Global Changes in Gene Expression in Mesorhizobium loti MAFF303099 upon an salt shock
Ontology highlight
ABSTRACT:
ORGANISM(S): Mesorhizobium japonicum MAFF 303099
PROVIDER: GSE43530 | GEO | 2016/12/31
SECONDARY ACCESSION(S): PRJNA186728
REPOSITORIES: GEO
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Project description:Purpose: Soil salinity is one of the main environmental factors that negatively influences yield, especially for sensitive crops such as rice. Studies report that a disturbing event can prepare the plant for a subsequent event through memory acquisition, involving physiological and molecular processes. Therefore, genes that provide altered responses in subsequent events define a category known as "memory genes." In this work, the RNA-Sequencing (RNA-Seq) technique was used to analyse the transcriptional profile of rice plants subjected to different salt shock events and to characterise genes associated with long-term memory. Methods: The mRNA of rice plants cv. Ligeirinho was generated using deep sequencing, in duplicate, using Illumina Hi-Seq 2500, for the following treatments:I) control (C): plants received irrigation with water and nutrient solution throughout the experiment; II) vegetative (SV), plants were exposed to saline shock only at the vegetative stage; III) reproductive (SR) plants were exposed to saline shock only at the reproductive stage; and IV) vegetative + productive (SV+R), plants were exposed to saline shock at the vegetative stage (first shock event) and at the reproductive stage (recurrent event). The sequence reads that passed quality filters were analyzed at the transcript level using this method: Mapping using STAR and identification of differentially expressed genes (DEGs) was performed with the edgeR (false discovery rates - FDRs of <0.05). RT–qPCR validation was performed using SYBR Green assays. Results: Plants subjected to recurrent salt shock showed differences in differentially expressed genes (DEGs). Additionally, the mammalian target of rapamycin (mTOR) pathways, and carbohydrate and amino acid associated pathways were altered under all conditions. Memory genes can be classified according to their responses during the first event (+ or –) and the second shock event (+ or –), being possible to observe a larger number of transcripts for groups [+/–] and [–/+], genes characterised as "revised response." Conclusions: This is the first long-term transcriptional memory study in rice plants under salt shock, providing new insights into the process of plant memory acquisition.
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Project description:Transcriptional differentiation in response to environmental stresses plays critical roles in adaptation. Mangroves are dominant in intertidal zones and form dense forest at the sea-land interface, but little is known about the impact of transcriptional phenotype on their adaptation to the saline environments. To address this issue, we prepared customized chips containing cDNA from the root cDNA library of a mangrove species, Ceriops tagal, and then monitored the time-course transcript profiles in the roots by conducting a series of microarray experiments. Five durations of salt shock with 500 mM NaCl, namely 2, 5, 10, 24 and 192 hours, were included. A total of 88 unigenes that were recognized to be up- or down-regulated by salt shock and both gene categories in relation to stresses-induced responses and transcription factor activity were over-predominant. The stresses-responsive genes were significantly overrepresented, some of which were regulated in differential manners from their homologues genes in Arabidopsis. Specific transcriptional regulations were employed by C. tagal to cope with salt shock, which could benefit the salt-tolerant lifestyle of this mangrove species and possibly contribute to establishment of adaptation to the saline environments. A reference design was used to analyze gene expression differences. Salt stressed young roots were harvested from seedlings of C. tagal at the ends of each shock duration. Young roots of unshocked seedlings were used as controls and harvested at the same time. Three biological replicates were set up for each treatment and corresponding control, respectively, each containing a pool of total RNA from 4 seedlings. Salt stressed samples were compared with the corresponding controls at each time point by co-hybridizing to the customized cDNA arrays
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