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ABSTRACT:
PROVIDER: PRJNA1133943 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: We aimed to provide a basis for the adaptive mechanism and a rich resource for the discovery and identification of novel genes involved in the cold stress response in Solenopsis japonica. Retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Solenopsis japonica was reared at lab condition, and incubated at 2 different temperature for 24h (9, and 25℃) under dark conditions. RNA was extracted using Trizol reagent and Illumina sequencing was performed at Macrogen. Illumina short reads were quality-filtered and Illumina-based de novo transcriptome assembly was performed. Differential Gene Expression Analysis was studied for different tempearture conditions. Results: Totally 89,657 unigenes was obtained which overall 43,375 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 GO functional sub-groups and 25 EggNOG terms resulted. DEGs with FC≥2 and FC≤-2, P-value<0.05 were screened and were compared at two different temperatures. We found 138 DEG down regulated and 271 DEG up regulated when the S. japonica incubated at 9 ℃ and compared with 25℃ treated group. Comparing transcriptome profiles for differential gene expression resulted various DE proteins and genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and HSP which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity up-regulated under high temperature stress. Conclusions: we compared the transcriptomes of S. japonica under normal room temperature and low-temperature using RNA-Seq technology based on the high-throughput sequencing. Comparative transcriptome analysis identified many genes and a large number of changes were discovered in metabolic pathway through the GO and KEGG enrichment analysis. Our data will facilitate further molecular investigations and genomic research. Many low-temperature significantly up-regulated genes were first identified in this study. These newly found genes may be important and necessary to S. japonica overwintering and its behavior for adaptation in new environment.
2020-08-01 | GSE155469 | GEO
Project description:Expression Data of Rice Crown and Growing Point Tissue Under Salt Stress imposed during the Panicle Initiation Stage Experiment Overall Design: Rice Genotypes a sensitive japonica, m103, tolerant japonica agami, sensitive indica ir29 and tolerant indica ir63731 were used for expression anlaysis using the tissue from crown and growing point under control and salt stressed conditions at the sensitive early reproductive stage (panicel initiation).
2008-11-05 | E-GEOD-4438 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to compare the different genetic mechanisms between Indica and Japonica rice under cadmium stress.
2023-01-02 | GSE196229 | GEO
Project description:Aluminum (Al) toxicity in plants is one of the primary constraints in crop production. Al³⁺, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. This data establish a comparative study of miRNAome profiles in ASR5 knockdown rice plants (ssp. Japonica cv. Nipponbare) under Al stress conditions.
2017-11-09 | GSE77046 | GEO
Project description:Comparative transcriptional profiling of two contrasting rice genotypes,IRAT109 (drought-resistant japonica cultivar) and ZS97 (drought-sensitive indica cultivar), under drought stress during the reproductive stage
2011-11-05 | GSE25176 | GEO
Project description:Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.
2021-06-15 | E-MTAB-10653 | biostudies-arrayexpress
Project description:Transcriptome analysis of Cryptomeria japonica seedlings under heat stress
| PRJDB8803 | ENA