Ontology highlight
ABSTRACT:
PROVIDER: PRJNA870326 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21101763_1.fastq.gz | Fastqsanger.gz | |||
| SRR21101763_2.fastq.gz | Fastqsanger.gz | |||
| SRR21101764_1.fastq.gz | Fastqsanger.gz | |||
| SRR21101764_2.fastq.gz | Fastqsanger.gz | |||
| SRR21101765_1.fastq.gz | Fastqsanger.gz |
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Project description:Protein kinases (PKs) are involved in plant growth and stress responses, and constitute one of the largest superfamilies due to numerous gene duplications. However, limited PKs have been functionally described in pecan, an economically important nut tree. Here, the comprehensive identification, annotation and classification of the entire pecan kinome was reported. A total of 967 PK genes were identified from pecan genome, and further classified into 20 different groups and 121 subfamilies using the kinase domain sequences, which were verified by the phylogenetic analysis. The receptor-like kinase (RLK) group contained 565 members, which constituted the largest group. Gene duplication contributed to the expansion of pecan kinome, 169 duplication events including 285 PK genes were found, and Ka/Ks ratio revealed they experienced strong negative selection. GO functional analysis indicated majority PKs involved in molecular functions and biological processes. The RNA-Seq data of PK genes in pecan were further analyzed at subfamily level, and different PK subfamilies performed various expression patterns across different conditions or treatments, suggesting PK genes in pecan involved in multiple biological functions and stress responses. Taken together, this study provided insight into the expansion, evolution and function of pecan PKs. Our findings regarding expansion, expression and co-expression analyses could lay a good foundation for future research to understand the roles of pecan PKs, and find the key candidate genes more efficiently.
2021-07-05 | GSE179336 | 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
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:ra06-02_staygreen - drought and salt stress response - Modification of the transcriptome by the eskimo mutation and response to stress. - Individual plants were grown in Fertiss clods in a culture chamber. 3 treatments were made to the plants : control, drought and salt. Keywords: gene knock out,treated vs untreated comparison
2008-09-11 | GSE10384 | GEO
Project description:Drought stress response involves vigorous reprogramming of transcriptome while the mechanism modulating this process remains elusive. The role of 3D-genome in the regulation of rice development has recently been unveiled in rice, which exhibited characteristics distinct from that in mammals and other plants. However, the relationship between spatial chromosome organization and drought responsive gene reprogramming is still poorly understood. In this study, we identified H3K9ac as an efficient histone mark that response dynamically to drought stress in rice and re-constructed high-resolution 3D genome contact maps based on these sites under the normal, drought, and recovery conditions. We discovered significant decondensation of chromatin contacts with over 10000 chromatin loops lost upon drought stress treatment while the recovery of 3D genome was limited after 4-day’s re-watering. We identified dominate promoter-promoter interacting (PPI) loops under each condition and identified their significant correlations to altered gene expressions in response to the corresponding condition. Based on the relative contact intensities of the PPI connections, we characterized super-promoter regions that integrate closer connections of genes with more vigorous inductions to condition shifts. Especially, about 75% of the drought stress-dominate PPI loops were associated to the binding by a well-defined drought stress-responsive transcription factor, OsbZIP23. The mutation of OsbZIP23 led to the diffuse of over 80% DS-dominate PPI loops and impaired the expression of the connected genes. As a case study, we showed how OsbZIP23 binding to a super-promoter region can integrate the PPI loop formation and transcriptional activation of four function-vital dehydrin genes upon drought stress. Our results shed light on the mechanisms of 3D genome dynamic in response to water supply variations in rice and highlight the role of OsbZIP23 in the regulation of chromatin loop formation under drought stress.
2024-09-19 | GSE242453 | GEO
Project description:Chickpea (Cicer arietinum) is the third largest legume grown worldwide and are prone to drought and various pathogen infections. These stresses often occur concurrently in the field conditions. Previous studies in other plant species indicated that plant senses concurrently occurring stresses as new state of stress however, the molecular events in response to that is largely unknown. In the present study, we studied the transcriptome changes in chickpea plants exposed to combination of drought stress and a potential wilt pathogen, Ralstonia solanacearum by microarray analysis. Chickpea plants were exposed to short duration individual drought (SD-drought, soil field capacity, FC-35%), long duration individual drought (LD-drought, FC-30%), short duration individual pathogen stress (SD-pathogen = 2 days pathogen infection), long duration individual pathogen stress (LD-pathogen = 4 days of infection) and short duration and long duration combined stress, SD-combined = 2 days of pathogen infection with progressive drought (FC-40% to FC- 35%), LD combined = 4 days of pathogen infection with progressive drought (FC-35% to 30%).Transcriptome analysis for the leaf samples from above treatment were done by microarray analysis using Agilent ChickpeaGXP_8X60K chip. Result indicated presence of specific molecular events and also some common but tailored events in response to combined stress. Global transcriptional analysis in chickpea leaves exposed to individual and combined drought stress and Ralstonia solanacearum infection.
2017-06-13 | GSE89228 | GEO
Project description:ra06-02_staygreen - drought and salt stress response - Modification of the transcriptome by the eskimo mutation and response to stress. - Individual plants were grown in Fertiss clods in a culture chamber. 3 treatments were made to the plants : control, drought and salt. Keywords: gene knock out,treated vs untreated comparison 6 dye-swap - CATMA arrays
2008-09-10 | E-GEOD-10384 | biostudies-arrayexpress
Project description:Under natural conditions, plants experience episodes of drought for periods of days or longer. Plants respond to drought stress by reconfiguring their transcriptome activity. Transcriptome changes in response to drought are dynamic, and are likely to be shaped by mitigating factors such as diel signals. To gain insights into the dynamics of transcriptome reconfiguration in response to gradual soil drying, the drought-induced transcriptomes of Arabidopsis thaliana were examined at four time points over a single diel period – midday, late day, midnight, and pre-dawn. A core set of genes was identified that was responsive to drought, independent of the time of day at which they were measured. Strikingly, the magnitude of the drought-induced changes for these genes varied in a time-of-day-dependent manner. An additional set of time-of-day-specific drought-responsive genes were also identified. The diurnal patterns of transcript accumulation for these genes was strongly influenced by drought stress. This study indicates that analysis of a single time point would miss suites of drought-responsive genes that are revealed through assessment of the dynamics of diurnal changes, emphasizing the value of characterizing multiple time-of-day-specific drought transcriptomes.
2010-07-01 | GSE19700 | GEO
Project description:Episodic drought stress negatively impacts the health of long-lived trees. Understanding the genetic and molecular mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. Here we aim to establish standardized drought stress protocols for transcriptome studies in poplar trees, to determine how hybrid poplars respond to prolonged and uniform exposure to drought; to determine if the responses to moderate and more severe growth-limiting drought stresses were qualitatively or quantitatively different; and, to determine how response to drought changes throughout the day. We established hybrid poplar trees (Populus x ’Okanese’) from unrooted stem cutting with abundant soil moisture for six weeks. We then withheld water to establish three soil water contents reflecting well-watered, moderate, and severe growth-limiting drought conditions. Plants were rewatered as needed for three weeks to maintain the soil water conditions. The mild and severe drought treatments elicited distinct changes in growth and development, photosynthetic rates and global transcriptomic changes. Notably, the time of day of sampling was strongest signal in the transcriptome data and it quantitatively and qualitatively affected drought responsive changes in gene expression. These analyses emphasize the complex nature of drought regulation in long-lived trees.
2021-12-20 | GSE191155 | GEO
Project description:Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. To gain insights into the genome-wide transcriptional regulation in lentil root and leaf under short- and long-term drought conditions, we performed RNA-seq on a drought-sensitive lentil cultivar (Lens culinaris Medik. cv. Sultan). After establishing drought conditions, lentil samples were subjected to de novo RNA-seq-based transcriptome analysis. The 207,076 gene transcripts were successfully constructed by de novo assembly from the sequences obtained from root, leaf, and stems. Differentially expressed gene (DEG) analysis on these transcripts indicated that period of drought stress had a greater impact on the transcriptional regulation in lentil root. The numbers of DEGs were 2915 under short-term drought stress while the numbers of DEGs were increased to 18,327 under long-term drought stress condition in the root. Further, Gene Ontology analysis revealed that the following biological processes were differentially regulated in response to long-term drought stress: protein phosphorylation, embryo development seed dormancy, DNA replication, and maintenance of root meristem identity. Additionally, DEGs, which play a role in circadian rhythm and photoreception, were downregulated suggesting that drought stress has a negative effect on the internal oscillators which may have detrimental consequences on plant growth and survival. Collectively, this study provides a detailed comparative transcriptome response of drought-sensitive lentil strain under short- and long-term drought conditions in root and leaf. Our finding suggests that not only the regulation of genes in leaves is important but also genes regulated in roots are important and need to be considered for improving drought tolerance in lentil.
2019-04-19 | GSE115199 | GEO