Showing 8 results for Rna-Seq
M. Sharifi Alishah, R. Darvishzadeh, M. Ahmadabadi, Y. Piri Kashtiban, K. Hasanpur,
Volume 10, Issue 4 (12-2019)
Abstract
Revealing DNA sequences is vital for all branches of biological sciences. Next-Generation Sequencing (NGS) is a different approach in this area so that it has created a great evolution in biology science and covers various aspects of genome, transcriptome, epigenome and metagenome-level studies. NGS is considered as a high-performance method for genomic and transcriptomic information analysis in comparison with traditional methods due to providing good genomic coverage, determining each single pairs of bases and eliminating the first generation sequencing disadvantages (Sanger sequencing). Use of NGS has begun since 2005 and 2006, after the commercialization of various apparatus companies such as ABI/SOLiD Illumina, Science Roch/454Life, and Solexa to study the transcriptome of the model and non-model organisms. Recently, RNA sequencing is used widely to identify genes associated with growth and development processes and their expression patterns in response to a variety of biological and non-biological stresses, in various organs and growth stages in different organisms. It helps scientists to determine the amounts of gene expression, differentiation of different isoforms of genes, detection of gene fusions and characterization of small RNA as well as alternative splicing events, duplicate elements, exon of genes, new transcripts, UTRs, SNPs, and somatic mutations. The RNA-seq method typically consists of providing suitable biological samples, isolation of total RNA, enrichment of non-ribosomal RNAs, conversion of RNA to cDNA, construction of a fragment library, selecting size and adding linkers and sequencing on high-throughput sequencing platform, alignment, and assembly of the reads and downstream analysis.
Volume 13, Issue 3 (12-2024)
Abstract
Botrytis cinerea is one of the most important harmful fungi affecting agricultural products. This study focused on the expression changes of Arabidopsis thaliana infected with this fungus. The expression dataset of a microarray and two RNA-sequencing were integrated using the respective software. The list of differentially expressed genes was extracted, and the key genes with altered expression were identified through Cytoscape software. These key genes co-expression patterns and functional enrichment were analyzed. Subsequently, microRNAs and transcription factors associated with these genes were predicted. Ten genes, including GAPA-2, SBPASE, CRB, HCEF1, CaS, ATPD, LIL3:1, PSAH2, PRK, and PMDH2, were identified as crucial down-regulated genes. Additionally, ten genes, namely WRKY33, CZF1, SZF1, STZ, ERF11, RHL41, BAP1, AT1G07135, CMPG2, and TET8, were highlighted as key up-regulated genes. The key roles of the hub genes with a decreased expression included processes and pathways associated with the reductive pentose phosphate cycle, photosynthesis, cold response, fructose and sucrose metabolism, defense response against bacteria, and gluconeogenesis. The key over-expressed genes played important roles in responding to chitin, oxygen deprivation, temperature fluctuations, injuries, fungal attacks, and gene transcription functions. Key genes were associated with ath-miR850, ath-miR393a-5p, and ath-miR393b-5p. Transcription factor SPL7 was linked to the transcription of down-regulated key genes, while transcription factors SARD1, PIF5, CAMTA1, HY5, WRKY33, TOC1, CAMTA3, CAMTA2, BZR1, FAR1, and CAMTA5 were also predicted to be associated with up-regulated genes. Some of these results have not previously been reported. Therefore, they could be used to design practical experiments exploring the interaction between plants and pathogenic fungi.
Volume 24, Issue 1 (1-2022)
Abstract
Salinity stress is one of the most important environmental stresses that decrease crop growth and yield. Barley is an important crop known as the salt-tolerant plant in cereals. In this study, the salt stress-responsive root transcriptome of tolerant (Afzal) and susceptible (Yusef) cultivars was investigated. The sequencing of mRNA transcripts (termed RNA-Seq) was performed using the Illumina HiSeq platform after filtering for RNA with 3' polyadenylated tails to include only mRNA. The Tuxedo pipeline was used to identify the altered expression of transcripts. Sequencing results showed that, after initial trimming of the reads, more than 20 million reads (92%) remained for all samples, of which 88% were aligned with the barley genome. Bioinformatics analysis showed the altered genes expressions in various processes such as membrane antiporter and transporter activity, an antioxidant, wide range of kinase and phosphatase cascades, internal signal transduction, metabolism of carbohydrates, amino acids, and lipids, binding processes, response to plant hormones, catalytic activity, and cell wall organization. Gene network analysis revealed that key genes, including proteins involved in systemic acquired resistance, peroxidase family proteins, cyclin-dependent protein kinase, phosphatidylinositol kinase, auxin-carrying proteins, mannose 6 phosphate isomerase, helicases and transcription factors play an important role in salt tolerance. These data can be used as a valuable source in future studies for genetic manipulation of barley and development of salinity tolerant cultivars.
Volume 24, Issue 5 (9-2022)
Abstract
Several viruses affect iris plants worldwide, and are major constraints in commercial production due to serious economic losses. The first genomic sequences of two potyviruses, namely, Iris Severe Mosaic Virus (ISMV) and Iris Mild Mosaic Virus (IMMV) from naturally infected iris plants (Iris versicolor) in Iran were determined using RNA deep sequencing and RT-PCR followed by sequencing of amplicons. Both viruses (ISMV-Ir and IMMV-Ir) had a typical potyvirus genetic organization, with a large open reading frame translated as a polyprotein, including nine autocatalytic cleavage sites, and a putative smaller protein P3N-PIPO. Phylogenetic analyses and sequence comparisons revealed close relationships between ISMV and members of group Onion Yellow Dwarf Virus (OYDV) of the genus Potyvirus. The ISMV-Ir showed > 92% nucleotide (nt) identity (> 96% amino acid (aa) identity) to the three previously reported ISMV isolates, the highest with the Japanese isolate J (94.10% nt identity, 97.41% aa identity) and the lowest with Chinese isolate BJ (92.73% nt identity, 96.77% aa identity). IMMV-Ir belonged to the Chilli Veinal Mottle Virus (ChVMV) group of potyviruses, had 82.36% nt identity (91.25% aa identity) with the BC32 isolate, and 75.55% nt identity (83.59% aa identity) with the WA-1 isolate from Australia. The genetic distance among IMMV polyprotein-coding genomic sequences or gene-specific sequences indicated a high genetic divergence of these isolates. Our analysis indicated that natural selection has contributed to the evolution of isolates belonging to the two identified potyviruses. The information on genomic sequences presented in this study will improve our understanding of virus function and pathogenicity leading to better control of the disease.
Volume 24, Issue 6 (11-2022)
Abstract
MicroRNAs are endogenous noncoding RNA that play vital roles in all plant cellular metabolic processes by mediating target gene expression. To date, miRNAs in Taraxacum spp., which is an important industrial plant, have remained largely unknown. In the present study, 970 miRNAs from 399 families were identified in Taraxacum spp by conducting computational approaches. The most frequent miRNAs in Taraxacum spp was miR5021. According to the KEGG results, miR5021, miR838, and miR1533 are related to the terpene biosynthesis pathway, while miR5015b, and miR1436 are involved in the starch and sucrose biosynthesis pathways. Quantitative real-time PCR assay was performed to validate the expression levels of five predicted miRNAs and 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase (HMGCR) and invertase as the target genes. Results indicated that the highest relative expression of miR1533 and miR1436 occurred in the flower, while the highest transcripts levels of miR5015b were observed in the stem. In addition, the higher relative expression level of the miR5021 and miR838 was consistent with the lower expression level of the HMGCR gene in all tissue, suggesting that miR5021 and miR838 are involved in regulating HMGCR gene expression. Since mevalonate pathway is the main source of isopentenyl pyrophosphate, which is used in the synthesis of rubber, miR5021 and miR838 play an important role in the production of rubber by regulating the expression of HMGCR enzyme. These findings will accelerate future perspective studies on the regulatory mechanisms of miRNAs in Taraxacum kok-saghyz.
Volume 26, Issue 1 (1-2024)
Abstract
An effort was made to analyze metabolome and transcriptome profiles of Ferula persica via GC-MS and RNA-seq data. The analysis of the essential oils extracted from both flower and root tissues demonstrated the prominence of monoterpene constituents, while sesquiterpene compounds were present in the lower magnitudes. Considering transcriptome analysis, 2127 differentially expressed genes were found between root and flower: 396 transcripts were up-regulated in root, while 1731 exhibited an up-regulation pattern in flower. Out of 2127 transcripts, 86 were annotated as Terpene Synthases (TPSs), of which 83 TPSs were classified subsequently into five individual sub-families of TPS-a (33), TPS-b (42), TPS-c (2), TPSe-f (3), and TPS-g (3). Several transcription factor families were recognized among the differentially expressed genes, suggesting their direct or indirect regulatory roles for the biosynthesis of terpenoids in F. persica. Finally, according to our phylogenetic results, both F. assa-foetida and F. gummosa were placed in the same clade, while F. persica was lonely settled in one monophyletic clade, with the estimated divergence time of 2.99 Million Years Ago (MYA) between F. gummosa and F. assa-foetida, and 3.87 MYA between F. persica and two other Ferula species.
Volume 26, Issue 3 (5-2024)
Abstract
Fatty Liver Hemorrhagic Syndrome (FLHS) is common in poultry. Long non-coding RNAs (lncRNAs) regulate gene expression in a variety of ways at epigenetic, chromatin remodeling, transcriptional, and translational levels. Chicken liver produces lipoproteins and most of the precursors to egg yolk with the help of RNA such as MicroRNAs (miRNAs) and lncRNAs. In order to analyze lncRNAs in liver, RNA-seq data of six samples were downloaded from National Center for Biotechnology Information (NCBI) (3 birds with fatty livers from the paternal group and 3 control birds).Then, using the DESeq2 package, the difference in expression of lncRNAs in the samples was analyzed. Functional enrichment analysis was established by STRING and the PPI network visualized by Cytoscape. Annotation of the data was carried out by DAVID 6.8. The biological pathways were searched in Kyoto Encyclopedia of Genes and Genomes (KEGG). The results of the analysis of Differentially Expressed Genes (DEGs) showed that there were 24356 annotated genes. Also, 101 lncRNAs were found. Gene Ontology (GO) term enrichment analysis suggested that DEGs significantly enriched in metallocarboxypeptidase activity, protein ubiquitination, etc. KEGG pathway analysis showed that DEGs related with biosynthesis of antibiotics and biosynthesis of amino acids (P< 0.05). Examination of gene loci revealed that the expression process of GCGR, PDK3 and PCK1 genes was in line with the expression of neighboring lncRNAs. Examination of this number of lncRNAs along with their target genes can help in selecting laying hen lines with less chance of developing fatty livers.
Volume 28, Issue 2 (3-2025)
Abstract
Introduction: Opioid Use Disorder (OUD) is a chronic neuropsychiatric condition driven by persistent neuroadaptive changes in reward, motivation, and stress-related circuits. While opioid receptors are central to OUD, the broader role of G protein-coupled receptors (GPCRs) in opioid-induced neuroplasticity remains underexplored. This study systematically characterizes GPCR dysregulation in OUD to identify potential pharmacological targets. Methods: We performed transcriptomic analysis of RNA sequencing (RNA-seq) datasets from addiction-related brain regions, including the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (GSE174409), Brodmann area 9 (GSE182321), and central amygdala (GSE194368). A curated set of ~900 GPCR genes was analyzed for differentially expressed genes (DEG), principal component analysis (PCA), and hierarchical clustering. Drug-targetable GPCRs were identified via DrugBank and ChEMBL, and their behavioral and stress-related roles were determined. Protein-protein interaction (PPI) networks were constructed using STRING. Results: We identified 58 GPCRs consistently dysregulated across brain regions, reflecting common molecular adaptations in OUD. PCA revealed a clear separation between OUD and control groups, indicating distinct receptor remodeling. Hierarchical clustering identified functional subgroups, including drug-targetable GPCRs and orphan GPCRs. Notably, 17 GPCRs—including DRD1, DRD3, DRD4, HTR1A, HTR2A, OXTR, and CNR1—are involved in behavioral regulation and addiction vulnerability. Network analysis highlighted key receptor hubs, suggesting novel therapeutic targets. Conclusion: The present study provides a receptor-centric framework for drug repurposing and precision medicine in OUD. Integrating transcriptomic and pharmacological data, we highlight GPCRs with translational potential. Further validation through functional assays and single-cell studies is warranted.
