Showing 9 results for Transcriptome
Volume 0, Issue 0 (1-2024)
Abstract
Crown rot, caused by Colletotrichum siamense, is a devastating hemibiotrophic fungal disease that poses a significant threat to the strawberry industry. Salicylic acid (SA) is known to play a critical role in plant defense responses to biotic stress. However, its contribution to mitigating strawberry crown rot remains unclear due to the microbial isolate-specific sensitivity and cultivar/tissue-specific responses in strawberries. In this study, we aimed to investigate how exogenous supply of SA influenced crown rot in strawberry. Exogenous SA application significantly reduced C. siamense infection in strawberry crowns, evidenced by the lesion size and pathological analysis. Transcriptomic data showed that for each sample of SA pretreatment and mock, owing to nearly 50 million reads, the ratio of Q20 ranged from 98% to 99%, and 91.63%-94.29% of the reads mapped to the reference genome. The SA pretreatment up-regulated genes encoding MLO-like protein 2, receptor-like kinase, peroxidase, and caffeic acid 3-O-methyltransferase involved in lignin biosynthesis. The SA pretreatment also down-regulated chalcone isomerase, naringenin 3-dioxygenase, bifunctional dihydroflavonol 4-reductase, anthocyanidin synthase, and anthocyanidin reductase expressions involved in flavonoid biosynthesis during C. siamense infection. Consistent with gene expression changes, the SA pretreatment remarkably enhanced peroxidase activity and lignin content and decreased flavonoid content and chalcone isomerase activity after C. siamense inoculation. The results suggest that exogenous SA enhanced strawberry resistance to crown rot caused by C. siamense by up-regulating defense-related genes and lignin biosynthesis.
Volume 5, Issue 4 (12-2016)
Abstract
One of the best strategies to control bacterial wilt caused by Ralstonia solanacearum (Smith) is generally based on breeding resistant cultivars. The information obtained from the expression of plant defense genes will provide new insight for improving plant resistance against pathogens. This study was to identify inducible genes under defense no death (DND) reaction of tobacco (Nicotiana tabacum)-R. solanacearum interaction using cDNA-AFLP technique. In this assay five different primer combinations were used. Out of 1320 Transcript derived fragments (TDF) that were detected, 101 fragments were identified as differentially expressed genes in 0, 24, 48 and 72 hours post inoculation. Most of the differentially expressed genes were obtained 48 hours post inoculation. Following sequencing, most of sequenced TDFs showed homology to known genes interfering in signaling, regulation and defense functions. DND phenotype in tobacco has some similarities specially in signaling process with mechanism associated with induction of the hypersensitive reaction and it is distinct from general defense mechanisms.
F. Shariari, Sh. Moradi, M. Totonchi, L. Satarian, S.j. Mowla, H. Baharvand,
Volume 10, Issue 3 (9-2019)
Abstract
Aims: The retinal pigment epithelium cells (RPE) have crucial roles in the health and functionality of retina. Any damage or dysfunction of these cells can lead to severe retinopathies. Identification of signaling pathways and biological processes involved in RPE differentiation can be useful in devising more robust therapeutic approaches.
Materials and Methods: In the present study, we used the intersection of three online prediction databases and their ::union:: with one experimental database to select microRNAs gene targets. Next, by the intersect of the targeted genes with an increase in their expression in epithelial to mesenchymal transition (EMT) of RPE cells, we tried to build a microRNA-mRNA integrative network. Further, several pathway analyses tools were used to perform a more accurate and comprehensive analysis of the signaling pathways and biological processes being regulated by selected miRs in the EMT of the RPE cells.
Findings: Our study revealed that among the 3406 genes being upregulated over the course of EMT in RPE cells, adj p-value≤0.05, fold change≥1.5, 93 genes were miR-204-5p and miR 211-5p target genes. Further analysis of the obtained target gene list demonstrated that these two microRNAs are mostly involved in maintaining RPE cells from going through EMT via regulation of cell adhesion and secretion subnetworks and also MAPK and TGF-β1 signaling pathways while preserving cells from apoptosis and neuronal fates.
Conclusion: This study indicated that miR-204-5p and miR 211-5p are involved in protecting RPE cells from EMT and reinforce their epithelial cell identity.
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.
Mojtaba Khayam Nekoui, Maryam Moazam Jazi, Mohsen Mardi, Saeid Kadkhodaei,
Volume 11, Issue 2 (6-2020)
Abstract
In stevia (Stevia rebaudiana), breeding programs are mainly aimed at developing plants with high Rebaudioside-A (RA) content. To this end, in order to screen stevia plants and selection of varieties with the highest amount of desired sweeteners (RA) using molecular markers, the present study was conducted on RNA-seq data of varieties having different amounts of RA. We took advantage of CLC to make de novo transcriptome assembly for each variety with k-mer and contig length values of 20 and 200bp, respectively. The assembly was annotated using the latest Arabidopsis proteome release. To identify signatures of candidate polymorphic SSRs among the stevia varieties, the assembled sequences were used as an input for CandiSSR, followed by designing primer pairs for identified polymorphic SSRs. We identified 368 potential polymorphic SSRs based on the stevia transcriptome analysis, among which 360 were qualified for primer design. Almost 89% of the contig sequences possessing polymorphic SSRs had the best blast hit against Arabidopsis proteome. We found contigs similar to the UDP-Glycosyltransferase protein family and Deoxyxylulose-5-phosphate synthase which are involved in biosynthesis pathway of steviol glycosides. Also, gene set enrichment analysis using PlantGSE through Hypergeometric test (FDR<0.05) identified enriched metabolic pathways in the sequences contained polymorphic SSRs; It is therefore most likely that such connections exist between the SSRs and biosynthesis of steviol glycosides. Hence, it could conceivably be hypothesized that the SSR markers developed in this study would be reliable in molecular breeding of stevia toward selection of varieties with high RA content.
Mehdi Sadeghi, Sajjad Safari,
Volume 13, Issue 4 (1-2023)
Abstract
Background and Objectives: Alzheimer’s disease is the most common neurodegenerative disease and the memory impairment is the main prominent symptom of this disease. The hippocampus of the brain, is the first region that undergoes changes in Alzheimer’s. Systems biology tools such as high-throughput techniques, enable us to explore signature genes involved in disease initiation and advancement which can be considered as new therapeutic and diagnostic candidates in complex diseases like Alzheimer’s.
Methods: A total of 85 samples obtained from the hippocampus of the brain of healthy individuals and individuals with Alzheimer’s were selected from two datasets. Differential expression analysis was performed independently for both datasets and the results were integrated. Genes with the same expression pattern in the two datasets were used to construct a gene-gene network using the STRING database. The obtained network analysis was performed to detect key genes associated with the disease.
Results: In this study, 73 genes with the same expression pattern were found in the two datasets. The obtained network analysis led to the identification of SNAP25, UNC13A, SYN2 and AMPH as key genes connected with Alzheimer’s disease.
Conclusion: The role of the reported key genes in endocytosis, neurotransmitters release and synaptic vesicle cycle facilitate proper functioning of memory. Expressional changes and mutations in each of these genes effect other pathways and lead to Alzheimer’s. Thus, the key genes reported in this study, can be considered as potential markers in developing diagnostic and therapeutic methods for Alzheimer’s.
Volume 18, Issue 4 (7-2016)
Abstract
The yellow-bud mutant hot pepper, 96-140YBM, which exhibits a yellow leaf phenotype in its young leaves but whose matured leaves are green, was isolated from wild type 96-140 in this study. The results of photosynthetic pigment determination and chloroplast ultrastructure observation revealed that the young mutant leaves displayed Chl a+b and Cars content, increased Chl a/b and Car/Chl a+b ratios, and delayed chloroplast development compared with the wild type leaves. Here, we obtained 95,714 transcripts from cultured yellow-bud mutant yellow leaves and cultured wild-type seedling leaves using the Illumina HiSeq-2000 (Illumina Inc., USA) platform. A total of 42,384 unigenes were identified, among which 37,949 were annotated using gene descriptions or gene ontology terms. Based on Differentially Expressed Genes (DEG) analysis, 1,056 of the 1,101 DEGs were annotated in the Nr database, and 302 unigenes were mapped to 130 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Finally, we found that 6 pathways were related to chloroplast and chlorophyll biogenesis.
Volume 19, Issue 3 (5-2017)
Abstract
Transition from vegetative to reproductive growth is an important stage in plant’s life. Flowering pathways including photoperiod, vernalization, gibberellins, and autonomous pathway are regulated by different genes. Identification of flowering genes is essential for the development of bolting-resistant sugar beet cultivars. In this study, a set of 118 Arabidopsis thaliana genes involved in flowering time control were used as a reference to identify homologous counterparts in Expressed Sequence Tags (ESTs) and Transcriptome Shotgun Assembly (TSA) sequence of sugar beet. Based on obtained ESTs, primers were designed for Suppressor of Frigida 4 (SUF4), Curly Leaf (CLF), Constitutive Photomorphogenesis1 (COP1), and Cycling Dof Factor (CDF) genes. SUF4 and CLF are components of vernalization pathway and COP1 and CDF are in photoperiod pathway. The sequence regions of these genes were amplified using cDNA PCR technique, and compared with other identified sequences in Gene Bank. Four genes namely CLF, COP1, CDF and SUF4 were deposited in Gene Bank. Results showed that most of the flowering pathway genes in Arabidopsis are detectable in sugar beet which can be contributed to the understanding of the genetic control of bolting resistance.
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.
