Circad_pop1-circadian rhythm in the expression of genes involved in the formation of poplar wood
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus sp. Populus tremula x Populus alba
PROVIDER: GSE16459 | GEO | 2010/06/05
SECONDARY ACCESSION(S): PRJNA116033
REPOSITORIES: GEO
Similar Datasets
Project description:affy_orleans_circad - circad_pop1 - Global transcriptome analysis of tension wood in poplar over a 24h period. Young differentiating xylem was harvested on the tension wood side of 6 month-old poplar trees grown in greenhouse conditions. The samples were harvested at 6 hour intervals throughout the day. The bioinformatic analysis will permit the identification of genes expressed in tension wood and that cycle with a nycthemeral oscillation pattern. Keywords: time course 10 arrays - poplar
2010-06-16 | E-GEOD-16459 | biostudies-arrayexpress
Project description:The Trametes versicolor genome is predicted to encode many enzymes that can effectively degrade lignin, making it a has potentially useful application intool for biopulping and biobleaching. Poplar is an important and widely cultivated species of tree species, which isand extensively applied used in the pulping industry. However, the wood degradation mechanism of T. versicolor from transcriptomic level is not clear. To reveal identify the enzymes that contributeing to lignocellulose degraredauction and its degradation mechanisms, we evaluated transcriptomic how study theof T. versicolor transcriptome was changes during evaluated growthing on the poplar wood relative to growth on glucose medium. 853 genes were differentially expressed;, 360 genes were up-regulated on poplar wood, and 493 genes were down-regulated on poplar wood. Notably, most genes relative involved into lignin degradation were up-regulated, including eight lignin peroxidase (LiP) genes, and two manganese peroxidase (MnP) genes etc. Genes encoding cellulose and hemicelluloses degrading-enzymesation were mostly down-regulated, including six endo-β-1, 4-glucanase genes, three cellobiohydrolase I genes, and one cellobiohydrolase II gene, etc. MeanwhileAdditionally, expression of more significant expansion of P450s in T. versicolor genome, along with differences in carbohydrate- and lignin-degrading enzymes, could bewere correlated withto poplar wood degradation. Our results revealed transcriptomic characterizeation transcriptomic changes related toof lignocellulose degradation. Therefore, our results cwould be benuseful for the development ofefit T. versicolor as a tool to improve the efficiency of lignin degradation, and provide a theoretical foundation for a new paper pulp manufacturing processe
2016-08-06 | GSE81742 | GEO
Project description:Ray cells were enriched from wood samples of poplar (Populus x canescens) by LMPC and transcripts monitored by poplar whole genome microarrays. Results provided insight into molecular processes during the transition from dormancy to flowering in early spring in contrast to the active growth phase in summer.
2012-12-05 | GSE33977 | GEO
Project description:The Trametes versicolor genome is predicted to encode many enzymes that can effectively degrade lignin, making it a has potentially useful application intool for biopulping and biobleaching. Poplar is an important and widely cultivated species of tree species, which isand extensively applied used in the pulping industry. However, the wood degradation mechanism of T. versicolor from transcriptomic level is not clear. To reveal identify the enzymes that contributeing to lignocellulose degraredauction and its degradation mechanisms, we evaluated transcriptomic how study theof T. versicolor transcriptome was changes during evaluated growthing on the poplar wood relative to growth on glucose medium. 853 genes were differentially expressed;, 360 genes were up-regulated on poplar wood, and 493 genes were down-regulated on poplar wood. Notably, most genes relative involved into lignin degradation were up-regulated, including eight lignin peroxidase (LiP) genes, and two manganese peroxidase (MnP) genes etc. Genes encoding cellulose and hemicelluloses degrading-enzymesation were mostly down-regulated, including six endo-β-1, 4-glucanase genes, three cellobiohydrolase I genes, and one cellobiohydrolase II gene, etc. MeanwhileAdditionally, expression of more significant expansion of P450s in T. versicolor genome, along with differences in carbohydrate- and lignin-degrading enzymes, could bewere correlated withto poplar wood degradation. Our results revealed transcriptomic characterizeation transcriptomic changes related toof lignocellulose degradation. Therefore, our results cwould be benuseful for the development ofefit T. versicolor as a tool to improve the efficiency of lignin degradation, and provide a theoretical foundation for a new paper pulp manufacturing processe 1,T.versicolor groewn on PDA medium. 2, T. versicolor growing on the a glucose carbon medium of glucose. 3, T. versicolor growing on poplar medium
2016-08-06 | E-GEOD-81742 | biostudies-arrayexpress
Project description:Young poplar stems show a preponderantly primary growth in the top internodes and differential cambium activity in the basal internodes after inclination with some tension wood formed after 45 min. This study was conducted in order to characterize the early changes in gene expression during early stages of the gravitropic response in the poplar.
2013-04-12 | GSE44981 | GEO
Project description:affy_rewatering_poplar - rewatering - Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.-The experimental design consisted in a differential water supply. Experiments were done on tilted trees to induce tension wood formation. Trees were regularly irrigated at full capacitance until July 18, 2007, the beginning of the experiment. Two sets of plants were designed. For each set, irrigation was withheld until July 25, 2007. At this time, one of the two sets (treated-sample) was re-irrigated at full capacitance during 14hrs (WDR) while the other one was maintained under water deficit (WD). Samples were collected after the 14hrs for all trees. Keywords: treated vs untreated comparison 6 arrays - poplar
2010-06-16 | E-GEOD-20061 | biostudies-arrayexpress
Project description:Ray cells were enriched from wood samples of poplar (Populus x canescens) by LMPC and transcripts monitored by poplar whole genome microarrays. Results provided insight into molecular processes during the transition from dormancy to flowering in early spring in contrast to the active growth phase in summer. 4 samples of summer (July) 4 of early spring (February) from Populus x canescens field-culture
2012-12-05 | E-GEOD-33977 | biostudies-arrayexpress
Project description:Lignocellulosic feedstock (i.e., wood) is gaining popularity as a source of fermentable sugars for liquid fuel production. To improve the quantity and quality of woody biomass, the developing xylem (DX) cell-specific genetic modification is desired. Bioinformatic analyses followed by the validation of cell type-specific transcriptomes led to the identification of 37 transcripts specifically expressed in DX. After further confirmation of DX-specific expression, we selected four genes (DX5, DX8, DX11 and DX15) to demonstrate the feasibility of our strategy. The promoter regions of selected DX genes were isolated and produced stable transformants of poplar by using transcriptional promoter:β-glucuronidase (GUS) fusion constructs. The GUS expression patterns of DX5 and ANAC073 (orthologous gene of Arabidopsis) revealed that these promoters were active in xylem cells in poplar at early seedling growth, and showed strongest expression in the developing xylem cells in the wood formation/development at later growth stages of poplar. DX specific and strong expression patterns of all the other DX promoters (DX8, DX11 and DX15) tested suggests that these promoters may be useful to control transgene expression in the DX cells of woody plants with the aim of the feedstock improvement.
2012-07-07 | GSE30507 | GEO
Project description:Lignocellulosic feedstock (i.e., wood) is gaining popularity as a source of fermentable sugars for liquid fuel production. To improve the quantity and quality of woody biomass, the developing xylem (DX) cell-specific genetic modification is desired. Bioinformatic analyses followed by the validation of cell type-specific transcriptomes led to the identification of 37 transcripts specifically expressed in DX. After further confirmation of DX-specific expression, we selected four genes (DX5, DX8, DX11 and DX15) to demonstrate the feasibility of our strategy. The promoter regions of selected DX genes were isolated and produced stable transformants of poplar by using transcriptional promoter:?-glucuronidase (GUS) fusion constructs. The GUS expression patterns of DX5 and ANAC073 (orthologous gene of Arabidopsis) revealed that these promoters were active in xylem cells in poplar at early seedling growth, and showed strongest expression in the developing xylem cells in the wood formation/development at later growth stages of poplar. DX specific and strong expression patterns of all the other DX promoters (DX8, DX11 and DX15) tested suggests that these promoters may be useful to control transgene expression in the DX cells of woody plants with the aim of the feedstock improvement. In order to identify specifically and strongly expressed genes from DX cells of woody plant, we generated the tissue/cell type-specific transcriptomes from poplar stem by using whole genome GeneChip technology (Affymetrix).
2012-07-06 | E-GEOD-30507 | biostudies-arrayexpress
Project description:affy_rewatering_poplar - rewatering - Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.-The experimental design consisted in a differential water supply. Experiments were done on tilted trees to induce tension wood formation. Trees were regularly irrigated at full capacitance until July 18, 2007, the beginning of the experiment. Two sets of plants were designed. For each set, irrigation was withheld until July 25, 2007. At this time, one of the two sets (treated-sample) was re-irrigated at full capacitance during 14hrs (WDR) while the other one was maintained under water deficit (WD). Samples were collected after the 14hrs for all trees. Keywords: treated vs untreated comparison
2010-06-03 | GSE20061 | GEO