Research Paper
Bioinformatics
Zahra Aminfar; Babak Rabiei; Masoud Tohidfar; Mohammad Hossein Mirjalili
Abstract
Isoprenoids and their derivatives represent the largest group of natural compounds in plants that are biosynthesized from isoprenyl diphosphate C5 units. These C5 units generated by two distinctive biosynthetic pathways in plants including mevalonate (MVA) pathway in the cytoplasm and methylerthritol ...
Read More
Isoprenoids and their derivatives represent the largest group of natural compounds in plants that are biosynthesized from isoprenyl diphosphate C5 units. These C5 units generated by two distinctive biosynthetic pathways in plants including mevalonate (MVA) pathway in the cytoplasm and methylerthritol phosphate (MEP) pathway in plastids. To perform a meta-analysis of two pathways of MVA and MEP, expression data of the microarray experiments in different tissues, developmental stages, biotic and abiotic stresses were used in Arabidopsis thaliana as a model plant. The transcriptom meta-analysis was carried out using Genevestigator as a large database containing transcriptomics data of GEO in NCBI and ArrayExpress in EBI. The results of the meta-analysis showed that the transcription of genes encoding the enzymes of MVA and MEP pathway did not coordinate and they had different expression patterns in developmental stages, various tissues and conditions. MVA pathway genes show the highest expression in the roots and reproductive organs, while the MEP pathway genes are expressed in photosynthetic tissues. The results obtained here can help to understand how the underlying pathway gene networks are organized and regulated in different conditions, tissues and developmental stages.
Research Paper
Biosafty
Negar Bagheri; Masoud Ahmadzadeh; Gholamreza Salehi Jouzani
Abstract
Co-inoculation of plant growth promoting bacteria and biological control agents, is a strategy to improve health, yield and quality of crop production. The objective of the present study was to evaluate interactions of two bacterial strains, Bacillus amyloliquefaciens UTB96 and Azospirillum oryzae NBT506, ...
Read More
Co-inoculation of plant growth promoting bacteria and biological control agents, is a strategy to improve health, yield and quality of crop production. The objective of the present study was to evaluate interactions of two bacterial strains, Bacillus amyloliquefaciens UTB96 and Azospirillum oryzae NBT506, on growth promotion of wheat and control of the causal agent of Fusarium head blight, Fusarium graminearum. The results showed that single and co-culture of these strains inhibit mycelium growth of F. graminearum by direct inhibition and volatile organic compounds. In germinator assays, different wheat growth features were increased and disease index was decreased. Results showed that co-inoculation or single application of the bacteria in the soil significantly enhanced root length (14-80%), root fresh weight (18-167%), root dry weight (4-110%,), shoot length (17-61%), shoot fresh weight (47-169%) and shoot dry weight (up to 90%). In addition, a significant decrease in disease index (62-100%) was observed in different single and co-culture treatments. In conclusion, the studied two bacterial strains showed synergistic effects on wheat growth promotion and fungal growth inhibition.
Research Paper
Molecular Genetics and Genetic Engineering
Niloufar Peykari; Katayoun Zamani
Abstract
Producing transgenic plants need new promoters. Due to the advent of next generation sequencing technologies and the production of massive genomic data for various crop plant species paralleled by the development of bioinformatics tools, there is an opportunity to identify, isolate and characterize ...
Read More
Producing transgenic plants need new promoters. Due to the advent of next generation sequencing technologies and the production of massive genomic data for various crop plant species paralleled by the development of bioinformatics tools, there is an opportunity to identify, isolate and characterize new promoters. Because of public concern about using viral promoters, there is a need for cloning and using plant promoters in transgenic food crops. Native plant constitutive promoters may be composed of non-specific elements that are simply more efficient at protein recruitment for transcription. Promoters are classified as inducible, constitutive and tissue specific according to the nature of gene expression they regulate. Housekeeping genes are the best and most important sources for isolating the constitutive promoters. In this study, -Glucoronidase reporter gene expression mediated by a polyubiquitin promoter (CaUBQ10) from chickpea (Cicer ariethinum) was analyzed in tobacco tissues. The functionality of the CaUBQ10 was confirmed in leaves, stems, and roots of stably transformed tobacco plants and suggested that the CaUBQ10 is a constitutive promoter and may provide a valuable choice for high-level expression of target genes during the life cycle of a plant.
Research Paper
Molecular Phsoiology
Razieh Rahmati; Mohammad Ali Ebrahimi; Hamid Sobhanian; Ghasem Hosseini Salekdeh; Mohammad Reza Ghaffari
Abstract
Hydrangea macrophylla is a plant that its blooms turn from pink to blue in the presence of aluminum (Al) and thereby could be considered as a model plant for studying blue color formation. In this study, the metabolite profiling analysis has been performed using ion chromatography coupled to mass spectrometry ...
Read More
Hydrangea macrophylla is a plant that its blooms turn from pink to blue in the presence of aluminum (Al) and thereby could be considered as a model plant for studying blue color formation. In this study, the metabolite profiling analysis has been performed using ion chromatography coupled to mass spectrometry (IC-MS/MS) and Ultra Performance Liquid Chromatography (UPLC) to investigate the regulatory connected network among metabolites during color turning from pink to blue in full bloom of H. macrophylla in the presence and absence of aluminum. The metabolite profiles resulted in identification of 35 metabolites including two soluble sugars, six sugar phosphates, two sugar nucleotides, four organic acids, four nucleotides and 17 amino acids. Further, a coordinated change was found in glycolytic metabolites showing changes in flux through a pathway during color formation. Moreover, there was a strong correlation among nitrogenous compounds including glutamine, aspartate, glutamate, glycine and threonine indicating the important role of nitrogen metabolism during blue color formation. These findings will facilitate comprehensive research on the regulatory networks of color change in full bloom in H. macrophylla.
Research Paper
Bioinformatics
Reza Mir Drikvand; Seyyed sajad Sohrabi; Seyyed Mohsen ُSohrabi; Kamran Samiei
Abstract
MicroRNAs (miRNAs) are a class of small and noncoding RNAs with length of 18-24 nucleotides that control the expression of target genes at the transcriptional and post-transcriptional levels in plants. The miRNAs play an important role in different processes such as growth and development, cell proliferation ...
Read More
MicroRNAs (miRNAs) are a class of small and noncoding RNAs with length of 18-24 nucleotides that control the expression of target genes at the transcriptional and post-transcriptional levels in plants. The miRNAs play an important role in different processes such as growth and development, cell proliferation and response to stresses in plants. Coriander or Coriandrum sativum L. is a plant of Apiaceae family with different nutritional and pharmaceutical applications. Up to now, the genome of this plant has not been sequenced and there is no report of miRNAs identification has been recorded for it. The present study was performed to identify the conserved miRNAs and their target genes in transcriptome of coriander plant. Firstly, Transcriptome of seed and leaf tissues was assembled and non-coding transcripts were identified and considered as miRNA precursor. Finally, among candidate sequences, three miRNAs named csa-miR162, csa-miR169 and csa-miR399 belong to three conserved families were identified after strict filtering. Identified miRNAs showed differential expression between seed and leaf tissues and also role of their target genes in different biological processes was confirmed. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of coriander plant in the present study, these miRNAs can be used as candidate genes to improve qualitative and quantitative yield and resistance to different stresses in this plant.
Research Paper
Biotic and Abiotic stress
Seyyed Hamidreza Hashemi-petroudi; Ghorbanali Nematzadeh; Markus Kuhlmann
Abstract
Genome-wide identification of orthologs and paralogs gene clusters across different species is considered as a common strategy for predicting gene function. Regarding to importance role of species-specific paralog genes in adaptation to specific environmental stresses, identification of paralog genes ...
Read More
Genome-wide identification of orthologs and paralogs gene clusters across different species is considered as a common strategy for predicting gene function. Regarding to importance role of species-specific paralog genes in adaptation to specific environmental stresses, identification of paralog genes in the Aeluropus littoralis, halophyte plant, was considered in this study. For this purpose, the proteome data of four species including A. littoralis, Oryza sativa, Brachypodium distachyon and Sorghum bicolor was compared genome-widely. Based on OrthoMCL analysis, by comparing of 15916 protein sequences of A. littoralis to proteome of other species, 10312 orthologs gene cluster were identified that shared in all given species while 70 unique paralog gene clusters were devoted to A. littoralis. Gene ontology annotation of these paralog clusters showed that they are involved in key biological processes such as cellular processes, metabolic DNA processes, chromatin organization, response to environmental stimuli and cell growth and cycle. The study of the largest cluster of this set led to the identification of a family of small polypeptides (72-39 aa) that is called DEVIL (DVL). Analysis of A. littoralis transcriptome data in a Heatmap display a divergence in gene expression patterns of DVL gene family that could be an evident for their sub‐functionalization in biological processes and molecular functions of the cell. Functional analysis of AlDVL peptide hormones (phytohormones) could be useful for identifying their potential role in the mechanisms involved in drought and salinity tolerance.
