Research Paper
Bioinformatics
Aboozar Soorni; Sepehr Meratian Esfahani; Badraldin Ebrahim Sayed-Tabatabaei
Abstract
Today, medicinal plants are used in the treatment of many diseases because of their secondary metabolites. Thyme as one of these plants contains a wide range of secondary metabolites such as terpenes. Various methods have been developed to increase these materials. In classical methods, environmental ...
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Today, medicinal plants are used in the treatment of many diseases because of their secondary metabolites. Thyme as one of these plants contains a wide range of secondary metabolites such as terpenes. Various methods have been developed to increase these materials. In classical methods, environmental factors are changed to produce the most effective substance in medicinal plants, but in newer approaches that are based on plant genetics, higher yields are observed. One of these approaches is the use of miRNAs. These miRNAs control gene expression after transcription by mRNA analysis or inhibition of their translation, and play different roles in biological and metabolic processes in plants and animals. One of the simplest and least expensive methods for identifying miRNAs is the use of bioinformatics tools and methods. To identify distinct miRNA in different species of thyme, a study based on homology search was conducted using transcriptomic data of thyme. First, this information was refined and then aligament performed against all known miRNAs in the miRBase database. After screening of results based on factors such as length and e-value level, the secondary structure of miRNAs was analyzed with UNAfold tool. Target genes were identified using psRNATARGET tool and phylogenetic relationships were investigated using maximum likelihood method and RaxML tool. In total 64 distinct candidate’s miRNAs were identified in different species of thymus and 14 miRNAs included miR172 and miR396 played an important role in terpenes synthesis and it has been proven in previous studies. The phylogenetic tree was able to show the relationship between miRNAs in different species.
Research Paper
Bioinformatics
Samira Mohammadi
Abstract
60 kDa heat shock proteins (HSP60s) also known as chaperonin (cpn60) play an important role in plant growth and stress response. In this study, 32 HSP60 genes were identified in the soybean genome through bioinformatics tools, which are distributed on 14 chromosomes. Most of these proteins are hydrophilic, ...
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60 kDa heat shock proteins (HSP60s) also known as chaperonin (cpn60) play an important role in plant growth and stress response. In this study, 32 HSP60 genes were identified in the soybean genome through bioinformatics tools, which are distributed on 14 chromosomes. Most of these proteins are hydrophilic, acidic, and unstable with a high aliphatic index The evolutionary tree divided HSP60 proteins of soybean, Arabidopsis, and rice into three main groups based on their cellular location. The proteins of different subgroups have highly conserved gene structure, conserved motifs, intron phase, and three-dimensional structure, which can indicate their functional similarities in different subgroups. Several cis-regulatory elements responsive to stresses, growth and hormones were found in the promoter of GmHSP60 genes, that indicate their role in plant growth and response to environmental stresses. Gene ontology (GO) analysis predicted that GmHSP60 genes were responsible for protein folding and refolding in an ATP-dependent manner in response to various stresses. Analysis of the transcriptome pattern (RNA-seq) showed that most of the GmHSP60 genes had high expression in response to salt, drought, cold, heat, submergence, and nutrient deficiency stresses, which indicates their role in improving soybean tolerance to abiotic stresses. Overall, these findings provide useful information to better understand the function of GmHSP60 genes in soybean and facilitate the way for the utilization of chaperonin family genes for achieving plant tolerance against abiotic stresses.
Research Paper
Proteomics
Samira Mardani Zonouz; Mahmoud Toorchi; Shaghayegh aslzad
Abstract
Drought is one of the most important factors causing abiotic stress in plants. Wheat, as a vital crop, is extensively cultivated in regions that face water scarcity at least during one period of the year. Proteomic approach is one of the ways to identify proteins involved in plant tolerance to water ...
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Drought is one of the most important factors causing abiotic stress in plants. Wheat, as a vital crop, is extensively cultivated in regions that face water scarcity at least during one period of the year. Proteomic approach is one of the ways to identify proteins involved in plant tolerance to water stress. In order to investigate the effect of water deficit stress on the root proteome pattern of desert-tolerant wheat, an experiment was conducted in the form of a completely randomized design with seven replications. Root proteins were extracted by TCA/acetone method and the protein expression pattern was analyzed using two-dimensional electrophoresis. Potential proteins involved in the response to water deficiency were identified by comparing the protein expression patterns under water deficit stress with the expression pattern in control conditions. The results revealed significant differences in root weight and root length at a 5% probability level, indicating the detrimental effects of water stress on plant roots. The proteomic analysis identified 98 reproducible protein spots, of which 10 exhibited statistically significant changes, with eight spots showing increased expression and one showing decreased expression. These protein spots were identified based on their molecular weight (MW) and isoelectric point (pI) through database searches. The identified proteins were classified into various functional categories related to stress response, including protein synthesis and accumulation, oxidative stress, response and defense against stress and metabolic pathways.
Research Paper
Biotic and Abiotic stress
Maryam Faramarzi Jafar Beiglou; Farhad Nazarian-Firouzabadi; Seyed Sajad Sohrabi; Ali Moghadam
Abstract
Plant diseases, particularly diseases caused by fungi and oomycetes pose significant challenges in modern agriculture worldwide. Pathogen associated molecular pattern (PAMP) like chitin found in the cell walls of fungi and oomycetes, trigger defence signalling, leading to expression of R-genes and the ...
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Plant diseases, particularly diseases caused by fungi and oomycetes pose significant challenges in modern agriculture worldwide. Pathogen associated molecular pattern (PAMP) like chitin found in the cell walls of fungi and oomycetes, trigger defence signalling, leading to expression of R-genes and the production of reactive oxygen species (ROS), and accumulation of a wide range of metabolites. Chitin elicitors prompt the expression of defence-related genes such as chitinases, ultimately the resulting in the breakdown of chitin in the pathogen's cell wall. To assess the expression level of certain chitinases in potatoes and the activity of antioxidant enzymes, leaves of a tolerant potato genotype (jelly) was challenged with chitin oligomers in vitro. Result of this study revealed that 48 hours post chitin induction, the expression of different classes of chitinase genes were significantly increased. Class I chitinase (Soltu.DM.10G017450) and class III chitinase (Soltu.DM.11G026160) genes, had respectively the highest (5.5-fold relative to control) and the lowest (1.1-fold relative to control) expression level after 48 hours post chitin inoculation. However, the activities of antioxidant enzymes catalase and ascorbate peroxidase did not change significantly compared to the control. These findings suggest that the application of chitin does not activate the signaling pathways involved in the biosynthesis of antioxidant enzymes 48 hours after chitin treatment. In addition, results of this study may imply that chitinase genes can be cloned by genetic engineering approaches to generate transgenic plants resistant to pathogens.
Research Paper
Molecular Plant Breeding
Leila Farhadi; Ali Arminian; sajad Rashidi Monfared
Abstract
MicroRNAs (miRNAs) are endogenous and noncoding small RNA molecules with a length of 19-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. In this study, several miRNAs in Camelina were identified, and their potential roles were reported. Camelina with its scientific ...
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MicroRNAs (miRNAs) are endogenous and noncoding small RNA molecules with a length of 19-24 nucleotides (nts) that regulate target genes at the post-transcriptional level in plants. In this study, several miRNAs in Camelina were identified, and their potential roles were reported. Camelina with its scientific name (Camelina Sativa L.) is an oil-medicinal plant belonging to the Brassicaceae family. First the RNA was extracted from C. sativa leaf and sent to the Beijing genome institute for RNA-sequencing. Then the data were assembled denovo with Trinity software after removing the reads with lower quality than the threshold level and trimming them. Detection of miRNAs was then performed by miRDeep2 software. Accordingly, we identified 33 miRNAs from the leaf dataset, and their secondary structures were evaluated. The target genes of the detected miRNAs were identified by the psRNAtarget website. Examining the target genes showed that a total of 1415 genes are regulated by these microRNAs, which belong to several gene families with different biological functions, including the genes of proteins that bind to the Squamusa promoter, the protein kinase family, etc. Comparing the expression of microRNA carrying genes (TPM) in the two studied doubled haploid lines, showed that except for miR296 and miR474 which were more expressed in line number 1, the other miRNAs had higher expression in line number 2. Considering the lower amount of oil production in line number 1 compared to line number 2, this indicates the relationship of these two microRNAs with oil production. miR483 was not expressed in any of the lines. miR113 and miR206 had the highest expression levels among all microRNAs. The higher expression of micro RNAs in line 2 probably indicates the higher activity of the silencing mechanism at the transcription level for the target genes in this line compared to line number 1.
Research Paper
Biotic and Abiotic stress
Alireza Tarang
Abstract
Rice (Oryza sativa) is very sensitive to drought stress because of its limited adaptation to water-deficit conditions. Drought stress alters morphological, physiological, biochemical, and molecular responses in plant. In this study, the effects of drought stress on morphological traits and expression ...
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Rice (Oryza sativa) is very sensitive to drought stress because of its limited adaptation to water-deficit conditions. Drought stress alters morphological, physiological, biochemical, and molecular responses in plant. In this study, the effects of drought stress on morphological traits and expression of transcription factor genes DREB2A and ZFP252 at vegetative and reproductive stages were investigated in TH1 line (drought sensitive) and Neda (drought tolerant). Drought stress was induced by stopping irrigation at tillering and heading stages. Investigation of morphological traits showed tiller and panicle numbers as production indices were significantly higher in Neda cultivar than TH1 line. Real Time PCR Neda genotype showed a significant increase (3.217 expression ratio) in expression of transcript level of ZFP252 at vegetative stage under drought stress. This indicates the importance of this drought stress responsive gene in acquisition of drought tolerance in this genotype at this stage. Investigation of expression level changes in TH1 line showed significant increase in DREB2A and ZFP252 genes expression under drought stress at the vegetative stage. Gene expression analysis in this study suggesting that tolerant and sensitive plants may be using genetic regulations and different mechanisms to be exposed to stress conditions. Deciphering of these molecular mechanisms will aid to better understand stress tolerance and to select strategies for improving crop productivity facing climate change.
