Ontology highlight
ABSTRACT:
PROVIDER: PRJNA993716 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25288229_1.fastq.gz | Fastqsanger.gz | |||
| SRR25288229_2.fastq.gz | Fastqsanger.gz | |||
| SRR25288230_1.fastq.gz | Fastqsanger.gz | |||
| SRR25288230_2.fastq.gz | Fastqsanger.gz | |||
| SRR25288231_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We developed a 60-mer oligonucleotide Agilent microarray representing about 20,000 cassava genes and applied it to expression profiling under drought stress. We demonstrated that our microarray is an useful tool for analyzing the cassava transcriptome and that it can be applied to various cassava species.
2012-06-15 | GSE31749 | GEO
Project description:Cassava is a drought–resistant food crop in tropical and subtropical regions. Although cassava is a relatively drought-tolerant species, the development and yields are greatly affected by the adverse drought conditions. Information about molecular breeding will obtain by studying genetic regulatory mechanism. In this study, we demonstrate the drought-tolerant mechanisms in leaves of both cassava varieties(Xinxuan048 and KU50) by using RNA-Seq technique. 1,880 and 2,066 differentially expressed genes(DEGs) were induced by drought stress in leaves of KU50 and Xinxuan048, respectively. DEGs in the response to drought stress involve in many regulated pathways. ROS- and ABA-associated signaling pathways and photosynthesis-associated regulation are mainly elucidated. In addition, alternative splicing and ingle nucleotide polymorphism also involve in drought-stress responses in both cassava varieties, showing their important roles in response to drought stress in leaves. This study not only increases the understanding of physiological and molecular mechanisms to the drought response in cassava, but also lays a solid foundation on the breeding of drought-resistant varieties using molecular methods.
2018-07-01 | GSE98537 | GEO
Project description:We developed a 60-mer oligonucleotide Agilent microarray representing about 20,000 cassava genes and applied it to expression profiling under drought stress. We demonstrated that our microarray is an useful tool for analyzing the cassava transcriptome and that it can be applied to various cassava species. After cutting of shoots from the cassava plants, the shoots were grown in a glass bottle containing MS medium supplemented with 2% sucrose and 0.3% gelrite for 4 weeks (16 hours light / 8 hours dark). The plantlets were subjected to drought treatment by removing the plantlets from the gelrite plate, placing on a plastic plate and keeping them for 1 hour under 40-80 M-NM-<mol photons m-2 sec-1 at 30M-BM-:C in 50% of relative humidity. Then total RNA was prepared from the shoots and used for the microarray hybridization. Three replicative hybridization experiments were carried out using the independent biological samples.
2012-06-14 | E-GEOD-31749 | biostudies-arrayexpress
Project description:Cassava Anthracnose Disease (CAD) that caused by the fungus Colletotorichum anthracnose is a serious disease of cassava in worldwide. In this study, we aim to establish the cassava oligo-DNA microarray representing approximately 30,000 cassava genes and apply it to investigate the molecular mechanisms against fungal infection using two cassava cultivars; Huay Bong 60 (HB60, resistant line for CAD) and Hanatee (HN, sensitive line for CAD). Based on expression profiling, we showed that the expression of various biotic stress-inducible genes, such as detoxification enzyme related genes is higher in HB60 under the treated conditions and non-treated condition, compared with HN. These results show that stress-inducible signaling pathways including ROS detoxification are constitutively activated in HB60 even under normal growth conditions without stress. These results suggest that our microarray is a useful tool for analyzing the cassava transcriptome and add new insight into the host responses of cassava against fungal infection.
2016-12-31 | GSE63223 | GEO
Project description:Background: Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is limited information about gene regulation and signaling pathways related to the cold stress response in cassava. The development of microarray technology has accelerated the study of global transcription profiling under certain conditions. Results: A 60-mer oligonucleotide 4X44K Agilent microarray representing 20,840 genes was used to perform transcriptome profiling in cassava apical shoots subjected to cold at 7M-BM-0C for 0 h, 4 h, and 9 h. A total of 508 transcripts were identified as early cold-responsive genes in which 319 sequences had descriptions when they were aligned with Arabidopsis proteins. Gene ontology (GO) annotation analysis identified many interesting categories including M-bM-^@M-^XResponse to abiotic and biotic stimulusM-bM-^@M-^Y, M-bM-^@M-^XResponse to stressM-bM-^@M-^Y, M-bM-^@M-^XTranscription factor activityM-bM-^@M-^Y, and M-bM-^@M-^XChloroplastM-bM-^@M-^Y. Various stress-associated genes comprising signal transduction components (e.g., MAP kinase 4), transcription factors (TFs; e.g., RAP2.11), and ROS scavenging enzymes (e.g., catalase 2), as well as photosynthesis-related genes (e.g., PSAL), were found. Seventeen major TF families were also identified as being involved in the early response to cold stress (e.g., AP2-EREBP). Meanwhile, KEGG pathway analysis uncovered many important pathways, including M-bM-^@M-^XPlant hormone signal transductionM-bM-^@M-^Y, M-bM-^@M-^XStarch and sucrose metabolismM-bM-^@M-^Y, and M-bM-^@M-^XPlant-pathogen interactionM-bM-^@M-^Y. Furthermore, the expression changes of 18 genes under cold and other abiotic stresses conditions were validated by real-time RT-PCR. As a response to cold stress in cassava, an increase in the ROS scavenging enzyme activities of catalase and superoxide dismutases and the accumulation of total soluble sugars were also detected. Importantly, most of the tested stress-responsive genes were primarily expressed in mature leaves, stem cambia, and fibrous roots rather than apical buds and young leaves. Conclusions: The dynamic expression changes reflect the integrative controlling and transcriptome regulation of the networks in the early cold stress response of cassava. The biological processes involved in the signal perception and physiological response might shed light on the molecular mechanisms related to cold tolerance in tropical plants and provide useful candidate genes for genetic improvement. Apical shoots subjected to cold at 7M-BM-0C for 0 h, 4 h, and 9 h were collected for RNA extractions from three independent healthy 3-month-old cassava (cultivar TMS60444) plants in the greenhouse.
2013-01-17 | E-GEOD-31073 | biostudies-arrayexpress
Project description:Background: Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is limited information about gene regulation and signaling pathways related to the cold stress response in cassava. The development of microarray technology has accelerated the study of global transcription profiling under certain conditions. Results: A 60-mer oligonucleotide 4X44K Agilent microarray representing 20,840 genes was used to perform transcriptome profiling in cassava apical shoots subjected to cold at 7°C for 0 h, 4 h, and 9 h. A total of 508 transcripts were identified as early cold-responsive genes in which 319 sequences had descriptions when they were aligned with Arabidopsis proteins. Gene ontology (GO) annotation analysis identified many interesting categories including ‘Response to abiotic and biotic stimulus’, ‘Response to stress’, ‘Transcription factor activity’, and ‘Chloroplast’. Various stress-associated genes comprising signal transduction components (e.g., MAP kinase 4), transcription factors (TFs; e.g., RAP2.11), and ROS scavenging enzymes (e.g., catalase 2), as well as photosynthesis-related genes (e.g., PSAL), were found. Seventeen major TF families were also identified as being involved in the early response to cold stress (e.g., AP2-EREBP). Meanwhile, KEGG pathway analysis uncovered many important pathways, including ‘Plant hormone signal transduction’, ‘Starch and sucrose metabolism’, and ‘Plant-pathogen interaction’. Furthermore, the expression changes of 18 genes under cold and other abiotic stresses conditions were validated by real-time RT-PCR. As a response to cold stress in cassava, an increase in the ROS scavenging enzyme activities of catalase and superoxide dismutases and the accumulation of total soluble sugars were also detected. Importantly, most of the tested stress-responsive genes were primarily expressed in mature leaves, stem cambia, and fibrous roots rather than apical buds and young leaves. Conclusions: The dynamic expression changes reflect the integrative controlling and transcriptome regulation of the networks in the early cold stress response of cassava. The biological processes involved in the signal perception and physiological response might shed light on the molecular mechanisms related to cold tolerance in tropical plants and provide useful candidate genes for genetic improvement.
2013-01-17 | GSE31073 | GEO
Project description:External application of acetic acid has been recently reported to enhance the survival to drought in plants such as Arabidopsis, rapeseed, maize, rice and wheat, but the effects of acetic acid application on increased drought tolerance in woody plants such as a tropical crop “cassava” remain elusive. A molecular understanding of acetic acid-induced drought avoidance in cassava will contribute to the development of technology that can be used to enhance drought tolerance without resorting to transgenic technology or advancements in cassava cultivation. In the present study, morphological, physiological and molecular responses to drought were analyzed in cassava after the treatment with acetic acid. Results indicated that the acetic acid-treated cassava plants had a higher level of drought avoidance than water-treated, control plants. Specifically, higher leaf relative water content, and chlorophyll and carotenoid levels were observed as soils dried out during the drought treatment. Leaf temperatures in acetic acid-treated cassava plants were higher relative to leaves on plants pretreated with water and the increase of ABA content was observed in leaves of acetic acid-treated plants, suggesting that stomatal conductance and the transpiration rate in leaves of acetic acid-treated plants decreased to maintain relative water contents and avoid drought. Transcriptome analysis revealed that the acetic acid treatment increased the expression of ABA signaling-related genes, such as OPEN STOMATA 1 (OST1) and protein phosphatase 2C; as well as drought response and tolerance-related genes, such as outer membrane tryptophan-rich sensory protein (TSPO), and heat shock proteins. Collectively, the external application of acetic acid enhances drought avoidance in cassava through the upregulation of ABA signaling pathway genes and several stress response- and tolerance-related genes. These data support the idea that adjustments of the acetic acid application to plants is useful to enhance drought tolerance in order to minimize the growth inhibition in the agricultural field.
2019-05-29 | GSE122140 | GEO
Project description:In this study, genome-wide transcriptome profiling was used to understand molecular genetic mechanism of drought tolerance in rice. Illumina High-Seq 2000 platform was used for sequencing RNA from leaf tissue of rice plants exposed to controlled drought stress and well-watered conditions. The differentially expressed genes were used to identify biological process and cis-regulatory elements enriched under drought stress compared to well-watered conditions.
2015-01-16 | GSE65022 | GEO
Project description:The members of bHLH transcription factor superfamily are known to play key role in plant development and abiotic stress response. Loss-of-function of OsbHLH148 gene resulted in increased sensitivity of rice plants to drought stress. To identify the targets of OsbHLH148 and dissect the drought stress response pathway regulated by it, we performed transcriptome profiling of Osbhlh148 mutant plants under drought stress as well as well-watered conditions by RNA-sequencing.
2015-01-16 | GSE65024 | GEO
Project description:Heat shock factors (Hsfs) are known to regulate heat and drought stress response by controlling the expression of heat shock proteins and oxidative stress responsive genes. Loss-of-function of OsHSFA2e gene resulted in increased sensitivity of rice plants to drought and heat stress. To identify the targets of OsHSFA2e and dissect the stress response pathway regulated by it, we performed transcriptome profiling of Oshsfa2e mutant plants under drought stress as well as well-watered conditions by RNA-sequencing.
2015-01-16 | GSE65025 | GEO