antioxidative. Rebaudioside A and stevioside are the major glycosides produced in stevia leaves. Development of new varieties of Stevia rebaudiana with a greater content of rebaudioside A and decreased content of stevioside is the main concern. This is due to rebaudioside A having a more desirable sweet flavour taste than stevioside which possesses bitter aftertaste. In respect to that, many biotechnological approaches are available for the industrial improvement and manipulation of steviol glycosides content in stevia. Transcriptome profiling has emerged as a useful tool to identify target genes involved in the steviol g...
Big Data In Agriculture, 2021
Stevia rebaudiana is among recognized medicinal plants used as an artificial sweetener in food an... more Stevia rebaudiana is among recognized medicinal plants used as an artificial sweetener in food and drinks as it contains very low sugar content. It is recognized that stevia contains component steviol glycoside which contains stevioside and rebaudioside A has 50 to 100 more sweetness than sucrose. Due to this, stevia extraction of steviol glycoside is very demanded in the food and pharmaceutical industries. Research shows that stevioside levels are the highest at the time of flower bud formation and lower at the time preceding and following flower bud formation. Hence, this study aims to identify and characterize the putative gene that may involve in the flowering of local S. rebaudiana accession MS007 from the analysis of bioinformatics tools. The outcome of this study will help further in the study of the manipulation of the flowering process to increase the outcome yield of steviol glycoside. This study involves characterization of putative zinc finger ZAT10 gene by homology sear...
Annals of Microbiology, 2021
Purpose Bacillus megaterium strain BHS1, isolated from an alkaline water sample taken from Mavi G... more Purpose Bacillus megaterium strain BHS1, isolated from an alkaline water sample taken from Mavi Gölü (Blue Lake, Turkey), can grow on minimal medium containing 2,2-dichloropropionic acid. We characterized this bacterium at the genomic level. Methods The HiSeq platform was used to carry out genome sequencing, de novo assembly, and scaffolding with strain BHS1. Next, genome data were analyzed to demarcate DNA regions containing protein-coding genes and determine the function of certain BHS1 genes. Finally, results from a colorimetric chloride ion–release assay demonstrated that strain BHS1 produces dehalogenase. Results De novo assembly of the BHS1 genomic sequence revealed a genome size of ~ 5.37 Mb with an average G+C content of 38%. The predicted nuclear genome harbors 5509 protein-coding genes, 1353 tRNA genes, 67 rRNA genes, and 6 non-coding (mRNA) genes. Genomic mapping of strain BHS1 revealed its amenability to synthesize two families of dehalogenases (Cof-type haloacid dehalog...
Pertanika Journal of Tropical Agricultural Science, 2021
Food security is the most crucial issue faced by humans considering the rising population. Rice, ... more Food security is the most crucial issue faced by humans considering the rising population. Rice, a staple food consumed by nearly 50% of the world’s population, faces challenges to meet the consumers’ demand to ensure self-sufficiency amidst various abiotic and biotic stresses. Drought, salinity, heat, and infection by bacteria and viruses are the main challenges in rice cultivation. Genome editing technology provides abundant opportunities to implement selective genome modifications. Moreover, it finds the functional implications of different genome components in rice and provides a new approach for creating rice varieties tolerant of stresses. This review focuses on rice production worldwide and challenges faced in rice cultivation, and current genome editing tools available that can be utilised for crop breeding and improvement. In addition, the application of genome editing to develop biotic and abiotic resistance rice varieties is critically discussed.
Journal of Tropical Life Science, 2020
An acid, 2,2-dichloropropionic acid (2,2-DCP) is an active ingredient in herbicide (Dalapon®). Us... more An acid, 2,2-dichloropropionic acid (2,2-DCP) is an active ingredient in herbicide (Dalapon®). Using 2,2-DCP as a model substrate, an alkalotolerant bacterium was successfully isolated from the Blue Lake, Turkey. This bacterium is a potential bioremediation agent of recalcitrant xenobiotic halogenated compounds. This study aimed to prove the efficacy of the alkalotolerance Bacillus megaterium BHS1 in degrading 2,2-DCP as the sole source of carbon. Biolog GEN III system and 16S rRNA analysis were used for the identification of the bacterium. It was discovered that the strain BHS1 is Bacillus megaterium, and the bacterium that was observed to thrive in alkaline conditions (pH 7.0−14.0), supplemented with varying concentrations of 2,2-DCP (from 20 to 60 mM). Growth of strain BHS1 was exceptional in 40 mM of 2,2-DCP at pH 9, corresponding to a cell doubling time of 17.7 hour, whereas was fully inhibited at 50 mM 2,2-DCP. Since halogenated pollutants can make their way into highly alkaline environments, therefore, identifying threshold levels of strain BHS1 with respect to alkaline-tolerance and maximum level of 2,2-DCP may prove pertinent. This is to ensure that an optimal environment is created for the bacteria to degrade 2,2-DCP-contaminated water. In addition, this is the first study exploring a Bacillus species isolated from an alkaline environment adept in utilizing 2,2-DCP as a sole source of carbon. Hence, the ability of this strain to degrade other types of haloalkanoic acids constitutes a worthy future study.
International Journal of Life Sciences and Biotechnology, 2019
Ripening is a complex developmental process and involves many events such as textural and constit... more Ripening is a complex developmental process and involves many events such as textural and constitutional changes. The texture of fleshy fruits is one of the major criteria for consumer choice. However, the molecular determinants of ripening- associated changes in texture or “softening” are relatively poorly understood and seem to involve a large number of cell wall remodelling factors. The recent completion of the tomato genome sequence has revealed more than 50 cell wall structure-related genes that are expressed during fruit development and ripening and may impact texture changes in this fruit. The aim of the project is to compare, on a genome-wide scale, ripening-related gene expression in a range of fleshy fruits and especially those linked with cell wall remodelling. Then by identifying orthologous genes in different fruit species to make predictions about those genes likely to important for the softening process in all fleshy fruits. Comparative genomics analysis of tomato (So...
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Papers by Hidayah Samsulrizal