Ontology highlight
ABSTRACT:
PROVIDER: PRJNA828517 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18835791.fastq.gz | Fastqsanger.gz | |||
| SRR18835792.fastq.gz | Fastqsanger.gz | |||
| SRR18835793.fastq.gz | Fastqsanger.gz | |||
| SRR18835794.fastq.gz | Fastqsanger.gz | |||
| SRR18835795.fastq.gz | Fastqsanger.gz |
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Project description:Trichomes are the hair-like structures that are widely present on the surface of aerial organs and function in plant defense against biotic and abiotic stresses. Previous studies focus on the single cell trichomes in Arabidopsis and cotton, or multicellular glandular trichomes in tomato, but the developmental process and molecular mechanisms controlling multicellular non-glandular trichome development are largely neglected. Here, we extensively characterized the fruit trichome (spine) development in wild type cucumber and in a tiny branched hair (tbh) mutant that contains a spontaneous mutation and has hairless foliage and smooth fruit surface. Our data indicated that cucumber trichome was multicellular and non-glandular, with no branches or endoreduplication. Further, the major feature of cucumber trichome development was spine base expansion. Transcriptome profiling through Digital Gene Expression indicated that meristem-related genes and transcription factors were implicated in the fruit spine development, and polarity regulators were upregulated during spine base expansion. qRT-PCR verified the reliability of our RNA-SEQ data, and in situ hybridization confirmed the enriched expression of meristem regulators CUP-SHAPED COTYLEDON3 (CUC3) and STM (SHOOT MERISTEMLESS) , as well as the abaxial identity gene KANADI (KAN) in cucumber fruit spine. Together, our results suggest a distinct regulatory pathway involving meristem genes and polarity regulators in multicellular trichome development in cucumber. Using Digital Gene Expression technology to compare the genome-wide gene expression profiles in the fruit spines of wild type cucumber and the tbh mutant, as well as the fruit spines on fruits of 0.5cm and 1.6cm long, repectively. Two biological repelicates were generated for each tissue.
2014-07-01 | E-GEOD-49607 | biostudies-arrayexpress
Project description:The plant vascular system is essential for the enlarged plant stature and successful colonizzation the land by delivering resources throughout the plants and providing mechanical support. Despite several regulators of vascular patterning have been reported, how vascular system mediates stress resistance remain largely unknown. Here we identified a CsIND transcription factor that is specifically expressed in the xylem and phloem tissues in cucumber. Knock down of CsIND by RNAi lead to dwarf plants with enlarged or disorganized vascular systems in all aerial organs. The content of both auxin and jasmonic acid were increased in the CsIND-RNAi lines. Transcriptome profiling by RNA-Seq hints CsIND-regulated gene networks for defense response and vascular development. Biochemical analyses verified that CsIND directly binds to well-known vascular regulators including CsCCR1, CsMYB116, CsYAB5, CsBP and CsAUX, and physically interacts with dorsiventral patterning genes CsKAN2 and CsYAB5. Further, CsIND-RNAi plants displayed significantly enhanced tolerance to nitrogen dificency and resistance to cucumber downy mildew. Therefore, CsIND regulates vascular formation and resistance to biotic and abiotic stresses in cucumber, through the combinarory interactions with well-known vascular regulaors and hormone metabolism and signaling pathways.
2019-09-02 | GSE86496 | GEO
Project description:Trichomes are the hair-like structures that are widely present on the surface of aerial organs and function in plant defense against biotic and abiotic stresses. Previous studies focus on the single cell trichomes in Arabidopsis and cotton, or multicellular glandular trichomes in tomato, but the developmental process and molecular mechanisms controlling multicellular non-glandular trichome development are largely neglected. Here, we extensively characterized the fruit trichome (spine) development in wild type cucumber and in a tiny branched hair (tbh) mutant that contains a spontaneous mutation and has hairless foliage and smooth fruit surface. Our data indicated that cucumber trichome was multicellular and non-glandular, with no branches or endoreduplication. Further, the major feature of cucumber trichome development was spine base expansion. Transcriptome profiling through Digital Gene Expression indicated that meristem-related genes and transcription factors were implicated in the fruit spine development, and polarity regulators were upregulated during spine base expansion. qRT-PCR verified the reliability of our RNA-SEQ data, and in situ hybridization confirmed the enriched expression of meristem regulators CUP-SHAPED COTYLEDON3 (CUC3) and STM (SHOOT MERISTEMLESS) , as well as the abaxial identity gene KANADI (KAN) in cucumber fruit spine. Together, our results suggest a distinct regulatory pathway involving meristem genes and polarity regulators in multicellular trichome development in cucumber.
2014-07-01 | GSE49607 | GEO
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: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.
2015-08-11 | GSE60346 | 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: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.
2015-08-11 | E-GEOD-60346 | 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