Research Paper
Bioinformatics
Mohammad Amin Baghery; Seyed Kamal Kazemitabar; Ali Dehestani; Pooyan Mehrabanjoubani; Hamid Najafi Zarrini
Abstract
Sesame (Sesamum indicum L.) is a nutritionally and medicinally important oilseed crop that environmental stresses limit its yield potential. Ethylene-responsive factor (ERF) is one of the largest transcription factor families that play key roles in regulating plant response to abiotic stress. In the ...
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Sesame (Sesamum indicum L.) is a nutritionally and medicinally important oilseed crop that environmental stresses limit its yield potential. Ethylene-responsive factor (ERF) is one of the largest transcription factor families that play key roles in regulating plant response to abiotic stress. In the current study, a total of 113 ERF genes were identified from the sesame genome and they were divided into two subfamilies including, 46 dehydration-responsive element-binding (DREB) members, and 67 ERF members. Phylogenetic relationships, physicochemical properties of proteins, structural properties of genes, and conserved amino acid motifs in the sesame ERF family were analyzed. Then, the expression profile of sesame ERF genes in various tissues as well as under environmental stresses was investigated. Overall, several genes of the ERF Family were expressed noticeably in different sesame tissues, especially in roots, capsules, and flowers. Expression profiles also showed that RAP2.2L, PTI6, ERF017L, and ERF096 genes were strongly induced by drought, osmotic, salinity, and waterlogging stresses, respectively. Moreover, the qPCR results showed that the relative expression of the ERF061L gene was higher in the sesame tolerant genotype compared to the susceptible one under drought conditions. This study provides important data for understanding the evolution and functions of the ERF family in sesame that can be used in future breeding programs for abiotic stresses tolerance.
Research Paper
Bioinformatics
Shadi Heidari; Peivand Heidari
Abstract
Brassica napus field plant, as an important oilseed, has undergone extensive genome reconstruction after interspecies hybridization of its ancestors. To elucidate the evolutionary mechanisms underlying the diversity of secondary metabolites, insilico comparative analysis of different genes between three ...
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Brassica napus field plant, as an important oilseed, has undergone extensive genome reconstruction after interspecies hybridization of its ancestors. To elucidate the evolutionary mechanisms underlying the diversity of secondary metabolites, insilico comparative analysis of different genes between three Brasica species was performed. After assembling the preliminary EST sequence of libraries using EGassembler software, the contigs were analyzed by X-blast using CLC Protein Workbench software against non-redundant proteins databank. IDEG6 software and Audic-Claverie statistics were used to determine the differential expression of genes. To identify orthologs and paralogs, the Ensembl Plants website and CLUSTALW were used for a pairwise alignment for each pair of proteins. The discovery of the DNA motif is a first step in many systems to study gene function, so the MEME website and STAMP webtool were used to explore the DNA binding motif and determine the similarity of the motif sequences of the paralogs. The results showed a significant difference between 18 genes in the functional groups of secondary metabolism and transcriptional regulation. Most of the genes involved in the glucosinolate diversity in B. napus have ortholog genes in the ancestral species and Arabidopsis, which have diverged during evolutionary processes. While most transcriptional regulatory genes, including MYB28 and bHLH, have paralog genes that have been functionally altered within B. napus as a result of duplication and mutation following changes in allopolyploidy. The ancestral genome of B. napus provides valuable resources for insilico analysis in understanding the genetic consequences of polyploidy, evolution and breeding of B. napus.
Research Paper
Biotic and Abiotic stress
Rahil Dowlatabadi; Hajar Shayesteh; Amin Mirshamsi Kakhki; Mohammad Zare Mehrjerdi; Alireza Seifi
Abstract
Broomrape (Orobanche aegyptica) is a notorious parasitic plant that cause significant production loss. Here we report analysis of publicly available RNA-seq data for broomrape, coupled with experimental verification of part of the results. After quality control of raw illumine reads, qualified reads ...
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Broomrape (Orobanche aegyptica) is a notorious parasitic plant that cause significant production loss. Here we report analysis of publicly available RNA-seq data for broomrape, coupled with experimental verification of part of the results. After quality control of raw illumine reads, qualified reads were mapped against Orobanch transcriptome. Differential gene expression analysis, performed by using DESeq package, identified 391 differentially expressed genes between seed imbibition and haustorium attachment stages. The expression of orthologs of these genes in close relatives of Orobanch, which are parasitic, hemi- or non-parasitic, was investigated. From 391 identified genes, 87 genes showed high levels of expression in parasitic relatives and not in non-parasitic ones. Based on these analyses the 87 genes were considered as candidate genes involved in establishment of parasitic interaction between Orobanch and its host. The expression of nine of these genes were checked experimentally in flower tissues of Orobanch and in tissues sampled from the attachment site on the host root. The expression of Or2094, which a putative serine-carboxy peptidase, was detected only in the attachment site, supporting the role of this gene in establishment of the parasitic interaction. The results of this work will pave the way for future genetic engineering projects to use host-induced gene silencing strategy to enhance resistance to Orobanch in host crop plants.
Research Paper
Tissue culture and Micropropagation
Eshaghali Bayati; Masoud Gomarian; Hossein Mirzaie Nodoushan; Mahdi Changizi; Shahab Khaghani
Abstract
In a laboratory experiment conducted in Kabudarahang, Hamadan, a promising potato genotype was selected through somaclonal variation from Agria commercial cultivar, based on the callus size on growth media, shoot and root regeneration. A field experimental design with three replications was carried out ...
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In a laboratory experiment conducted in Kabudarahang, Hamadan, a promising potato genotype was selected through somaclonal variation from Agria commercial cultivar, based on the callus size on growth media, shoot and root regeneration. A field experimental design with three replications was carried out to assess the new genotype along with its parental commercial cultivar for several morphological traits. Results revealed that total dry matter per plant (13.5%), total number of tubers (12.3%), tuber weight per plant (8.6%), and stolon length (4%) were significantly higher than in the new genotype. Also, days to 50% flowering (11.4%) and maturity date (7.6%) were significantly less in comparison with the parental cultivar. Several nutritional traits were also studied by which more antioxidant activity was observed on the new genotype (35.6%) than Agria cultivar (25.3%). Furthermore, the new genotype had a lower nitrite (81.2%) and higher iron (20.7%) and starch content (21.2%) comparing with Agria cultivar. Therefore, it seems that the new genotype has an acceptable potential for cultivation and replacement with existing cultivars.
Research Paper
Bioinformatics
Zahra Pakbaz; Asa Ebrahimi; Martina Rickauer; Cecile Ben; Abdollah Mohammadi
Abstract
Metal tolerance proteins (MTP) are plant membrane divalent cation transporters, which plays an important role during plant growth and development. They involve in minerals uptake and provide resistance for plants in polluted soil by heavy metal. However, information about MTPs proteins in Fabceace family ...
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Metal tolerance proteins (MTP) are plant membrane divalent cation transporters, which plays an important role during plant growth and development. They involve in minerals uptake and provide resistance for plants in polluted soil by heavy metal. However, information about MTPs proteins in Fabceace family are scarcely known. Therefore, in this study we provided an extensive evaluation of MTP genes in three important members of this family including: Glycine max, Medicago truncatula and Phaseolus vulgaris by providing phylogenetic assessments, chromosomal distributions, gene structures and expression in different tissue. According to the results 14, 12 and 23 MTP genes respectively were found in M. truncatula, P. vulgaris and G. max. 13 duplicated MTP genes in G. max were found meanwhile we did not find any duplication in the MTP genes of M. truncatula and P. vulgaris. All studied MTPs were classified into three major cation diffusion facilitator (CDFs) groups; Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. In silico subcellular location results revealed that these proteins have the maximum activity in the vacuole in all three plants, and a small number are located in the cell wall and nucleus. According to gene structure and protein motifs of studied MTPs, they are highly conserved but their expression measurement showed that each one of them have different levels of expression during growth stage. It confirms their importance for plants during growth and development.
Research Paper
Mahdieh Shojaee; Razieh Sarabadani
Abstract
Immune system disorders have been recognized as a cause of the autism spectrum disorder (ASD). TNFα and IL-6 are significant markers of the ASD. Increased levels of these cytokines in the brain and blood of the ASD-engaged patients not only affect the immune system disorders but also contribute to many ...
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Immune system disorders have been recognized as a cause of the autism spectrum disorder (ASD). TNFα and IL-6 are significant markers of the ASD. Increased levels of these cytokines in the brain and blood of the ASD-engaged patients not only affect the immune system disorders but also contribute to many common behavioral abnormalities exhibited by such patients. In this research, we investigated the effect of the broccoli extract and its sulforaphane content on two immune system factors, namely TNFα and IL-6. For this purpose, with its effectiveness confirmed via gas chromatography – mass spectroscopy (GC-MS) and MTT assay, the broccoli extract was subjected to immune system induction to maximize the activity of the immune system factors. The cells were treated with the broccoli extract at three different dosages, namely 1, 1.5 and 2 mg of the cell per milliliter of the broccoli extract, enzyme-linked immunosorbent assays (ELISA) were performed for three treatment times, namely 1, 2, and 3 days. A comparison between the stimulated immune system cells without treatment against those treated with the 2 mg of broccoli extract for 3 days clearly demonstrated the effectiveness of the broccoli extract for attenuating the activity of the TNFα and IL-6 factors. It was also observed that higher concentrations of the extract and longer treatment time were more effective in reducing these two factors. In general, the results of the present experiment suggest the effect of broccoli extract on reducing the inflammation of the immune system caused by these two factors.
