Sisymbrium irio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA203232 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE27548: cRNA hybridizations of 10 Spring annual accessions of Arabidopsis thaliana under well-watered and mild soil drying GSE27549: Genomic dna hybridizations of 10 Spring annual accessions of Arabidopsis thaliana GSE27550: cRNA hybridizations of 18 accessions of Arabidopsis thaliana under well-watered and mild soil drying GSE27551: Genomic dna hybridizations of 8 winter annual accessions of Arabidopsis thaliana Refer to individual Series
2012-03-09 | E-GEOD-27552 | biostudies-arrayexpress
Project description:<p>Common vetch (Vicia sativa L.) is an important annual leguminous forage crop commonly used for green manure, fodder, and soil improvement. It is widely cultivated as a green manure and forage crop in Yunnan Province during winter and spring. However, the dry conditions and minimal rainfall during these seasons greatly limit common vetch growth. Therefore, screening for drought-tolerant, high-yielding common vetch varieties is a critical objective in breeding programs.</p>
2026-01-31 | MTBLS13368 | MetaboLights
Project description:Seasonal cycles of light, temperature and precipitation provide signals that set the timing of gene expression and growth for trees. Conifers possess evergreen needles to sense and respond to year-round external signals. We monitored gene activity in Douglas-fir needles for one year and found that gene expression is dependent on light at daily and annual scales. The majority of rhythmic genes achieve maximum activity +/- 2 hours from sunrise and sunset, and +/- 20 days from the winter and summer solstices. Remarkably, the dormant period is characterized by significant gene activation, with thousands of genes achieving peak activity. This study identifies annual gene rhythms in conifers needles, and provides a framework for identifying genes that respond to other environmental cues. Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x10^9 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
2017-01-04 | GSE93066 | GEO
Project description:Seasonal cycles of light, temperature and precipitation provide signals that set the timing of gene expression and growth for trees. Conifers possess evergreen needles to sense and respond to year-round external signals. We monitored gene activity in Douglas-fir needles for one year and found that gene expression is dependent on light at daily and annual scales. The majority of rhythmic genes achieve maximum activity +/- 2 hours from sunrise and sunset, and +/- 20 days from the winter and summer solstices. Remarkably, the dormant period is characterized by significant gene activation, with thousands of genes achieving peak activity. This study identifies annual gene rhythms in conifers needles, and provides a framework for identifying genes that respond to other environmental cues. Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x10^9 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
2017-01-04 | GSE93067 | GEO
Project description:Photoperiodic Time Measurement (PPTM) is the ability of plants and animals to measure differences in day/night-length (photoperiod, PP) and use that information to anticipate seasonal changes in key environmental factors such as annual changes in average temperature. This timekeeping phenomenon, which is well documented for higher organisms, enables processes such as gonadal growth/regression, flowering, hibernation, and diapause to optimally adapt to annual transformations of the environment. We discovered PPTM capability in cyanobacteria, which is unexpected since cyanobacteria are unicellular prokaryotes with generation times as short as 5-6 hours. Therefore PPTM is not confined to eukaryotes with long generation times. Here we show that cyanobacteria can distinguish between short and long daylengths (photoperiods) and respond to short winter-like days by developing an enhanced resistance to cold. This capability develops over several cycles of photoperiod, and therefore they harbor a “photoperiodic counter” that is a common characteristic of PPTM in higher organisms. These photoperiodic responses are dependent on the presence of the kaiABC genes that encode the central circadian clockwork in cyanobacteria. Short days that herald winter stimulated desaturation of membrane lipids, which is a seasonally adaptive response to lower temperatures. Long vs. short days evoke differential programs of gene transcription, including differential expression of stress response genes, suggesting that PPTM originally evolved from stresses that recur seasonally. Therefore, PPTM is a property of much simpler organisms than previously appreciated, with important implications for the evolution of biological timekeeping mechanisms.
2024-06-01 | GSE252562 | GEO
Project description:Thlaspi arvense Winter and Spring Annual Genome Resequencing
| PRJNA237017 | ENA
Project description:Comparison of stress response among Brassicaceae species at single cell resolution
| PRJNA1113801 | ENA
Project description:Early maize planting requires cold tolerance in temperate regions, which is not present in current elite maize. By extending the growing season of annual crops, net primary productivity and yield can be improved and the mismatch between soil nitrate availability and crop nitrate demand can be addressed. Wild PACMAD grasses have each independently evolved freezing tolerance. To uncover the molecular basis of this convergence, we performed TMT‐based shotgun proteomics on rhizome tissues—a perennial storage organ—sampled during winter dormancy and summer activity from five species: Panicum virgatum, Andropogon gerardii, Miscanthus giganteus, Sorghastrum nutans and Tripsacum (maize’s sister genus), all grown in Ithaca, NY (where winter lows reach –29 °C). From between ~2,400 and 4,500 proteins quantified per species per season, 330 protein families showed consistent upregulation in winter, yet only three—late embryogenesis abundant 3 (LEA3), aldose reductase, and phosphatidylethanolamine‐binding protein (PEBP)—were shared across all five lineages. Functional enrichment highlighted recurrent use of lipid transfer proteins, heat shock proteins, LEAs, and other drought‐associated cryoprotectants. Comparing rhizome proteomic data with tissue‐specific mRNA expression surprisingly revealed Tripsacum seedling leaf tissues showed substantially higher transcriptional responsiveness to cold than underground tissues, a pattern less pronounced in cold sensitive maize seedlings. Overall, the independent evolution of rhizome frost tolerance in PACMAD grasses appears to be governed by similar mechanisms driven primarily by expression‐level changes and complemented by protein structural adaptations—particularly within the LEA family—offering candidate targets for improving freezing tolerance in maize.
2026-01-23 | PXD063668 | Pride
Project description:Parrya nudicaulis is a perennial of Brassicaceae family
| PRJNA62305 | ENA