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ABSTRACT:
PROVIDER: PRJNA1090639 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptome analysis may provide means to investigate the underlying genetic causes of shared and divergent phenotypes in different populations and help to identify potential targets of adaptive evolution. Applying RNA sequencing to whole male Drosophila melanogaster from the ancestral tropical African environment and a very recently colonized cold-temperate European environment at both standard laboratory conditions and following a cold shock, we seek to uncover the transcriptional basis of cold adaptation. In both the ancestral and the derived populations, the predominant characteristic of the cold shock response is the swift and massive upregulation of heat shock proteins and other chaperones. Although we find ~30% of the genome to be differentially expressed following a cold shock, only relatively few genes (n=26) are up- or down-regulated in a population-specific way. Intriguingly, 24 of these 26 genes show a greater degree of differential expression in the African population. Likewise, there is an excess of genes with particularly strong cold-induced changes in expression in Africa on a genome-wide scale. The analysis of the transcriptional cold shock response most prominently reveals an upregulation of components of a general stress response, which is conserved over many taxa and triggered by a plethora of stressors. Despite the overall response being fairly similar in both populations, there is a definite excess of genes with a strong cold-induced fold-change in Africa. This is consistent with a detrimental deregulation or an overshooting stress response. Thus, the canalization of European gene expression might be responsible for the increased cold tolerance of European flies.
2016-11-28 | GSE77404 | GEO
Project description:Abstract: In order to understand the expression patterns of miRNAs in alfalfa under alkali stress, small RNA sequencing was performed on alfalfa roots at different time points under alkali stress, and miRNAs were identified and analyzed.
2023-05-08 | GSE231697 | GEO
Project description:Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially control almost all aspect of plant growth and development. Although miRNAs have been reported from alfalfa but their expression profiles in different tissues and novel miRNAs as well as their targets have not been confirmed in this plant species. Therefore, we sequenced small RNAs in whole plantlets, shoots and roots of three different alfalfa genotypes (Altet-4, NECS-141 and NF08ALF06) to identify tissue-specific profiles. After comprehensive analysis using bioinformatics methods, we have identified 100 miRNA families, of which 21 belongs to the highly conserved families whereas the remaining 79 families are conserved between M. truncatula and M. sativa. The profiles of the six highly expressed conserved miRNA families (miR156, 159, 166, 319, 396, 398,) were relatively similar between the plantlets, roots and shoots of three genotypes. Contrastingly, the differenecs were robust between shoots and roots for miR160 and miR408 levels, which were low in roots compared to shoots. The study also has identified 17 novel miRNAs that also differed in their abundanecs between tissues of the alfalfa genotypes. Additionally, we have generated and analyzed the degradome libraries from three alfalfa genotypes that has confirmed 69 genes as targets for 31 miRNA families in alfalfa. The identification of conserved and novel miRNAs as well as their targets in different tissues of three genotypes not only enhanced our understanding of miRNA-mediated gene regulation in alfalfa but could also be useful for practical applications in alfalfa as well as related legume species.
2019-01-15 | GSE119460 | GEO
Project description:We studied the application of transcriptome technology in alfalfa selenium (Se) treatment. Alfalfa had different states after different concentrations of Se treatment. It shows that lower concentration promoted growth and higher concentration produced toxicity. The positive regulatory effects of moderate Se (100 mg / kg) on alfalfa was determined through preliminary experiments, and the gene expression of Alfalfa under this treatment was further analyzed by transcriptome.
2023-08-09 | GSE192349 | GEO
Project description:Heat stress and extreme temperatures negatively affect plant development by disrupting regular cellular and biochemical functions, ultimately leading to reduced crop production. Recently, our group has shown through physiological experiments that miR156 overexpression resulted in an improved alfalfa response to heat stress. To further expand the scope of miR156 research, we employed a label-free quantification based quantitative proteomics approach to explore the effects of heat stress on protein levels in miR156OE alfalfa. Our major objective was to identify miR156-regulated gene products with differentially altered abundance under heat stress in alfalfa.
2020-10-16 | PXD019560 | Pride
Project description:Alfalfa (Medicago sativa) is the most widely grown and most important forage crop in the world. However, alfalfa is susceptible to waterlogging stress, which is the major constraint for its cultivation area and crop production. So far, the molecular mechanism of alfalfa response to the waterlogging is largely unknown. Here, comparative transcriptome combined with proteomic analyses of two cultivars (M12, tolerant; M25, sensitive) of alfalfa showing contrasting tolerance to waterlogging were performed to understand the mechanism of alfalfa in response to waterlogging stress. Totally, 748 (581 up- and 167 down-regulated) genes were differentially expressed in leaves of waterlogging-stressed alfalfa compared with the control (M12_W vs M12_CK), whereas 1193 (740 up- and 453 down-regulated) differentially abundant transcripts (DATs) were detected in the leaves of waterlogging-stressed plants in comparison with the control plants (M25_W vs M25_CK). Furthermore, a total of 187 (122 up- and 65 down-regulated) and 190 (105 up- and 85 down-regulated) differentially abundant proteins (DAPs) were identified via iTRAQ method in M12_W vs M12_CK and M25_W vs M25_CK comparison, respectively. Compared dataset analysis of proteomics and transcriptomics revealed that 27 and 8 genes displayed jointly up-regulated or down-regulated expression profiles at both mRNA and protein levels in M12_W vs M12_CK comparison, whereas 30 and 27 genes were found to be co-up-regulated or co-down-regulated in M25_W vs M25_CK comparison, respectively. The strongly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for co-up-regulated genes at mRNA and protein levels in M12_W vs M12_CK comparison were ‘Amino sugar and nucleotide sugar metabolism’, ‘Arginine and proline metabolism’ and ‘Starch and sucrose metabolism’, whereas co-up-regulated protein-related pathways including ‘Arginine and proline metabolism’ and ‘Valine, leucine and isoleucine degradation’ were largely enriched in M25_W vs M25_CK comparison. Importantly, the identified genes related to beta-amylase, Ethylene response Factor (ERF), Calcineurin B-like (CBL) interacting protein kinases (CIPKs), Glutathione peroxidase (GPX) and Glutathione-S-transferase (GST) may play key roles in conferring alfalfa tolerance to waterlgging stress. The present study may contribute to our understanding the molecular mechanism underlying the responses of alfalfa to waterlogging stress, and also provide important clues for further study and in-depth characterization of waterlogging-resistance breeding candidate genes in alfalfa.
2019-11-11 | PXD013025 | Pride
Project description:In this study, MeDIP-seq and RNA-seq were performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cell line (ZF4) and its variation under cold environment.This study puts a new insight into the genome-wide epigenetic regulation under cold environment. ZF4 cells were cultured at 28 °C as control and at 18 °C for 5 days and 30 days, seperately. Each condition has three biological replica.
2016-07-30 | E-GEOD-71567 | biostudies-arrayexpress
Project description:By comparing transcriptomes of tolerant and intolerant plants of sickle alfalfa subject to intensive animal grazing, we identified pathways involved in nutrient-responsive signaling, light and wound response, cell wall formation, and energy metabolism. In these pathways, grazing suppressed 39 genes, but less severe in the tolerant plant, and activated 5 genes all carrying polymorphisms in their homologous transcripts between the tolerant and intolerant plants. These genes and pathways - responsive to grazing and differentially expressed between the tolerant and intolerant plants â?? underline a defense mechanism in alfalfa against grazing stresses. We examined transcriptomes of 3 alfalfa plants: grazing tolerant and grazed, grazing tolerant and not grazed, grazing intolerant and grazed, all at single replicate each.
2016-08-24 | E-GEOD-50430 | biostudies-arrayexpress