Digital gene expression (DGE) of alkali-stressed cucumber leaves
Ontology highlight
ABSTRACT: 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-
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 SNP’s 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.
Project description:Alkali-salinity is a major abiotic stress that limits plant growth and productivity. Studying mechanisms of alkali-salinity tolerance in halophytic plants will provide valuable information for underlying plant alkali-salinity tolerance. Puccinellia tenuiflora is considered as an ideal model plant for studying the alkali-salinity tolerant mechanisms in plants. In this study, the NaHCO3-responsive molecular mechanisms in P. tenuiflora leaves were investigated using a combined physiological and proteomic approaches. Our results implied some specific NaHCO3-responsive mechanisms in leaves from P. tenuiflora. They are (1) reduction of photosynthesis attributed to the decrease of the abundance of Calvin cycle enzymes, (2) accumulation of Na+ and K+ caused ion-specific stress, (3) accumulation of proline, soluble sugar and betaine enhanced the ability of osmotic regulation, (4) diverse reactive oxygen species (ROS) scavenging mechanisms under different NaHCO3 concentrations, and (5) alternative protein synthesis and processing strategies in chloroplast and cytoplasm. All these provide important evidence for understanding NaHCO3-responsive mechanisms in P. tenuiflora.
Project description:Here we performed a transcriptomic study on PaWB phytoplasma-infected Paulownia sp. using Solexa/IlluminaM-bM-^@M-^Ys 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. To investigate the response of Paulownia sp. to PaWB infection, we collected four samples in two groups, namely the tissue cultured group (containing healthy sample TH and diseased sample TD) and field-grown group (containing healthy sample FH and diseased sample FD). Four individual tag libraries from these samples were constructed in parallel. For the gene expression analysis, the digital gene expression (DGE) data of diseased sample were compared to that of healthy sample in each group to obtain the gene expression variations.
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.
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.
Project description:Cucumber (Cucumis sativus L.) fruit is a type of fleshy fruit that is harvested immaturely. Early fruit development directly determines the final fruit length and diameter, and consequently the fruit yield and quality. Different cucumber varieties display huge variations of fruit length, but how fruit length is determined at the molecular level remains poorly understood. To understand the genes and gene networks that regulate fruit length in cucumber, high throughout RNA-seq data were used to compare the transcriptomes of early fruit from two near isogenic lines with different fruit lengths. 3955 genes were found to be differentially expressed, among which 2368 genes were significantly up-regulated and 1587 down-regulated in the line with long fruit. Microtubule and cell cycle related genes were dramatically activated in the long fruit, and transcription factors were implicated in the fruit length regulation in cucumber. Thus, our results built a foundation to dissect the molecular mechanism of fruit length control in cucumber, a key agricultural trait of significant economic importance. Comparative analysis of fruit from two near-isogenic lines, 408 (long fruit) and 409 (short fruit), was employed to discover genes and networks that regulate the fruit length. Two biological replicates were used from each line.
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
Project description:Versatile roles of REVOLUTA (REV), a Class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, have been mainly depicted in Arabidopsis and Populus. In this study, we investigated the functions of its tomato homolog, namely SlREV. Over-expression of a microRNA166-resistant version of SlREV (35S::REVRis) not only resulted in vegetative abnormities such as curly leaves and fasciated stems, but also caused dramatic reproductive alterations including continuous production of flowers at pedicel abscission zone (AZ) and ectopic fruit formation on receptacles. Microscopic analysis showed that meristem-like structures continuously emerged out from the exodermises of pedicel AZs and ectopic carpels formed between the first and the second whorl of floral buds in 35S::REVRis plants. Therefore, we performed Illumina’s digital gene expression (DGE) system, a tag-based transcriptome sequencing methodTranscriptional data to dicover differential expressed genes in early buds (1-2 mm floral buds at stage 6-8) of overexpression line SlREVRis-1. The result suggests that SlREV may regulate genes related to meristem maintenance and cell differentiation in the development of flower pedicel abscission zone, and modulate genes in homodomain and MADS-box families and hormone pathways during fruit formation. These results reveal important roles of SlREV in tomato. 1-2 mm floral buds at stage 6-8 were sampled from three individual plants of 35S::REVRis-1 and corresponding WT control. Three aliquots of RNA from transgenic or WT plants were pooled. Then, the digital expression profile were generated by Illumina Cluster Station and Illumina HiSeq™ 2000 System (BGI Inc.).
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.
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.