Payame Noor UniversityCrop Biotechnology2252-078313220240119Analyzing the expression data (RNA-Seq) in Catharanthus roseus plant in order to identify key genes of the active substances (vinblastine and vincristine) in different organs (root, leaf and flower) and to investigate their anticancer effects using docking analysis and molecular dynamics.Analyzing the expression data (RNA-Seq) in Catharanthus roseus plant in order to identify key genes of the active substances (vinblastine and vincristine) in different organs (root, leaf and flower) and to investigate their anticancer effects using docking analysis and molecular dynamics.1111056610.30473/cb.2024.70157.1945FAMasoudTohidfarDepartment of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, IranYousefSaeedi HonarDepartment of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, IranNaserFarrokhiDepartment of Cell & Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, IranJournal Article20231004Catharanthus roseus is one of the most important medicinal plants that contains two antitumor substances, vinblastine and vincristine. It is important to identify the involved genes and their expression pattern and anti-tumor effect in different tissues of this plant. By using the expression data of RNA sequencing of different tissues, differential expression genes and their antitumor effects were investigated as in silico. The results showed that the total number of differentially expressed genes in the organs varied between 120 and 1238. The highest number of DEGs compared to the root was related to the leaf and the lowest number was related to the flower. Subsequently, 13 common genes between three different organs and 22 common genes were observed between leaves versus flowers and leaves versus roots. Among them, 6 common genes were observed in all three tissues, and the annotation analysis showed that these genes are involved in the biosynthetic pathway of two important compounds, vinblastine and vincristine. The highest expression of these genes was related to leaves and the lowest was related to roots. Protein network analysis determined that a number of genes that showed the most interaction with other genes were related to the genes of the biocentric pathway of antitumor compounds. Docking and molecular dynamics analysis showed that vinblastine and vincristine, while having good interaction as inhibitors with phosphoglycoprotein (drug resistance protein in tumor cells), also have good stability in interaction with phosphoglycoprotein. Generally DAT, STR, TDC, G10H, D4H, T16H2, Tryptophandecar-boxylase and Strictosidine synthase genes that were in the biosynthesis pathway of vinblastine and vincristine had an effective role in different organs. The obtained results give new insights about the mechanism of treatment with natural products, which can be used to improve the patients.Catharanthus roseus is one of the most important medicinal plants that contains two antitumor substances, vinblastine and vincristine. It is important to identify the involved genes and their expression pattern and anti-tumor effect in different tissues of this plant. By using the expression data of RNA sequencing of different tissues, differential expression genes and their antitumor effects were investigated as in silico. The results showed that the total number of differentially expressed genes in the organs varied between 120 and 1238. The highest number of DEGs compared to the root was related to the leaf and the lowest number was related to the flower. Subsequently, 13 common genes between three different organs and 22 common genes were observed between leaves versus flowers and leaves versus roots. Among them, 6 common genes were observed in all three tissues, and the annotation analysis showed that these genes are involved in the biosynthetic pathway of two important compounds, vinblastine and vincristine. The highest expression of these genes was related to leaves and the lowest was related to roots. Protein network analysis determined that a number of genes that showed the most interaction with other genes were related to the genes of the biocentric pathway of antitumor compounds. Docking and molecular dynamics analysis showed that vinblastine and vincristine, while having good interaction as inhibitors with phosphoglycoprotein (drug resistance protein in tumor cells), also have good stability in interaction with phosphoglycoprotein. Generally DAT, STR, TDC, G10H, D4H, T16H2, Tryptophandecar-boxylase and Strictosidine synthase genes that were in the biosynthesis pathway of vinblastine and vincristine had an effective role in different organs. The obtained results give new insights about the mechanism of treatment with natural products, which can be used to improve the patients.https://cropbiotech.journals.pnu.ac.ir/article_10566_30c0de2d38eec3dc207cada1c4e4d87d.pdfPayame Noor UniversityCrop Biotechnology2252-078313220240120Genome-wide bioinformatic analysis of MYB gene family in monocotyledons and dicotyledonsGenome-wide bioinformatic analysis of MYB gene family in monocotyledons and dicotyledons13291056410.30473/cb.2024.70059.1939FASaraDezhsetanAssociate Prof., Department of Plant Production. Genetics, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, IranParivashNezami AnbaranM.Sc. Student, Department of Plant Production. Genetics, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, IranMahdiBehnamianAssociate Prof., Department of Horticultural Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, IranJournal Article20230925The MYB transcription factor superfamily has a fundamental role in plant growth and development, activation of stress-responsive genes, and in some cases biosynthesis of key metabolites. The availability of potato, Arabidopsis (dicotyledonous), maize and barley (monocotyledonous) genome sequences provided the opportunity to identify 121, 139, 190 and 144 non-redundant MYB genes in these linages, respectively. In the study of the evolutionary characteristics of MYB conserved domains in two monocotyledonous plants, corn and barley, they were remarkably similar to each other in terms of alignment and order of placement. This characteristic was also true in relation to two dicotyledonous plants, potato and Arabidopsis, but the difference between MYB conserved domains in monocots and dicots was significant. In other words, it seems that despite the similarity of MYB genes in monocots and dicots, this gene family in the evolution in monocots and dicots have derived from each other. The 2R-MYB members were the most common subgroup of the MYB family in monocots and dicots and only one member of the 4R-MYB subfamily was observed in maize. In all four plants, the main reason for the functional differentiation of genes in this gene family was segmental duplication that has led to positive and purifying evolutionary selection. MYB gene family was located on all chromosomes of potato, Arabidopsis, maize and barley with non-uniform distribution. The expression pattern of AT1G57560, AT2G47190, AT3G23250 and AT1G56650 genes changed in more than one test of abiotic stress and hormonal response. Also, the expression pattern of AT1G74080, AT4G12350, AT4G22680, AT2G47190, AT1G48000, AT2G39880, AT5G40330 and AT5G16600 genes changed in more than one biotic stress test. On the other hand, the expression pattern of the AT2G47190 gene showed increased expression in several biotic and abiotic stresses. The presence of diverse and numerous regulatory Cis elements in response to stresses and hormones in the promoter region of MYB genes and the investigation of the expression profiles of this gene family in biotic and abiotic stresses in Arabidopsis indicates the functional diversity of the genes of this superfamily. In silico investigation of MYB gene superfamily in monocots and dicots provides a framework for comparative, evolutionary and functional studies of the members of this important gene superfamily.The MYB transcription factor superfamily has a fundamental role in plant growth and development, activation of stress-responsive genes, and in some cases biosynthesis of key metabolites. The availability of potato, Arabidopsis (dicotyledonous), maize and barley (monocotyledonous) genome sequences provided the opportunity to identify 121, 139, 190 and 144 non-redundant MYB genes in these linages, respectively. In the study of the evolutionary characteristics of MYB conserved domains in two monocotyledonous plants, corn and barley, they were remarkably similar to each other in terms of alignment and order of placement. This characteristic was also true in relation to two dicotyledonous plants, potato and Arabidopsis, but the difference between MYB conserved domains in monocots and dicots was significant. In other words, it seems that despite the similarity of MYB genes in monocots and dicots, this gene family in the evolution in monocots and dicots have derived from each other. The 2R-MYB members were the most common subgroup of the MYB family in monocots and dicots and only one member of the 4R-MYB subfamily was observed in maize. In all four plants, the main reason for the functional differentiation of genes in this gene family was segmental duplication that has led to positive and purifying evolutionary selection. MYB gene family was located on all chromosomes of potato, Arabidopsis, maize and barley with non-uniform distribution. The expression pattern of AT1G57560, AT2G47190, AT3G23250 and AT1G56650 genes changed in more than one test of abiotic stress and hormonal response. Also, the expression pattern of AT1G74080, AT4G12350, AT4G22680, AT2G47190, AT1G48000, AT2G39880, AT5G40330 and AT5G16600 genes changed in more than one biotic stress test. On the other hand, the expression pattern of the AT2G47190 gene showed increased expression in several biotic and abiotic stresses. The presence of diverse and numerous regulatory Cis elements in response to stresses and hormones in the promoter region of MYB genes and the investigation of the expression profiles of this gene family in biotic and abiotic stresses in Arabidopsis indicates the functional diversity of the genes of this superfamily. In silico investigation of MYB gene superfamily in monocots and dicots provides a framework for comparative, evolutionary and functional studies of the members of this important gene superfamily.https://cropbiotech.journals.pnu.ac.ir/article_10564_c3a83ee2d8fa9b6c9d8a6b9fc3fd692a.pdfPayame Noor UniversityCrop Biotechnology2252-078313220231222genetic diversity of the green oak leaf roller moth, Tortrix viridana (Lep., Tortricidae) in Zagros oak forests using s rDNA28genetic diversity of the green oak leaf roller moth, Tortrix viridana (Lep., Tortricidae) in Zagros oak forests using s rDNA2831331131410.30473/cb.2023.69145.1926FARezvanMousivandDepartment of Plant Production and Genetics, University of Kurdistan, Sanandaj Iran.MohammadMajdiUniversity of KurDepartment of plant production and Genetics, University of Kurdistan, Sanandaj IrandistanّFoadFatehiDepartment of Agriculture, Payame Noor University, Tehran, Iran0000-0003-3261-080XHamedGhobariDepartment of plant Protection, University of Kurdistan, Sanandaj IranJournal Article20230909the genetic diversity of the T. viridana on the host oak species Quercus branti was investigated using the 28s gene sequence in some Zagros forests. The samples were collected from the forest area of West Azarbaijan, Lorestan, Kurdistan and Kermanshah provinces. The Collected samples, which were in the larval stage, were grown in laboratory conditions until they turned into paup and then into complete insects, for DNA extraction. DNA extraction was done by CTAB method. 21 samples were selected to investigate genetic diversity using the 28s gene, and 18 sequences DNAs were of suitable quality for further investigations. In order to amplify 28s region, based on the sequence obtained from the NCBI site.The desired region in the collected samples was amplified using the PCR method and the resulting product was sequenced. The sequences were edited using Bioedit software and aligned with the help of MegaX software, and the phylogenetic tree was drawn by UPGMA method with 1000 sampling repetitions. The results of this study, based on the phylogenetic tree, showed that the different samples of the oak saplings have genetic diversity based on the geographical distance. Assessment of genetic structure of the populations showed that higher diversity was demonstrated in intrapopulations than interpopulations geographically. 28s gene showed the presence of 5 haplotypes in these populations. The presence of low diversity between populations indicated the existence of gene flow between populations as well as genetic compatibility in the studied populations.the genetic diversity of the T. viridana on the host oak species Quercus branti was investigated using the 28s gene sequence in some Zagros forests. The samples were collected from the forest area of West Azarbaijan, Lorestan, Kurdistan and Kermanshah provinces. The Collected samples, which were in the larval stage, were grown in laboratory conditions until they turned into paup and then into complete insects, for DNA extraction. DNA extraction was done by CTAB method. 21 samples were selected to investigate genetic diversity using the 28s gene, and 18 sequences DNAs were of suitable quality for further investigations. In order to amplify 28s region, based on the sequence obtained from the NCBI site.The desired region in the collected samples was amplified using the PCR method and the resulting product was sequenced. The sequences were edited using Bioedit software and aligned with the help of MegaX software, and the phylogenetic tree was drawn by UPGMA method with 1000 sampling repetitions. The results of this study, based on the phylogenetic tree, showed that the different samples of the oak saplings have genetic diversity based on the geographical distance. Assessment of genetic structure of the populations showed that higher diversity was demonstrated in intrapopulations than interpopulations geographically. 28s gene showed the presence of 5 haplotypes in these populations. The presence of low diversity between populations indicated the existence of gene flow between populations as well as genetic compatibility in the studied populations.https://cropbiotech.journals.pnu.ac.ir/article_11314_641143c8e51a60681419d16ed4f16a22.pdfPayame Noor UniversityCrop Biotechnology2252-078313220240118Bioinformatics study of reverse transcriptase sequence in virusesBioinformatics study of reverse transcriptase sequence in viruses45521056310.30473/cb.2023.69786.1933FASamiraKarimiM.Sc. Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran.MahinPouresmaeilPost Doctoral Researcher, Faculty of Agriculture and Natural Resources, University of Mohaghegh ArdabiliJournal Article20230921Bioinformatics is an interdisciplinary science that utilizes information technologies to organize and analyze biological data. This science enables researchers to perform comprehensive and documented investigations on various biological problems without the need for expensive and time-consuming laboratory experiments .In this study, we acquired the reverse transcriptase (RT) sequence of eight virus strains from NCBI with the following accession numbers: NC_001497.2, NC_001648.1, NC_001839.2, NC_003977.2, AF053008.1, EF428979.1, NC_001802.1. We investigated the structural and functional characteristics, domains, and motifs. The analysis revealed that the proteins from the eight virus strains, belonging to different families, exhibited distinct properties that set them apart from one another. The analysis also showed that these proteins are found in the membrane, cytoplasm, and periplasm, and all of them contain at least one specific domain of the reverse transcriptase enzyme. Based on all the analyses performed, Cauliflower mosaic virus, Cassava vein mosaic virus, and Soybean chlorotic mottle virus, all belonging to the Caulimoviridae family, were suitable for producing RT enzymes. The ability of these viruses to adapt to different plant hosts could potentially lead to the development of more efficient and cost-effective methods for producing RT enzymes. This adaptability could also open up new possibilities for genetic engineering and biotechnology, enabling the development of more effective enzymes.Bioinformatics is an interdisciplinary science that utilizes information technologies to organize and analyze biological data. This science enables researchers to perform comprehensive and documented investigations on various biological problems without the need for expensive and time-consuming laboratory experiments .In this study, we acquired the reverse transcriptase (RT) sequence of eight virus strains from NCBI with the following accession numbers: NC_001497.2, NC_001648.1, NC_001839.2, NC_003977.2, AF053008.1, EF428979.1, NC_001802.1. We investigated the structural and functional characteristics, domains, and motifs. The analysis revealed that the proteins from the eight virus strains, belonging to different families, exhibited distinct properties that set them apart from one another. The analysis also showed that these proteins are found in the membrane, cytoplasm, and periplasm, and all of them contain at least one specific domain of the reverse transcriptase enzyme. Based on all the analyses performed, Cauliflower mosaic virus, Cassava vein mosaic virus, and Soybean chlorotic mottle virus, all belonging to the Caulimoviridae family, were suitable for producing RT enzymes. The ability of these viruses to adapt to different plant hosts could potentially lead to the development of more efficient and cost-effective methods for producing RT enzymes. This adaptability could also open up new possibilities for genetic engineering and biotechnology, enabling the development of more effective enzymes.https://cropbiotech.journals.pnu.ac.ir/article_10563_e49eb218f1ac8f819fa138109124aeaa.pdfPayame Noor UniversityCrop Biotechnology2252-078313220231222A review on reactive oxygen species (ROS): production, function, and their influence on plantsA review on reactive oxygen species (ROS): production, function, and their influence on plants53701056510.30473/cb.2024.70071.1940FAArminSaed-MoucheshiCrop and Horticulture Reseach Department, Kermanshah Agricultural and Natural Resources Research and Education Center (AREEO), Kermanshah, Iran.FatemehSohrabiPh.D. Student in Plant Biotechnology, Faculty of Agriculture University of Shiraz, IranAliShirkhaniCrop and Horticulture Reseach Department, Kermanshah Agricultural and Natural Resources Research and Education Center (AREEO), Kermanshah, Iran.Journal Article20231225Reactive oxygen species (ROS) produced in organelles such as mitochondria, chloroplast, and peroxisome play an important role in plant signaling and signal transduction pathways. ROSs basically are able to regulate oxidation-reduction (known as redux) reactions, plant growth and defense responses to environmental stimuli. Therefore, they affect every aspect at all life cycle stages of plants. ROSs such as hydrogen peroxide, superoxide, hydroxyl radicals, and singlet oxygen act as secondary messengers in plant cells to regulate a diverse range of protein functions (with post-translational modifications) and gene expression. They are produced naturally during the plant responses to environmental conditions and intra-/inter-cellular communications. Recent researches are indicating that ROS compounds play a key role in the plants response under both biotic and abiotic stresses. Biotic stresses such as fungi, viruses, mites, insects and other organisms, along with abiotic stresses such as drought, salinity and heavy metals, increase the production of ROS in plant cells. Plants possess various mechanisms to deal with the destructive effects of ROS increased production. ROS removal in plants is usually performed by two main groups of enzymatic and non-enzymatic antioxidant molecules. Antioxidant molecules play important roles in plant tolerance under stressful conditions by neutralizing ROS and converting them into water molecules. However, under severe stress conditions, plants are not able to eliminate the entire content of extra produced ROS molecules; as a result, the high amount of ROS causes oxidative stress in plants leading to various damages to the main components of the cells, such as proteins, lipids, DNA, carbohydrates, and ultimately cell death. There are still many unanswered questions regarding the plant specific responses to oxidative stress and regulation of cell communication during stress conditions. This review article tries to introduce the origin, location, and pathways of ROS production along with their types and effects on the cellular signal transduction system in stimulating adaptive responses of plants under stress conditions. Moreover, this review discusses the effectiveness of antioxidants systems in maintaining cell homeostasis and neutralizing the negative impacts of oxygen free radicals in plants.Reactive oxygen species (ROS) produced in organelles such as mitochondria, chloroplast, and peroxisome play an important role in plant signaling and signal transduction pathways. ROSs basically are able to regulate oxidation-reduction (known as redux) reactions, plant growth and defense responses to environmental stimuli. Therefore, they affect every aspect at all life cycle stages of plants. ROSs such as hydrogen peroxide, superoxide, hydroxyl radicals, and singlet oxygen act as secondary messengers in plant cells to regulate a diverse range of protein functions (with post-translational modifications) and gene expression. They are produced naturally during the plant responses to environmental conditions and intra-/inter-cellular communications. Recent researches are indicating that ROS compounds play a key role in the plants response under both biotic and abiotic stresses. Biotic stresses such as fungi, viruses, mites, insects and other organisms, along with abiotic stresses such as drought, salinity and heavy metals, increase the production of ROS in plant cells. Plants possess various mechanisms to deal with the destructive effects of ROS increased production. ROS removal in plants is usually performed by two main groups of enzymatic and non-enzymatic antioxidant molecules. Antioxidant molecules play important roles in plant tolerance under stressful conditions by neutralizing ROS and converting them into water molecules. However, under severe stress conditions, plants are not able to eliminate the entire content of extra produced ROS molecules; as a result, the high amount of ROS causes oxidative stress in plants leading to various damages to the main components of the cells, such as proteins, lipids, DNA, carbohydrates, and ultimately cell death. There are still many unanswered questions regarding the plant specific responses to oxidative stress and regulation of cell communication during stress conditions. This review article tries to introduce the origin, location, and pathways of ROS production along with their types and effects on the cellular signal transduction system in stimulating adaptive responses of plants under stress conditions. Moreover, this review discusses the effectiveness of antioxidants systems in maintaining cell homeostasis and neutralizing the negative impacts of oxygen free radicals in plants.https://cropbiotech.journals.pnu.ac.ir/article_10565_e02831d0fb0c2ad16e6a8bd41a88256b.pdfPayame Noor UniversityCrop Biotechnology2252-078313220240207Germination of Iranian and European barley cultivars under salinity stress and its relationship with seed storage proteinsGermination of Iranian and European barley cultivars under salinity stress and its relationship with seed storage proteins71831059810.30473/cb.2023.69761.1932FAAliMalekiDepartment of Plant Production and Genetics, Razi University, Kermanshah, Iran.LeilaZareiDepartment of Plant Production and Genetics, Razi University, Kermanshah, Iran.SohbatBahraminejadDepartment of Plant Production and Genetics, Razi University, Kermanshah, Iran.KianooshCheghamirzaDepartment of Plant Production and Genetics, Razi University, Kermanshah, Iran.LeilaAkbariDepartment of Plant Production and Genetics, Razi University, Kermanshah, Iran.FardinFatahiDepartment of Plant Production and Genetics, Razi University, Kermanshah, Iran.Journal Article20231118Germination is one of the most important stages of crop plant growth and proper germination in a wide range of environmental conditions is necessary for plant establishment. In this research, 20 varieties of Iranian barley and 24 varieties of European barley were used in three salinity levels (100, 200 and 300 mM sodium chloride) and a control level (distilled water) in order to investigate the tolerance of salinity stress in the germination stage, as a factorial test based on a completely randomized design with three replications in the mushroom cultivation chamber with controllable temperature and light and sterile conditions in the Nosoud agricultural service center by a protein marker in the biotechnology laboratory of the agriculture and natural resources of Razi university. The results of analysis of variance of traits related to germination showed that the effect of salinity, cultivar and salinity × cultivar were significant for all traits. By increasing the salinity level from 0 to 300 mM, all traits and indices decreased except the average germination time. The germination percentage had a positive and significant correlation with the total seedling length, shoot length, seed germination index, average germination rate and germination rate index. Stepwise regression analysis of different traits with protein markers showed that there were 13 bands associated with different traits. The most significant correlation with traits was related to the 60 kDa marker which was related four indices of seed germ, average germination speed, shoot length and cleoptile length. After the validation studies and confirmation of the results, the identified markers can be used in marker-assisted selection for related traits.Germination is one of the most important stages of crop plant growth and proper germination in a wide range of environmental conditions is necessary for plant establishment. In this research, 20 varieties of Iranian barley and 24 varieties of European barley were used in three salinity levels (100, 200 and 300 mM sodium chloride) and a control level (distilled water) in order to investigate the tolerance of salinity stress in the germination stage, as a factorial test based on a completely randomized design with three replications in the mushroom cultivation chamber with controllable temperature and light and sterile conditions in the Nosoud agricultural service center by a protein marker in the biotechnology laboratory of the agriculture and natural resources of Razi university. The results of analysis of variance of traits related to germination showed that the effect of salinity, cultivar and salinity × cultivar were significant for all traits. By increasing the salinity level from 0 to 300 mM, all traits and indices decreased except the average germination time. The germination percentage had a positive and significant correlation with the total seedling length, shoot length, seed germination index, average germination rate and germination rate index. Stepwise regression analysis of different traits with protein markers showed that there were 13 bands associated with different traits. The most significant correlation with traits was related to the 60 kDa marker which was related four indices of seed germ, average germination speed, shoot length and cleoptile length. After the validation studies and confirmation of the results, the identified markers can be used in marker-assisted selection for related traits.https://cropbiotech.journals.pnu.ac.ir/article_10598_e07f44545254643cf330cb4191a3fe63.pdf