Digital gene expression (DGE) of PaWB phytoplasma-infected Paulownia witches
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ABSTRACT:
ORGANISM(S): Paulownia
SUBMITTER: Jie Lu
PROVIDER: E-GEOD-42087 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Here we performed a transcriptomic study on PaWB phytoplasma-infected Paulownia sp. using Solexa/Illumina’s high-throughput digital gene expression (DGE) system. 4 DGE libraries (from 2 virus-infected samples and 2 healthy samples) were constructed, and the gene expression variations between the PaWB phytoplasma-infected (diseased) sample and the corresponding healthy sample were compared. Thousands of differentially expressed genes were obtained by the comparison, and KEGG pathway analysis of these genes suggested that many biological processes were responded to PaWB infection.
2014-10-01 | GSE42087 | GEO
Project description:Here we performed a transcriptomic study on complete symptom development process of CMV-infected Nicotiana tabacum using Solexa/Illumina's high-throughput digital gene expression (DGE) system. 12 DGE libraries (from six virus-infected samples and six corresponding mock-inoculated samples) were constructed, and the gene expression variations between the virus-infected sample and the mock-inoculated sample in each symptom stage were compared. Thousands of differentially expressed genes were obtained by the comparison, and KEGG pathway analysis of these genes suggested that many biological processes (such as phtosynthesis, pigment metabolism and plant-pathogen interaction) were related to the symptom development. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes. We sequenced a cDNA library constructed from mixture of total RNA from six virus-infected samples and six mock-inoculated samples to get gene information for tobacco leaves in different symptom stages, including vein clearing, mosaic, severe chlorosis, partial recovery, total recovery and re-mosaic, and 95,916 Unigenes were obtained Tobacco leaves were inoculated by CMV-infected leaf homogenate and healthy leaf homogenate, respectivley. Six time points with different symptom stage were selected, and one virus-infect sample and one mock-inoculated sample were collected at each time. In order to average out variation of different plants, five leaves from five different plants were mixed to prepare every RNA sample. Twelve individual tag libraries of samples (six infected samples and six mock-inoculated samples) were constructed in parallel. For the gene expression analysis, the twelve samples were grouped into six groups, and each group contained a virus-infected sample and a mock-inoculated sample collected at the same time. In each group, the DGE data of virus-infected sample were compared to that of mock-inoculated sample to obtain the gene expression variations. Illumina sequencing of transcripts from virus-infected and mock-inoculated samples to get gene information for tobacco leaves in different symptom stages. In order to get more gene information, the systemically infected leaves and mock-inoculated leaves were harvested at six time points and five leaves from five different plants were collected at each time point. The RNA-Seq analysis provided gene information for mock-inoculated and virus-infected tobacco leaves in different symptom stages.
2012-11-09 | E-GEOD-30162 | biostudies-arrayexpress
Project description:Here we performed a transcriptomic study on the effect of sodium nitroprusside (SNP) on cucumber leaves under alkali stress using Solexa/Illumina's high-throughput digital gene expression (DGE) system. Two DGE libraries (from one NaHCO3-treated sample and one NaHCO3 + SNP-treated sample) were constructed, and the gene expression variations between the two samples were compared. Hundreds of differentially expressed genes were obtained by the comparison, and GO analysis of these genes suggested that many biological processes, molecular function, cellular components were related to SNPM-bM-^@M-^Ys mitigated effect on alkaline stress. The authenticity of the DGE data was further confirmed by analyzing real-time RT-PCR using several random-selected genes. The experiment had 2 treatments: 30 mM NaHCO3 (alkali stress treatment, indicated as Na) and 30 mM NaHCO3+100 M-NM-<M sodium nitroprusside (indicated as SNP). Samples from Na- and SNP-treated leaves, used for RNA isolation, were harvested, and the two corresponding tag libraries of samples were constructed in parallel. Illumina sequencing of transcripts from Na- and SNP-treated samples to get gene information for cucumber leaves in different treatments.
2013-11-26 | E-GEOD-42439 | biostudies-arrayexpress
Project description:4,392 differentially expressed genes were generated by DGE analysis, and 3,074 had good comparability with known gene sequences in existing species. 1,152 differentially expressed sequences were mapped to the reference canonical pathways in the KEGG database, and were assigned to 110 KEGG pathways, 11 pathways less then with the transcriptome database. Differentially expressed genes were classed according to their function, which includes phytohormones, growth and developmental processes, defense, peroxidase and P450-related genes. Pathway analysis also revealed that the principal secondary metabolites in the C. odorata cuttings were phytohormones and flavonoids. Examination of 2 different stage of adventitious root formation
2012-11-16 | E-GEOD-42283 | biostudies-arrayexpress
Project description:Background: WitchesM-bM-^@M-^Y broom disease of Mexican lime (Citrus aurantifolia L.), which is caused by the phytoplasma M-bM-^@M-^\Candidatus Phytoplasma aurantifoliaM-bM-^@M-^], is a devastating disease that results in significant economic losses. Plants adapt to abiotic stresses by regulating gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are a recently identified family of molecules that regulate plant responses to environmental stresses through post-transcriptional gene silencing. Methods: Using a high-throughput approach to sequence small RNAs, we compared the expression profiles of miRNAs in healthy Mexican lime trees and in plants infected with M-bM-^@M-^\Ca. Phytoplasma aurantifoliaM-bM-^@M-^]. Results: Our results demonstrated the involvement of different miRNAs in the response of Mexican lime trees to infection by M-bM-^@M-^\Ca. Phytoplasma aurantifoliaM-bM-^@M-^]. We identified miRNA families that are expressed differentially upon infection with phytoplasmas. Most of the miRNAs had variants with small sequence variations (isomiRs), which are expressed differentially in response to pathogen infection. Conclusions: It is likely that the miRNAs that are expressed differentially in healthy and phytoplasma-infected Mexican lime trees are involved in coordinating the regulation of hormonal, nutritional, and stress signalling pathways, and the complex interactions between them. Future research to elucidate the roles of these miRNAs should improve our understanding of the level of diversity of specific plant responses to phytoplasmas. Small mRNA profiles of healthy (H) and Phytoplasma-infected Mexican lime trees were generated by deep sequencing, six replicate, using Illumina Hiseq2000
2013-03-09 | E-GEOD-44279 | biostudies-arrayexpress
Project description:The genomes of three major mosquito vectors of human diseases, including Anopheles gambiae, Aedes aegypti, and Culex pipiens quinquefasciatus, have been previously sequenced. C. p. quinquefasciatus has the largest number of predicted protein-coding genes, which partially results from the expansion of three detoxification gene families: cytochrome P450 monooxygenases (P450), glutathione S-transferases (GST), and carboxylcholinesterases (CCE). However, unlike A. gambiae and A. aegypti, which have large amounts of gene expression data, C. p. quinquefasciatus has limited transcriptomic resources. Knowledge of complete gene expression information is very important for the exploration of the functions of genes involved in specific biological processes. In the present study, the three detoxification gene families of C. p. quinquefasciatus were analyzed for phylogenetic classification and compared with those of three other dipteran insects. Gene expression during various developmental stages and the differential expression responsible for parathion resistance were profiled using the digital gene expression (DGE) technique. Results: A total of 291 detoxification genes were found in C. p. quinquefasciatus, including 70 CCE, 186 P450, and 35 GST genes. Compared with three other dipteran species, gene expansion in Culex mainly occurred in the CCE and P450 families, where the genes of M-NM-1-esterases, juvenile hormone esterases, and CYP325 of the CYP4 subfamily showed the most pronounced expansion on the genome. A total of 13314 genes were expressed in five DGE libraries. Genes with signal transduction and odorant binding functions were prominently expressed during egg development. Genes involved in proteolysis, glycosphingolipid biosynthesis, and purine metabolism were preferentially expressed at the larval stage. Seventy five percent of the detoxification genes were found to be expressed. One fourth of the CCE and P450 genes were expressed at unique stages, indicating their developmentally regulated expression. Fifteen detoxification genes, including 2 CCEs, 6 GSTs, and 7 P450s, were expressed at higher levels in a parathion-resistant strain than in a susceptible strain. Conclusion: The results of the present study provide new insights into the functions and evolution of three detoxification gene families in mosquitoes and comprehensive transcriptomic resources for C. p. quinquefasciatus, which will facilitate the elucidation of molecular mechanisms underlying the different biological characteristics of the three major mosquito vectors. Raw data were deposited in SRA and assigned accession number SRA049959: http://www.ncbi.nlm.nih.gov/sra?term=SRA049959 Five DGE libraries were sequenced: the egg, third instar larval, pupal, and adult stages of the SG strain, and the third instar larval stage of the S-lab strain.
2012-12-30 | E-GEOD-35744 | biostudies-arrayexpress
Project description:More than 3.5 million raw DGE tags were obtained in each library. The clean tags in each sample ranged from 3.35 to 3.63 million, and the distinct clean tags ranged from 93,593 to 139,389. The 21 bp DGE clean tags were mapped to sweet potato transcripts. Then, we compared 7 libraries pair-wisely so that 21 pairs of comparisons were implemented. Among these comparisons, we found that 4,721 to 12,151 transcripts had significant changes in expression, and the average number was 9,657. We also observed a large number of specifically expressed transcripts between each two libraries. The expression profiles of those genes involved in root development and carbohydrates accumulation were characterized. Moreover, other genes of interest, such as potentially abiotic stress tolerance and insect resistance, were also characterized. 7 samples are examined: young leaves, mature leaves, stems, fibrous roots, initial tuberous roots, expanding tuberous roots and harvest tuberous roots.
2012-02-18 | E-GEOD-35929 | biostudies-arrayexpress
Project description:Volvariella volvacea is one of a few commercial cultivated mushrooms mainly using straw as carbon source. In this study, the genome of V. volcacea was sequenced and assembled. A total of 286 genes encoding carbohydrate-active enzymes (CAZymes) in V. volvacea were identified and annotated. Among 15 fungi with sequenced genomes, V. volvacea ranks the seventh in the number of genes encoding CAZymes. In addition, the composition of glycoside hydrolases in V. volcacea is dramatically different from other basidiomycetes: it is particularly rich in members of the glycoside hydrolase families GH10 (hemicellulose degradation) and GH43 (hemicellulose and pectin degradation), and the lyase families PL1, PL3 and PL4 (pectin degradation) but lacks families GH5b, GH11, GH26, GH62, GH93, GH115, GH105, GH9, GH53, GH32, GH74 and CE12. Analysis of genome-wide gene expression profiles of 3 strains using 3'-tag digital gene expression (DGE) reveals that 246 CAZyme genes were expressed even in potato destrose broth medium. Our data also showed that the formation of a heterokaryon strain could dramatically increase the expression of a number of genes which were poorly expressed in its parental homokaryon strains. Using the 3'-tag digital gene expression (DGE), we compared the gene expression profiles among 2 homokaryotic V. volvacea strains PYd15 and PYd21, and one heterokaryotic strain H1521, which is a hybrid strain of PYd15 and PYd21.
2014-12-19 | E-GEOD-43019 | biostudies-arrayexpress
Project description:Cassava mosaic disease caused by cassava begomoviruses is the most serious disease of cassava in Africa. However, the molecular mechanisms leading to symptom development of infected cassava plants are poorly understood. Here a high throughput digital gene expression profiling (DGE) based on Illumina Solexa sequencing technology was used to investigate the global transcriptional response of cassava to the African cassava mosaic virus infection. Results showed that 3,210 genes were differentially expressed in virus-infected cassava leaves. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that photosynthesis related genes were most affected, which was consistent with the chlorotic symptom on the infected leaves. The upregulation of chlorophyll degradation genes, e.g. the genes encoding chlorophyllase and pheophorbide a oxygenase, as well as the downregulation of the major apoproteins genes in light harvesting complex II (LHCII) identified by the DGE analysis were confirmed by qRT-PCR. Together with the reduction of chlorophyll b content and fewer grana stacks in the infected leaf cells, this study reveals that the degradation of chlorophyll plays an important role during ACMV symptom development for the first time. Meanwhile, we believe that the non-lethal effect on photosystem is a trick for virus to avoid fierce host immune response and a result of the long-term co-evolution. This study will provide a road map for future investigations into virus symptom development. ACMV-infected cassava leaves mixture from three independent replicates were collected for RNA extractions at 20 dpi. Control samples were harvested from empty agrobacteria treated leaves incubated under the same conditions.
2014-04-01 | E-GEOD-47224 | biostudies-arrayexpress
Project description:Drought is a main environment stress which severely inhibits the stem growth of ramie and lead to a decrease of the fiber yield. The mechanisms of ramie responding to drought stress are poorly understood. Using Illumina sequencing, approximately 4.8 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from the drought-stressed ramie (DS), and about 4.7 M were sequenced in the cDNA library constructed from the control ramie under well water condition (CO). The tags generated from two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in two libraries revealed that 1101 and 505 genes were respectively up- and down- regulated under drought stress. Pathway enrichment analysis identified a set of significantly enriched pathways of DEGs. A series of candidate genes and pathways that may contribute to drought tolerance in ramie will be helpful for further improving ramie drought tolerance ability. 3' tag-based DGE libraries were generated to exam the differentially expressed gene between drought-stressed and well-watered ramie
2013-04-23 | E-GEOD-46253 | biostudies-arrayexpress