Bioinformatics
Ehsan Pourabed; Zahra-Sadat Shobbar
Volume 7, Issue 18 , November 2017, , Pages 73-92
Abstract
Rice is one of the most valuable crops, and water deficiency is the most important constraint to rice production. Due to the complexity and multigenic characteristics of the drought tolerance trait, the objective of the current research were reconstruction of the involved gene networks and identification ...
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Rice is one of the most valuable crops, and water deficiency is the most important constraint to rice production. Due to the complexity and multigenic characteristics of the drought tolerance trait, the objective of the current research were reconstruction of the involved gene networks and identification of the key genes in rice plants using microarray data analysis. To achieve the goal, all the differentially expressed genes (DEGs) with fold changes ≥+2.5 and ≤-2.5 at drought stress compared to normal conditions were identified among all the microarray data-series in rice using Genevestigator online tools. Totally, 101 DEGs were identified and their gene regulatory as well as protein-protein interactions (PPIs) networks was reconstructed. The hub genes (genes with the most interactions) were distinguished using nine Cyto-hubba computational algorithms on Cytoscape software. Based on the hub analysis results, 14 unique (non-redundant) genes were identified as the most effective genes in response to drought stress and their co-expression networks were constructed. According to the gene ontology analysis of the DEGs, their co-expressed genes and the hub genes, regulation of transcription were among the major groups indicating the importance of transcription factors (TFs) roles in drought tolerance mechanism. Amongst the TFs, ABA-responsive binding factors (AREBs), AP2, bZIP, WRKY and MYB gene families were observed. We hope that the obtained results would be beneficial toward finding the smart strategies for drought tolerance improvement.
Bioinformatics
Masoumeh Fallah Ziarani; Masoud Tohidfar; Zahra Aminfar
Volume 7, Issue 17 , July 2017, , Pages 15-29
Abstract
The biosynthesis pathway of fatty acids is one of the important pathways in the body of most organisms that an enzyme Acyl carrier protein (ACP) plays an important role in it. The purpose of this study is phylogenetic and in silico analysis of gene ACP. More analysis indicate that ACP gene has 4 exons, ...
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The biosynthesis pathway of fatty acids is one of the important pathways in the body of most organisms that an enzyme Acyl carrier protein (ACP) plays an important role in it. The purpose of this study is phylogenetic and in silico analysis of gene ACP. More analysis indicate that ACP gene has 4 exons, 3 introns and and 2 mRNA in prokaryotes and 13 exons, 12 introns and 9 mRNA in eukaryotes. This protein has target mitochondrial in plant eukaryotes and non-mitochondrial target in prokaryotes and it is not also included of secreted proteins. The results of multiple alignments by T-Coffee server showed that the ACP genes between bacterial species are more protected than plant species. Phylogenetic analysis of ACP proteins in prokaryotes is revealed that except for a cluster, in other case Gram-positive bacteria are in one cluster and gram-negative bacteria are in another cluster. In eukaryotes, different plant species are scattered in different clusters. These results indicated that clustering in eukaryotes are not relate to species. In addition, the study of ACP proteins in eukaryotes and prokaryotes revealed that both eukaryotes and prokaryotes are placed together in some clusters that is due to the similarities of sequences in species. Comparison of the secondary structure of the protein in eukaryotes and prokaryotes showed that the number of alpha and beta sheets in prokaryotes are more than of eukaryotes. Three-dimensional modeling of this protein was done by homology modeling using Swiss Model database in wheat (as representative of eukaryotic) and bacteria Clostridioides difficile 630 (as represented prokaryotes). The best templates were extracted with high similarity from PDB database. To validation of modeled structure and esterochemical analysis, Ramachandran plot was drawn and dihydral angles were calculated. Structural quality evaluation results showed that the proposed models are good quality and stability. The study of protein structure may help to understand protein function and the details of its structure can be useful in studies of the active site of the protein and docking.
Bioinformatics
Maryam Mortezaeefar; Reza Fotovat; Farid Shekari; Shahryar Sasani
Volume 7, Issue 17 , July 2017, , Pages 55-71
Abstract
Environmental conditions lead to biosynthesis of signaling molecules including phytohormones in plants which have important functions as primary messengers in signal transduction and regulating cell metabolism. Jasmonic acid hormone by controlling the transcription factors can play key roles in response ...
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Environmental conditions lead to biosynthesis of signaling molecules including phytohormones in plants which have important functions as primary messengers in signal transduction and regulating cell metabolism. Jasmonic acid hormone by controlling the transcription factors can play key roles in response to various stresses and developmental processes in plants. Despite numerous studies, plant responses to the hormone are not completely understood. Here, microarray data of Arabidopsis from GEO database was used for analysis of co-expression network. WGCNA (Weighted Gene Co-expression Network Analysis) analysis determines 25 gene groups (modules) that their expression profiles correlated highly significant with each other in response to jasmonic acid. Gene ontology was utilized to investigate each module for statistical significance. This analysis indicated that jasmonic acid controls many processes including photosynthesis, cell programmed death, and response to various stresses. In addition, many of transcription factors such as 11 genes of NAC family and 12 genes of bHLH family play roles in the regulation of jasmonic acid responses and adjust processes including response to biotic and abiotic stresses, flower development and response to light.
Bioinformatics
Amin Abedi; Reza Shirzadian-Khorramabad; Mohamad mehdi Sohani
Volume 6, Issue 16 , March 2017, , Pages 13-29
Abstract
Strictosidine synthase is a key enzyme in the monoterpenoid indole alkaloids biosynthesis pathway. Proteins with Str_synth domain have been identified in plants, bacteria, insects and even mammalians and called Strictosidine synthase-like due to unknown functional roles. With the Arabidopsis and rice ...
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Strictosidine synthase is a key enzyme in the monoterpenoid indole alkaloids biosynthesis pathway. Proteins with Str_synth domain have been identified in plants, bacteria, insects and even mammalians and called Strictosidine synthase-like due to unknown functional roles. With the Arabidopsis and rice genome sequence completed, SSL genes were also identified in these plants. However, little is known about evolutionary path, gene structure, expansion and function of SSL family in rice. In this study, through bioinformatic analysis, a total of 23 SSL genes were identified in rice genome. A phylogenetic analysis of the SSL genes in rice and Arabidopsis clarified that these genes could be divided into four different groups and the evolutionary paths are different in rice and Arabidopsis. The OsSSL genes contained zero to five introns and were distributed across 10 out of 12 chromosomes at different densities and tandem duplication was a major cause in expanding this family. Promoter analysis showed the presence of several cis-regulatory elements related to stress and hormone response in regulatory region, indicating probable their role in stress response. Microarray-based expression analysis of OsSSL genes indicated that a few number of these genes were widely expressed in various tissues and also in response to some abiotic stresses. This study is the first report about SSL gene family in rice and provides a framework for further analysis of the biological functions of SSL genes in either rice or other crops.
Bioinformatics
ِSedigheh Akhtartavan; Majid Talebi
Volume 6, Issue 15 , December 2016, , Pages 53-67
Abstract
Drought is one of the major environmental stresses that greatly affects growth and development of plants. The plants reaction against this stress is associated with showing massive changes in complex gene networks. In the present study, the changes of gene expression patterns in two sensitive and tolerant ...
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Drought is one of the major environmental stresses that greatly affects growth and development of plants. The plants reaction against this stress is associated with showing massive changes in complex gene networks. In the present study, the changes of gene expression patterns in two sensitive and tolerant genotypes of rice (as C3 plant) and maize (as C4 plant) were investigated using maize genome arrays containing 17,734 probe sets and the rice genome containing 57/381 probe set. The microarray data were taken from the GEO/NCBI database on both stress and control conditions to identify the genes involved in responses to the stress. The results indicated that 1861 (10.49%) and 1753 (8.9%) genes in the sensitive and tolerant maize, respectively, and 9252 (16%) and 7971 (13.8%) genes in the sensitive and tolerant rice, respectively, changed significantly after drought stress at the level of one percent. From of these genes, 1012 and 175 genes in the sensitive and tolerant genotype leaf of rice and maize, were significantly up-regulated, respectively. The Venn diagram showed that 663 genes of rice and 158 genes of maize, have significantly down-regulated. Rice plant, as a C3 plant, showed five times wider reaction to drought stress in compared with maize plant, as a C4 plant. The functional grouping of the up-regulated genes in two species revealed that functional group of ribosomal proteins and phosphatases in maize plant have the most abundant categories, whereas the functional groups of metal-binding, stress response, response to biological stimuli and signals in rice plant contained the highest percentage of the genes.
Bioinformatics
Manzar Heidari; Zahra-Sadat Shobbar; Parisa Koobaz; Mohammad javad Heydari
Volume 6, Issue 14 , August 2016, , Pages 1-15
Abstract
Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. ...
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Rice is the staple food for more than half the world's population, especially in developing countries. Drought is the most yield-limiting factor for rice production in Asia. The current study was conducted to identify the drought stress responsive genes through EST data analysis of two rice leaves libraries. EST libraries data under normal and drought stress conditions were downloaded from NCBI databank. Preprocessing, clustering and assembly of the EST sequences were done using EGassembler software. Generated contig and singleton sequences were used as template for BLASTx analysis against rice protein database and functional category assignment using CLC Protein Workbench software and AgriGO. The identified proteins in the normal and drought libraries were allocated to 70 and 82 functional categories, respectively. IDEG6 were used to identify significant differences between functional categories in control and drought stress libraries. Gene ontology analysis, revealed significant differences in 20 groups of molecular function, 35 groups of biological processes and 12 groups of the intracellular components. In order to find the significant differential expression between the two libraries, 4012 ESTs with unigene accession numbers were implemented through applying an algorithm by MATLAB software and were analyzed by IDEG6 software, where 42 genes were found to be differentially expressed between drought and normal conditions (31 up-regulated and 11 down-regulated genes). The up-regulated genes were involved in environmental and oxidative stress response, homestasis, proteolysis and glycolysis, while photosynthesis related genes were down-regulated.
Bioinformatics
Yaser Panahi Fakoor; Zahra-Sadat Shobbar; Ehsan Pourabed; Farzan Ghane Golmohamadi; Seyed Morteza Razavi
Volume 5, Issue 12 , February 2016, , Pages 25-38
Abstract
Abiotic stresses are among major factors limiting crop yields, and SnRK2 protein kinases are one of the key regulators of plant response to abiotic stresses. Due to the economic importance, cultivation area, and tolerance of barley to the abiotic stresses, identification and characterization of SnRK2 ...
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Abiotic stresses are among major factors limiting crop yields, and SnRK2 protein kinases are one of the key regulators of plant response to abiotic stresses. Due to the economic importance, cultivation area, and tolerance of barley to the abiotic stresses, identification and characterization of SnRK2 family members in barley is performed in present research. SnRK2 conserved sequences were used as a query for tBLASTn analysis in different databases such as NCBI and international barley sequencing consortium against all of the reported barley sequences. As a result, 10 members were identified (HvSnRK2.1 to HvSnRK2.10) which 8 of them were not yet reported. These HvSnRK2 members were aligned with AtSnRK2s and OsSnRK2s and a phylogenetic tree was constructed. Detection of chromosomal localization, promoter analysis and gene structure determination was also performed. Half of the family members were located on chromosome 2 and the rest on chromosomes 1, 4, 5 and 6. Number of introns in the gene family members varied from 0 to 8. Totally, 19 sorts of cis elements including abiotic stress responsive elements were found in HvSnRK2s promoter sequences. Expression pattern of the family members were evaluated in different tissues, treatments and genotypes, based on the microarray data. Expression of HvSnRK2.6 was up-regulated by drought, salt and cold stresses implementing its important role in signal transduction of these stresses and tolerance induction to them. It is expected that this gene could be used in plant manipulation and breeding programs aimed for tolerance enhancement to abiotic stresses especially drought.
Bioinformatics
Mohammad Amin Baghery; Hamid Najafi Zarini
Volume 5, Issue 11 , December 2015, , Pages 38-49
Abstract
Identification and quantification of proteins and genes that expressed in the salinity stress conditions could lead to better understanding of the response mechanisms. So, in this study iTRAQ comparative proteomic method was used to investigate the protein changes and quantification of them under salinity ...
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Identification and quantification of proteins and genes that expressed in the salinity stress conditions could lead to better understanding of the response mechanisms. So, in this study iTRAQ comparative proteomic method was used to investigate the protein changes and quantification of them under salinity stress. Then, more studies about the function of identified genes were done using gene expression and co-expression data obtained from databases and analysis of related sequences. According to the results of iTRAQ-2DLC-MS/MS a set of proteins including P5CS1, KIN1, KIN2, ERD10, ERD14 and COR47 were identified. Results showed that expressions of the related genes were not just restricted to salinity stress. They were also involved in other osmotic stresses. Gene network based on identified proteins was evaluated by String software. Based on the results, during the expression of these genes, protective compounds such as compatible solutes, dehydrin proteins and etc. were produced in the cells. Presence of the compounds led to induction of resistance and tolerance mechanisms in plants against osmotic stress such as salinity.
Molecular Plant Breeding
Mahdieh Safarzadeh; Reza Fotovat; Mohammadreza Azimi; Ehsan Mohsenifard; Behnam Bakhshi
Volume 4, Issue 6 , October 2014, , Pages 21-33
Abstract
Growth and metabolism of plants are affected by a variety of stimuli, including biotic and abiotic environmental stresses that could leads to responses of the plant through hormone regulation. miRNAs, are a group of Non-coding RNAs that some of them are involved in signaling of plant hormones. In this ...
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Growth and metabolism of plants are affected by a variety of stimuli, including biotic and abiotic environmental stresses that could leads to responses of the plant through hormone regulation. miRNAs, are a group of Non-coding RNAs that some of them are involved in signaling of plant hormones. In this study, the expression patterns of miR159a,b, miR160, miR167a,b and miR171a have been studied in both drought susceptible and drought tolerant varieties in wheat using qRT-PCR. miR159a,b, miR160, miR167a,b and miR171a could play important roles in MYB, ARF, ARF, and SCL, transcription factors regulation, respectively. High conservation among the studied miRNA families was observed in the mature miRNA producer regions by multiplex alignment of pre-miRNAs. Results of qRT-PCR analysis indicated that expressions of miR160 and miR167a,b in tolerant Variety and miR159a,b in susceptible Variety are increased significantly. However, no significant changes in expression were observed for miR171a in both tolerant and sensitive varieties. Presumably, up-regulation miR159a,b in susceptible variety could be resulted to reduction in the expression of MYB genes involved in drought response. On the other hand, up-regulation of miR160 and miR167a,b in tolerant variety, may lead to regulation of auxin and abscisic acid pathways interaction and probably these miRNAs could contribute in stress tolerance in tolerant variety. In addition, no significant change in miR171a expression demonstrated that expression of SCL could be regulated through other mechanisms in plant.
Molecular Plant Breeding
Parvaneh Mahmodi; Ahmad Moeini; Seyed Mojtaba Khayam Nekoie; Mohsen Mardi; Ghasem Hosseini Salekdeh
Volume 4, Issue 6 , October 2014, , Pages 35-46
Abstract
Saffron (Crocus sativus L.), is the most valuable and popular spice in the word. It is a triploid species of the Iridaceae family. Its long, red, and aromatic stigma distinguishes this species from others in its family. With the rapid advances in next generation sequencing technology, RNA sequencing ...
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Saffron (Crocus sativus L.), is the most valuable and popular spice in the word. It is a triploid species of the Iridaceae family. Its long, red, and aromatic stigma distinguishes this species from others in its family. With the rapid advances in next generation sequencing technology, RNA sequencing has risen as a cost-effective and powerful method for transcriptome study. De novo assembly of transcripts provides main solution to transcriptome analysis for organisms without reference genome. Precise sequencing and assembly of transcriptome reliable data are necessary for the downstream analysis. Accordingly, this work was analyzed by two of the most popular software's Trinity and SOAPdenovo for saffron stigma transcriptome to study the effective programs for transcriptome assembly. The results showed that the mean sequence length and the number of unigenes obtained by Trinity were more than SOAPdenovo (Trinity: 689, SOAPdenovo: 624). Translation of the better results produced by the appropriate assembler to protein led to a significant increase in the number of its records obtained at databases. Furthermore, these unigenes might help to identify more metabolite pathways. Assembled unigenes by Trinity had no lacking distance and were about twice the unigenes assembled by SOAPdenovo. As a general conclusion, it seems that selection of an appropriate software and its parameters is not easy without comprehension understanding of different software operation and their setting. Thus, comparison of the different softwares efficiency on the different organisms could provide some practical suggestions and choose an appropriate software.
Bioinformatics
Reyhaneh Ebrahimi; Behrouz Shiran; Esmaeil Ebrahimi; Hossein Fallahi
Volume 3, Issue 5 , February 2013, , Pages 49-51
Abstract
microRNAs are small non-coding RNAs approximately 21-22 nucleotides long and have been identified as negative regulators of gene expression in the post-transcriptional level in plants and animals. Temperature is one of the most important climate change factors and higher temperatures affect agriculture ...
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microRNAs are small non-coding RNAs approximately 21-22 nucleotides long and have been identified as negative regulators of gene expression in the post-transcriptional level in plants and animals. Temperature is one of the most important climate change factors and higher temperatures affect agriculture and crop production adversely. In this study, the expression pattern of miR398 and its target gene NtGT5b were measured in root and leaf tissues of sunflower (Helianthus annuus) in various heat stress conditions (0h, 1.5h, 3h , 6h) at 42 °C by qRT-PCR. The results showed different pattern of miRNA expression in both root and leaf tissues during mild, moderate and severe heat stress, respectively. miR398 was highly up regulated and its target gene down regulated in leaf tissue that showed thermo tolerance of this tissue in term of heat stress. There is a different miRNA expression patterns in leaf and root tissues under various stress conditions which is an indication of induced signal transmission after heat stress. Investigating miR398 network shows that this miRNA through presences of important genes and transcription factors such as AFO and INO has the ability to change the pattern of gene expression of many processes such as growth, development and response to stress.
Molecular Plant Breeding
maasoumeh Habibi; Asadollah Abiar Fini; Neda Mirakhorli; Mohsen Mardi
Volume 3, Issue 5 , February 2013, , Pages 85-92
Abstract
Bread wheat (Triticumaestivum) is one of the most important world food crops that are exposed to many pathogen. During the previous expression-profiling experiments, in addition to major resistant genes to disease in wheat, some defense-related genes such as S-Like RNase gene have been identified. Here ...
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Bread wheat (Triticumaestivum) is one of the most important world food crops that are exposed to many pathogen. During the previous expression-profiling experiments, in addition to major resistant genes to disease in wheat, some defense-related genes such as S-Like RNase gene have been identified. Here to study expression pattern of this gene in several fungal wheat diseases, some bioinformatics and laboratory studied were performed. In bioinformatics studies, several microarray libraries infected with Fusarium, Spike blight and Stripe rust were considered. In laboratory experiments Septoria tritici bloth was studied. So the level of expression was measured at 8 time interval, from 0h to 6 days after inoculation by Mycosphaerella graminicola in Wangshuibai as a resistant wheat cultivar and Falat as a susceptible wheat cultivar by semi quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). The results show that the maximum expression of this gene, depending on types of disease and resistant cultivars, is obtained up to 24 hours after the inoculation. Thus, according to this results it can be concluded that this gene plays an important role in resistance to diseases and ,along with the main gene, increase and maintain resistance to many fungal diseases in wheat. Also this gene was confirmed by Nucleotide Blast.
Molecular Plant Breeding
Zahra Sadat Shobbar; John Bennett
Volume 1, Issue 1 , March 2012, , Pages 23-33
Abstract
Protein phosphatase 2C family consists of a group of evolutionary conserved serine/threonine phosphatases which play a role in stress signal transduction. A subfamily of this Protein phosphatases in Arabidopsis, including ABI1 and ABI2, are known as components of ABA signal transduction pathway. Their ...
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Protein phosphatase 2C family consists of a group of evolutionary conserved serine/threonine phosphatases which play a role in stress signal transduction. A subfamily of this Protein phosphatases in Arabidopsis, including ABI1 and ABI2, are known as components of ABA signal transduction pathway. Their mutants are hypersensitive to ABA showing increased expression during seed dormancy and adaptive responses to drought. Considering sensitivity of rice to abiotic stresses, particularly drought, identification of this gene family in rice and studying their role in response to stress would be beneficial. In this research, nine OsPP2C proteins were found in rice (OsPP2C1 to OsPP2C9), carrying all the conserved motifs of this subfamily. Among them, only OsPP2C5 transcript levels were significantly up-regulated by drought and abscisic acid which is down-regulated by re-watering or ABA removal. Drought stress induced OsPP2C5 gene expression in all the studied tissues. Based on RNA in situ hybridization experiments, OsPP2C5 transcripts were observed in almost all cells and accumulated more in the nuclei in divisional zone of the drought stressed peduncles. However, the transcripts of this gene were accumulated at higher level in the primary and secondary vascular bundles, phloem and xylem parenchyma, epidermal cells and sclerenchyma / chlorenchyma precursors. Based on the achieved results, it seems that OsPP2C5 gene is playing a role in ABA/ drought stress signal transduction. It is expected that appropriate genetic manipulations to this gene family would increase the tolerance to the abiotic stresses.
