جستجوی مقالات مرتبط با کلیدواژه "bioinformatics" در نشریات گروه "زراعت"

Since the introduction of Next-Generation Sequencing (NGS) in the early 2000s, this technology has emerged as a transformative advancement in the life sciences, significantly propelling genomic, transcriptomic, epigenomic, and other related research fields. The core principles of NGS technology encompass library preparation, sequencing, and the analysis of the resulting data. By enabling the parallel sequencing of millions of DNA fragments with high accuracy, low cost, and rapid turnaround, NGS has effectively replaced older methods like Sanger sequencing. It has revolutionized our understanding of genetic complexities, genome structures, and genetic diversity through the swift and precise sequencing of entire genomes and target regions. Key applications of NGS in the life sciences include the identification and study of genes related to quantitative and qualitative traits, genetic diversity studies, population genetics, the diagnosis of genetic diseases, epidemiology, microbiome analysis, forensic science, phylogenetics, systems biology, genetic engineering, genome editing, and plant and animal breeding. However, the effective use of NGS data necessitates the development of robust computational infrastructure and advanced algorithms, as well as the expansion of researchers' knowledge regarding the bioinformatic applications and challenges associated with NGS data analysis and interpretation.

The present article is a review paper, conducted through content analysis by searching for keywords related to Next-Generation Sequencing (NGS), types of NGS sequencing, NGS data analysis, and the applications of NGS in relevant articles found in online databases such as PubMed, Web of Science, Google Scholar, and Scopus.

This study aims to provide a comprehensive guide for the efficient and optimal analysis of NGS data by thoroughly reviewing first-, second-, and third-generation sequencing methods, examining NGS data analysis pipelines, and exploring the broad applications of NGS in various fields, including cereal research. The first section reviews first-generation sequencing (Maxam-Gilbert and Sanger), second-generation sequencing (Illumina, ABI/SOLID, Roche/454 pyrosequencing, Ion Torrent), and third-generation sequencing (Heliscope, SMRT, and Oxford Nanopore). The second section introduces various NGS sequencing methods, such as Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), Bulk RNA-Seq, and others, and examines their analysis pathways. The subsequent discussion elaborates on the application of NGS in diverse areas, including the identification of structural genomic variations (SVs), the study of epigenetic changes, microbial population analysis, and agriculture (with an emphasis on cereal breeding). Finally, the advantages and challenges of NGS are discussed.

As a revolutionary technology in genomics, Next-Generation Sequencing has profoundly impacted life sciences research. The reduction in sequencing costs, coupled with increased accuracy and the development of new methods, has positioned NGS as a critical tool for a deeper understanding of genetics and the development of personalized therapeutic strategies. With ongoing advancements in this field and the integration of NGS with artificial intelligence, the future of NGS in enhancing the precision of genetic data analysis and improving therapeutic processes appears promising.

Potato (Solanum tuberosum L.) is an economic crop that is grown and consumed worldwide. Potato is considered as the fourth important crop for human consumption after maize, wheat, and rice. Potato contain more carbohydrates, proteins, minerals, and vitamins per unit area than cereals. However, this crops exposed environmental stresses during growth and developmental stages particularly, drought stress. Potato is sensitive to drought condition because of narrow root system. As a result, it is necessary the investigation of molecular mechanism involved in drought stress in potato. Drought stress affected on the integrity and structure maintain of biological membrane. The actin-based myosin is necessary for the growth and organization of the endomembrane system. Given that myosin genes allow to move intercellular and intracellular providing the possibility of repair of damaged membrane areas under drought stress in plants. In eukaryotic cells, organelle movement, positioning and communications are critical for maintaining cellular functions and are highly regulated by intracellular trafficking. Directional movement of motor proteins along the cytoskeleton is one of the key regulators of such trafficking. Most plants have developed a unique actin–myosin system for intracellular trafficking. Myosins participate in a different cellular processes, endocytosis, containing cell polarization, intracellular and organellar transport, transcriptional regulation, and signal transduction. Motions are as molecular motors in biological systems. These can bind to filamentous actin and produce physical forces through hydrolyzing ATP. Myosins is one of the most diverse and largest protein families in eukaryote. Class XI and VIII motor proteins are characterized as a slow and fast motor proteins. Myosin XI possess many genes in Angiosperms. Whereas, myosin-VIII contain fewer members against class XI. Further, molecular size of myosin-VIII is smaller than myosin-XI.

Protein file of A.thaliana was downloaded and matrix file of hidden Markov Model (HMM) of myosin gene family was used. Here, phylogenetic analysis, gene structure, and gene expression were surveyed. Gene expression of two genes (StMyoXI-F and StMyoXI-B) was performed in different tissues (root, stem, leaves, and tuber). For analysis of expression in different tissues (leaves, stem, and root), sampling was performed 2 weeks after mother tuber growth. However, tubers were sampled 6 weeks after cultivated in Karaj. To evaluate expression under drought stress, after 6 weeks of growth, the water stress was induced by irrigation suppression in 2 weeks while, daily irrigation was maintained for control plants. Leaves and tuber sampling were performed under two conditions.

The seven StMyo genes were unevenly distributed in the two subgroups. The seven StMyo genes were unevenly distributed in the two subgroups. Class XI was the largest subfamily, which class VIII had the lowest subfamily. Drought treatment significantly increased expression of StMyoXI-B and StMyoXI-F genes by 80 and 8 fold compared to the control treatment, repectively. Under control conditions, StMyoXI-B and StMyoXI-F enhanced expression in root by 25 and 20 fold while, it showed low expression in leaves under control conditions. Under control conditions, StMyoXI-F gene showed the 3 and 4 fold change higher mean relative expression than the reference gene. The relative expression of StMyoXI-B gene has been increased 5 and 10 fold change in leaves and stem under non-stress conditions as compared to the reference gene. Among myosin genes, the number of exons varied from 1 to 39. Most of class-VIII proteins had fewer introns whereas, class-XI proteins possess more proteins than class VIII. This results indicated that occurred splicing process in the myosin genes.

Based on the obtained results, it is considered that these genes highly do not influenced in stem development. However, it had significantly affected in root, leaves, and tuber development. It seems this gene can be potentially a good candidate for drought tolerance breeding programs in potato.

 Polymerase chain reaction (PCR) is a critical and practical technology in various biological and medical sciences fields. Using this technique, millions of copies of a specific pattern can be reproduced in vitro with a minimal amount of DNA. This has made significant advances in molecular biology and medicine. This technique has many applications in biological sciences. PCR primers are an integral part of PCR. Well-designed primers allow the PCR system to work accurately. To create a good PCR primer pair, several factors must be considered, including base pair length, melting and annealing temperature, base pair repeats, etc. Carefully designed PCR primers increase sensitivity and specificity and reduce the effort spent on experimental optimization. The poorly designed primer and the lack of optimization of the reaction conditions probably lead to decreased technical accuracy and false positive or negative detection in the amplification of the target DNA fragments. Bioinformatics has become an essential tool for basic research and applied research in life sciences. Primer designing tools provide optimal and efficient design of primers by automating complex and accurate calculations in the shortest possible time.

 This review article is a content analysis study performed by searching Polymerase Chain Reaction (PCR), PCR type, and primer design for PCR in related articles on Google Scholar, Web of Science, PubMed and Scopus.

 This article aims to provide an almost complete guide for designing efficient and optimal primers for PCR and qPCR analyses by reviewing the PCR method, its types and applications and using the links and web-based services. In this regard, in the first part of the article, various methods, such as standard PCR, reverse transcription PCR (RT-PCR), quantitative PCR (qPCR), combined RT-PCR/qPCR, etc., will be explained with suitable figures. The following summarizes the use of PCR types, emphasizing cereal research. In the end, primer design methods, especially for qPCR, classification and review of existing software and their capabilities, methods and software for testing the features of primers to obtain maximum specificity and PCR efficiency, extracting the gene sequence for PCR primer designing is presented with practical examples.

 A PCR with weak primers can produce little or no product due to non-specific amplification or primer dimer formation. Several online tools were introduced that are used to prepare effective primers for PCR in the field of molecular biology. 

Soil and water salinity has significantly reduced crop yields and threatened human food security worldwide. Understanding the molecular basis of how crop plants receive and respond to salinity and identifying the main components of their stress tolerance are essential for developing tolerant plants through genetic manipulation. Today, functional genomics methods such as transcriptomics, proteomics, and metabolomics have revolutionised the study of plant stress response and facilitated the identification of important pathways and components governing stress tolerance. For example, the production and analysis of EST sequences, RNA microarray, and RNA-sequencing technology (RNA-seq) have made it possible to study and identify gene transcripts in genome-wide stress response networks. Accordingly, this study aimed to analyse the transcript of forage turnip (Brassica rapa L.) under salinity stress, determine the functional orientation of the genome, and identify the important components and genes involved in salinity tolerance.

Two Expressed Sequenced Tags (ESTs) libraries of forage turnip under non-stress and salinity stress conditions were analysed using bioinformatic and statistical methods. Non-stress and salinity stress libraries had 8408 and 6894 sequences, respectively. After sequences trimming, the genome functional orientation of forage turnip in response to salinity stress was determined based on Fisher's exact test using the DAVID tool. Differentially expressed genes (DEGs) were assigned using the Audio and Claverie statistical test (AC test) implemented in the IDEG6 tool, at a significance level of 5%. Based on Fisher's exact test, a hierarchical gene network among DEGs was predicted. Then, gene network topology analysis was performed using the NetworkAnalyzer plugin in Cytoscape 4.3. One gene was identified as an important gene (Hub gene) based on gene network topology analysis. In a greenhouse experiment using a tolerant genotype and a susceptible genotype of forage turnip, the expression profile of the identified important gene along with some traits related to the plant antioxidant system, including anthocyanin content, antioxidant enzymes activity, and malondialdehyde content, were evaluated in response to different salinity time points. Finally, the relationship among the changes in gene expression, evaluated traits, and salinity tolerance was determined using Correspondence Analysis (CA).

Pre-processing of 8408 EST sequences of the non-stress library resulted in 8,403 high-quality sequences. Also, out of 6894 EST sequences from the salinity stress library, 6894 high-quality sequences were obtained. BlastX against Arabidopsis proteins showed that 8075 (96.1%) of the non-stress EST sequences had at least one specific hit. 6597 (95.7%) of the EST sequences of the salinity stress library also had at least one specific hit in BlastX. Based on Fisher's exact test, 15 functional groups were significantly (FDR≤0.01) more active in salinity stress conditions than in non-stress conditions. These results clearly showed that under salinity conditions, the genome functional activity of forage turnip was oriented towards response to stresses, especially oxidative stresses, response to internal inductions such as plant hormones, control of metabolic activities, and photosynthetic reactions. Audic and Claverie’s statistical test showed 344 genes were differentially expressed in response to salinity stress; among them, 242 genes were upregulated, and 102 genes were downregulated. The predicted gene network indicated a complex relationship among DEGs, regulatory molecules (especially melatonin and plant hormones), and downstream responsive pathways. Among identified DEGs, the gene encoding transcription factor ZAT6 was assigned as an important gene in the salinity response gene network. The expression profile of the ZAT6 gene, quantity of anthocyanin, the activity of antioxidant enzymes and content of malondialdehyde were significantly different between the two studied genotypes. ZAT6 was significantly more expressed in the stress-tolerant genotype than the stress-susceptible genotype at all time points. In addition, the antioxidant system of the tolerant genotype was more potent than the susceptible genotype. Also, results revealed a significant relationship between the expression profile of ZAT6 and evaluated traits in the context of salinity tolerance. Based on the results, changes in ZAT6 gene expression are directly or indirectly involved in regulating forage turnip plant responses to salinity stress, especially through the control of evaluated traits.

Transcriptome study clarified some of the molecular bases of the forage turnip response to salinity stress. Accordingly, it seems that the gene encoding the ZAT6 transcription factor plays an important role(s) in the salinity stress tolerance of forage turnip. There was a significant relationship between high expression levels of this gene and enhanced antioxidant activities, which could confirm the hypothesis. However, further studies are needed to assign detailed functions of ZAT6, particularly the association of this gene with the regulatory pathway of melatonin as a major regulatory molecule in plants. This can be an effective starting point for further studies.

Crocus sativus is a triploide plant and propagating by vegetative propagation. Therefore, trait segregation and genetic diversity are limited in this plant. EST-SSR markers have some priority, for example co-dominant inheritance, locus specific and highly polymorphic against all other markers. Due to the availability of transcriptome data, it is possible to develop EST-SSR markers and polymorphism studies in saffron. Development of EST-SSR markers in C. sativus make it possible to study genetic diversity and molecular polymorphism in different genotypes. In order to develop EST-SSR marker for C. sativus, we downloaded public available C. sativus RNA-seq data. Quality control and preprocessing of raw reads were done using FastQC and Trimmomatic tools, respectively. We performed de novo transcriptome assembly using RNA-Bloom. CD-HIT-EST was used in order to reduce redundancy in transcriptome assembly. The assembly quality was evaluated using the BUSCO software and completeness of transcriptome assembly was 90%. After achieving to high quality transcriptome assembly of C. sativus, EST-SSRs were identified by MISA tool. The EST-SSRs primers were designed using Primer3. 35459 SSR-containing sequences were detected and primer pairs were designed for them. Ten EST-SSR primer pairs were randomly selected to amplify C. sativus DNA. Seven pairs of the primers (70%) generated clear and reproducible bands with the expected size. These EST-SSR markers can be functional and useful for C. sativus genetic studies.

Tocopherols (Vitamin E) are an important group of organic compounds that realize vital activities in plant cells. They protect the photosynthetic system from photooxidation damages and prevent the lipid peroxidation of the chloroplast membrane. The presence of this plant organic compound in human nutrition is essential. In this research, six genes involved in the biosynthesis pathway of vitamin E including HPPD/ PDS1, VTE5, HPT/ VTE2, VTE3/ APG1/ IE35, TC/ VTE1, γ-TMT/ VTE4 and their products are identified in lentil plant using databases and bioinformatics software. After this identification, genes are implemented for breeding purposes of lentil through traditional breeding or modern biotechnology methods. According to the phylogenetic tree obtained by the MEGA 7 program, it was observed that most of these genes in the lentil have high homology to legume plants such as chickpea and alfalfa. In addition, the prediction of the presence of conserved domains revealed that the HPPD protein had two domains and one subdomain, and each of the proteins γ-TMT and VTE3 had only one conserved domain. Moreover, the results of the proteins description using ProtParam tool showed that the highest frequency with respect to the amino acids belonged to leucine, serine and glycine; by contrast, selenocysteine and pyrrolysine had the lowest frequency. The use of the DeepLoc-1.0 program predicted that only HPPD proteins were soluble in the cytoplasm, while five other proteins were located in the intermembrane space.

MicroRNAs (miRNAs) are a class of short and endogenously initiated non-coding RNAs that post-transcriptionally control gene expression via either translational repression or mRNA degradation. Mature miRNAs are reported to be highly conserved throughout the plant kingdom; therefore, comparative genomics approaches are used to predict the novel miRNA genes and their target genes. In this study, bioinformatics and laboratory approaches followed by the EST and miRNA sequences in the databases for chicory species were employed for the identification of potential miRNAs and their potential targets either in Cichorium intybus or Cichorium endivia. To identify the potential miRNAs in the C. intybus and C. endivia, all the publicly available EST sequences of the plant were blasted against the previously known Plant miRNAs. Ultimately, four novel miRNAs belonging to four different families of miR166, miR156, miR162 and miR393 were identified. Also, a large number of genes, such as TIR1, Squamusa promoter binding proteins genes were identified as target genes of these miRNAs. Furthermore, the results of Real Time PCR showed that the transcriptional activities of miR156 in the leaf tissue of C. endivia are extremely high, not only than those observed for flower tissue of the same species, but also as compared with the leaf and flower tissues of the another species of C. intybus.

MicroRNAs(miRNAs) are a group of small non-coding RNAs of approximately 18 - 24 nucleotides that play a negative role in post-transcriptional changes in eukaryotes. The miRNAs are then loaded onto the argonate family proteins (AGO) to form a protein complex (RISC). The primary activity of the RISC complex is to direct the mature miRNA to the target RNA and to stop protein production (Megah et al., 2018). miRNAs are involved in response to abiotic stresses in plants such as drought; several miRNA families have been reported in response to drought stress in rice, tomato, Arabidopsis, Medicago truncatula, peach, barley and wheat (Akdogan et al., 2015). The purpose of this study was to identify new microRNAs and their role in suppressing and preventing expression of some of their target genes in rapeseed.

A total of 38589 known mature miRAN sequences were downloaded from the miRBase database. The miRNA sequences were used as known sequences to find conserved miRNAs based on homology search for miRNAs with rapeseed GSS sequences.103369 GSS for rapeseed was downloaded from NCBI database. Mature miRNA sequences were uploaded to the BLASTn algorithm to search for homology with rapeseed GSSs in Linux. The miRNA sequences as known sequences and the GSS sequences as sequences were compared with each other for homology search. GSSs with mature miRNA sequences up to four mismatches were selected as candidates (Zhang, 2005). GSS sequences were used instead of EST sequences because miRNAs can generate GSS sequences in addition to EST sequences. Consequently, GSSs were sequenced between the BLASTx miRNA sequences and the GSS coding sequences were deleted and only non-coding GSS sequences remained (Karimi et al., 2017). Mfold software was used to predict the secondary structure of candidate miRNAs (Vivek, 2018). ath-miR5021 and ath-miR8175 from Arabidopsis, bol-miR9410 and bol-miR9411 from wild cabbage and cas-miR11592 from Camelina sativa were selected from the psRNATarget website (Dai and Zhao, 2011.

For miR5021: The NST1 target gene encodes a protein called Stress response protein NST1, which plays a role in regulating secondary wall thickness in plants and preventing its destruction against a variety of stresses (Mitsuda et al., 2005). For miR9410: The HST gene is one of the target genes that encodes an enzyme called Shikimate O-hydroxycinnamoyltransferase in plants, which participates in the phenylpropanoid biosynthesis and heat stress control in plants, propanoids as secondary metabolites during developmental stages. The plant is synthesized in response to stress conditions (Lukasik et al., 2013).

Types of microRNAs and their role in suppressing target genes during live and abiotic stresses in barley, wheat, soybean, cucumber, alfalfa, olive, rice have been reported (Ozhuner et al., 2013). In this study, we tried to identify new microRNAs and their role in suppressing target genes for the first time in rapeseed. The results of this study showed that among the newly identified microRNAs, miR5021 and miR9410 families play an important role in suppressing NST1 and HST target genes, respectively, especially during stress in canola.. Therefore, identifying the molecular mechanism of these microRNAs and their target genes can help us in selecting drought and heat resistant varieties for rapeseed. A study of microRNAs for boron stress tolerance in leaves and roots of barley showed that of the four new microRNAs identified, miR408 was more involved in regulating cell signaling in leaves than the other three microRNAs (Ozhuner et al., 2013). Also, no response has been reported in hybrid and maize inbred lines for miR172 under drought and salt stress conditions (Kong et al., 2010). Therefore, understanding the cellular regulation mechanism for new microRNAs, including how to regulate the activity pathway of antioxidant enzymes such as superoxide dismutase in organs such as leaves, roots and shoots of canola, requires further investigation.

MicroRNAs can be used as a new molecular tool alongside existing classical breeding methods to improve the genetic status of plants to promote tolerance to a variety of biotic and abiotic stresses in plant breeding.

Nowadays, saffron is considered as a strategic medicinal plant in Iran. Apocarotenoids are also known as economic compound in saffron stigmas. Therefore, isolation and functional analysis of genes involving in carotenoid metbolism in saffron has a great importance. In this study, regarding the role of CsCCD1 gene in saffron apocarotenoids biosynthesis, it was targeted for studying the genomic structure of Iranian saffron CCD1. ProtParam, SOPMA, ProtScale, Pfam, ProtComp, SignalP, TMHMM, TargetP and ChloroPwre are the softwares used for studying the physicochemical and physiological charachterizations of CCD1 protein. Swiss-Model server was used for investigate the 3D structure of CCD1 protein followed by Ramachandran plotting for structural validation of 3D model. The results of phylogenetic analysis showed that amino acid structure of CsCCD1 protein have the most similarity to CaCCD. It is also found that CsCCD1 protein has no signal sequence and transmembrane domains. In addition, the results of this study demonstrated that CCD1 protein belongs to carotenoid oxidase family and it is stable In vitro. The results of this study can provide valuable information on the behavior and response of the CCD1 enzyme in the pathway for the synthesis of apocarotenoids in saffron, and these results can be useful in future protein engineering programs.

Rice, as one of the most important crops, has the smallest genome among cereals and is considered as a model plant for genetic studies. The small size of this plant’s genome has led to comprehensive studies on it, resulting in a large amounts of data to be obtained. Properly collecting and storing these data and managing data from various experiments in a database for accessing researchers to them to avoid re-work and to compare their results with the results of other researchers is very important. To achieve these, bioinformatics can be great help. Therefore, the creation and development of specialized databases and the use of bioinformatics tools for data processing, efficient organization, analysis and visualization are necessary. In this paper, the major databases for studying gene expression at three levels, RNA, protein and metabolome in rice are reviewed and the characteristics of these databases for each level are discussed.

Polyamines are oxidativelydeaminated by amine oxidases (AOs), including copper amine oxidases (CuAOs) and FAD-dependent polyamine oxidases (PAOs). PAOs are associated with polyamine catabolism in peroxisome, apoplast and cytoplasm. In plants, increasing evidences support that PAO genes play an essential roles in growth and developmental processes such as organogenesis, senescence, and also responses to abiotic and biotic stresses. The availability of the maize genome sequences has provided an excellent opportunity for whole-genome annotation, classification and comparative genomics research. In this study, through bioinformatics analysis approaches, nine putative PAO (ZmPAO1–ZmPAO9) were identified in maize genome. According to Phylogenetic analysis ZmPAOs can be divided into three major groups as found in their orthologous in Arabidopsis and rice. It is also demonstrated that maize PAO proteins are more closely related to rice than those in Arabidopsis. Gene structural analysis showed that the ZmPAOs have zero to nine introns and they are distributed across 4 out of 10 chromosomes in maize. Duplication pattern analysis shows that segmental and tandem duplication are the main reasons for maize PAOs expansion. Using public microarray data, the roles of ZmPAOs in growth and development processes were assessed. These results have been provided evidences regarding the important functions of the gene family in maize developmental regulation. These results provide a basis for further functional characterization of ZmPAOs at the tissue/developmental level and in response to stresses. Using public microarray data, ZmPAO expression profiles strongly suggested that ZmPAOs have a role in growth and development processes.

MicroRNAs (miRNAs) are A group of 17_22 nucleotides that derived from its precursor sequence and show an enormous role in various biological and metabolic processes in both animals and plants. There are several ways to identify miRNAs. One of the easiest and cheapest way to identify miRNAs is bioinformatics methods. In this study¡ a bioinformatics approach was used to identify potential miRNAs in Papaver somniferum. We blasted publicly available EST sequences obtained from NCBI GenBank against previously known plant miRNAs and ultimately distinguished seven potential miRNA in Papaver somniferum. Target genes predicted miRNA are a protein serine / threonine kinase (signal transduction)¡ PPR protein family (Edit and stability of RNA) and globulins 7 S (hydration and dehydration cells), phototropin (response phototropism), protein of serine / threonine phosphatase (glycogen metabolism), TIR protein family (defense against bacteria). These genes play an important role in growth and development¡ metabolism¡ morphology and determine flowering time and response to biotic and abiotic stresses.

Advances of technology and the speed of genetic researches have enhanced genetic data in different fields like nucleotides and amino acids sequences, genes and proteins functions, mutants and their phenotypes, markers and etc. In addition to its volume, genetic information is complex and has subtle differences in the experimental manners which can influence on the quality and interpretation of the data. Thus it is crucial to describe and categorize the data related to genes and its phenotype information in the way that rapid and easy comparison of them be available. The use of genetic databases can help researchers to complete and update their researches and it awards them of the latest acquisitions of the science. Application of genetic databases in research for cereal is prevalent in recent years. This article will review databases which offer comprehensive information of rice genome and then one of the most usage cereal databases will be introduced.