Acalymma vittatum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA493105 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7902384_1.fastq.gz | Fastqsanger.gz | |||
| SRR7902384_2.fastq.gz | Fastqsanger.gz | |||
| SRR7902385_1.fastq.gz | Fastqsanger.gz | |||
| SRR7902385_2.fastq.gz | Fastqsanger.gz | |||
| SRR7902386_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: BurrowsâWheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRTâPCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens. mRNA profiles of infection and anti-infection cucumber were generated by deep sequencing, using Illumina Hiseq 2500 .
2016-08-01 | E-GEOD-72191 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens.
2016-08-01 | GSE72191 | GEO
Project description:Cucumber (Cucumis sativus L.) is one of the most important fruit vegetable crops and is widely grown worldwide (FAO STAT 2016, http://faostat3.fao.org). Astringency greatly affects the flavor quality of cucumber fruits and can be irritating due to the unpleasant oral sensation it causes. However, there are no available report addressing the molecular mechanisms driving the development of cucumber fruit astringency at the transcriptome level. A few relatively basic research efforts have been carried out in our previous studies. In this study, genome-wide analysis of gene expression in the highly astringent cucumber inbred line ‘YB’ was performed using RNA-seq. The aims of this research were to identify the genes responsible for fruit astringency development and to provide new insights into the mechanism underlying the synthesis of astringent compounds in cucumber fruits.
2018-12-01 | GSE112666 | GEO
Project description:Cucumber (Cucumis sativus L.) is an economically important vegetable cultivated all over the world. Grafting can produce bloomless or sparse-bloom cucumber, which is welcomed by increasing consumers. Bloom granule is tine glandular hair, which is hard and rare studied on its formation and related genes. Mutifunctional RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing and has been recently applied to a wide variety of organisms, which provide us reliable technical means detect bloom formation and related genes. In this study, we chose a cucumber inbred line (Shannong No.5) and two pumpkin rootstock lines as materials, and constructed four tested cucumbers, grew plants in “Yamazaki cucumber nutrient solution formula” prepared by deionized water, treated plants with or without 1.7mM potassium silicate 2 hours before collecting pericarp. Each treatment were duplicated twice.16 cDNA libraries were constructed from pericarp of a cucumber inbred line (own-rooted cucumber), C/C (self-grafted cucumber), M/C (More bloom, cucumber grafted onto “3225” rootstock) and L/C(Less bloom, cucumber grafted onto “3212” rootstock). We obtained 17,215,769~17,529,047 high quality reads, and 18,804~19,358 genes from each sample. All reads can be mapped to the cucumber genome (Version 2). By RPKM comparing, we got 38 comparing combinations with differentially expressed genes (DEGs), obtained 38 significantly expressed combinations by FDR≤0.001 and the absolute value of log2Ratio≥1 as the thresholds. These results suggest that there are many differences and genes expression mode among effects of grafting or added silicon. This study addresses a preliminary analysis and offers a foundation for future genomic research in the bloom formation of cucumber.
2020-04-02 | GSE79829 | GEO
Project description:We report the transcriptional response to Colorado potato beetle herbivory in leaves of the highly beetle resistant Solanum chacoense diploid line USDA8380-1 (80-) and a susceptible F2 individual (EE501F2_093) derived from a cross between 80-1 and a beetle susceptible line S. chacoense M6. Sampling tissue in a time course during adult Colorado potato beetle feeding provides novel insight to the transcriptomic defense response to this important pest.
2023-03-08 | GSE169331 | GEO
Project description:Nitrogen is the most important mineral nutrient of plant. As a worldwide and economically important vegetable, cucumber (Cucumis sativus L.) has a strong nitrogen-dependence. We took whole transcriptome sequencing approach to compare the gene expression profiles of cucumber leaves and roots grown under sufficient or insufficient nitrate supply. Analysis of the transcriptome data revealed that the root and leaf adapt different response mechanisms to long-term nitrogen deficiency. Photosynthesis and carbohydrate biosynthetic process were pronouncedly and specifically reduced in leaf, while the ion transport function, cell wall and phosphorus-deficiency response function seem systematically down-regulated in root. Genes in nitrogen uptake and assimilation are decreased in root, but some are increased in leaf under nitrogen deficiency. Several lines of evidence suggest that the altered gene expression networks support the basic cucumber growth and development likely through successful nitrogen remobilization involving in the induced expression of genes in ABA and ethylene pathways. cucumber leaf and root mRNA of 28-day after sowing nitrogen deficiency and sufficiency deep sequencing, using Illumina HiSeq 2000
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