Transcriptomic changes during cell wall biogenesis and modifications during xylogenesis in stems and pioneer roots of Populus trichocarpa
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PROVIDER: PRJNA523444 | ENA |
REPOSITORIES: ENA
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Project description:We studied the changes that occur in gene transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in xylem formation. Pioneer roots were examined in segments corresponding to their developmental stage: apical meristem (PR1), primary development (PR2), and secondary development (PR3). Comparative segments were used to analyze xylogenesis in stems: apical meristem with primary development (PS1), secondary development (PS2), and isolated secondary xylem (PS3). Results indicated that only approximately 10% of the genes that were identified to be differentially expressed during xylogenesis were common to both pioneer roots and stems. Despite the dissimilarity in gene expression, however, many fundamental mechanisms were similar, e.g. the pattern of expression of genes involved in the biosynthesis of cell wall proteins, polysaccharides and lignins. While hemicellulose degradation was typical for stems, possibly due to the intensive level of cell wall lignification. Our study is the first to conduct a comprehensive analysis, at the structural and molecular level, of xylogenesis, and clearly reveals the great complexity of molecular mechanisms underlying cell wall formation and modification during xylogenesis.
2019-10-14 | GSE126842 | GEO
Project description:au10-13_cellwall - cell wall mutants - What is the impact of the loss of function of monolignol exporters? How does the plant cope with these transporters? Is there any compensation mechanism induced? What is the impact on lignin and cell wall biosynthesis? Does expression of a hydroxycinnamoyl-CoA hydratase/lyase in Arabidopsis stems generate a stress and affect genes involoved in cell wall biosynthesis? - Determine differentially expressed genes in stems of Arabidopsis plants lacking 2 monolignol exporter proteins. mRNA from stems of wild-type and transgenic 7-week-old plants grown in the same conditions were extracted and used for transcriptomic analysis. Three independant cultures were conducted for biological replicates. Determine differentially expressed genes in stems of Arabidopsis plants that express a hydroxycinnamoyl-CoA hydratase/lyase. mRNA from stems of wild-type and transgenic seven-week-old plants grown in the same conditions were extracted and used for transcriptomic analysis. Three independant cultures were conducted for biological replicates.
2012-01-01 | GSE31975 | GEO
Project description:Regulation of gene expression, as determined by the genetics of the tree species, is a major factor in determining wood quality. Therefore, the identification of genes that play a role in xylogenesis is extremely important for understanding the mechanisms shaping the plant phenotype. Efforts to develop new varieties characterized by higher yield and better wood quality will greatly benefit from recognizing and understanding the complex transcriptional network underlying wood development. The present study provides a detailed comparative description of the changes that occur in genes transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Even though results of microarray analysis indicated that only approximately 10% of the differentially expressed genes were common to both organs, many fundamental mechanisms were similar; e.g. the pattern of expression of genes involved in the biosynthesis of cell wall proteins, polysaccharides, and lignins. Gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) shows that the composition of monosaccharides was also very similar, with an increasing amount of xylose building secondary cell wall hemicellulose and pectins, especially in the stems. While hemicellulose degradation was typical for stems, possibly due to the intensive level of cell wall lignification. Notably, the main component of lignins in roots were guiacyl units, while syringyl units were dominant in stems, where fibers are especially needed for support. Our study is the first comprehensive analysis, at the structural and molecular level, of xylogenesis in under- and aboveground tree parts, and clearly reveals the great complexity of molecular mechanisms underlying cell wall formation and modification during xylogenesis in different plant organs.
| S-EPMC6861220 | biostudies-literature
Project description:By characterizing the cell wall proteomes of different sugarcane organs (leaves and stems) at two developmental stages (young vs mature/apical vs basal), it was possible to address unique characteristics in each of them. Four-month-old leaves showed a higher proportion of oxido-reductases and proteins related to lipid metabolism (LM), besides a lower proportion of proteins acting on polysaccharides, in comparison to four-month-old internodes. It was possible to note that sugarcane leaves and young stems have the highest LM rate than all species, which was assumed to be linked to cuticle formation. The data generated enriched the number of cell wall proteins (CWPs) identified in sugarcane, reaching 277. To our knowledge, sugarcane has now the second higher coverage of monocot CWP in plants
2018-01-05 | PXD007893 | Pride
Project description:au10-13_cellwall - cell wall mutants - What is the impact of the loss of function of monolignol exporters? How does the plant cope with these transporters? Is there any compensation mechanism induced? What is the impact on lignin and cell wall biosynthesis? Does expression of a hydroxycinnamoyl-CoA hydratase/lyase in Arabidopsis stems generate a stress and affect genes involoved in cell wall biosynthesis? - Determine differentially expressed genes in stems of Arabidopsis plants lacking 2 monolignol exporter proteins. mRNA from stems of wild-type and transgenic 7-week-old plants grown in the same conditions were extracted and used for transcriptomic analysis. Three independant cultures were conducted for biological replicates. Determine differentially expressed genes in stems of Arabidopsis plants that express a hydroxycinnamoyl-CoA hydratase/lyase. mRNA from stems of wild-type and transgenic seven-week-old plants grown in the same conditions were extracted and used for transcriptomic analysis. Three independant cultures were conducted for biological replicates. 6 dye-swap - gene knock in (transgenic),normal vs transgenic comparaison
2012-01-01 | E-GEOD-31975 | biostudies-arrayexpress
Project description:In the autumn, stems of woody perennials such as forest trees undergo a transition from active growth to dormancy. We used microarray transcriptomic profiling in combination with a proteomics analysis to elucidate processes that occur during this growth-to-dormancy transition in a conifer, white spruce (Picea glauca [Moench] Voss). Several differentially expressed genes were likely associated with the developmental transition that occurs during growth cessation in the cambial zone and the concomitant completion of cell maturation in vascular tissues. Genes encoding for cell wall and membrane biosynthetic enzymes showed transcript abundance patterns consistent with completion of cell maturation, and also of cell wall and membrane modifications potentially enabling cells to withstand the harsh conditions of winter. Several differentially expressed genes were identified that encoded putative regulators of cambial activity, cell development, and of the photoperiodic pathway. Reconfiguration of carbon allocation figured centrally in the tree’s overwintering preparations. For example, genes associated with carbon-based defenses such as terpenoids were downregulated, while many genes associated with proteinbased defenses and other stress mitigation mechanisms were upregulated. Several of these correspond to proteins that were accumulated during the growth-to-dormancy transition, emphasizing the importance of stress protection in the tree’s adaptive response to overwintering.
2011-10-17 | GSE31090 | GEO
Project description:Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. The application of genomic approaches would advance development of alfalfa as a cellulosic feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. These ESTs were de novo assembled into 132,153 unique sequences. By combining the de novo assembled ESTs (132,153 sequences) with our previously identified EST sequences (341,984 sequences, unpublished data), and the ESTs available from GenBank (12,371 sequences), we built the first Alfalfa Gene Index (MSGI 1.0). MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1, 294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Transcript profiling of stem internodes of genotypes 708 and 773 was conducted by quantifying the number of Illumina EST reads that were mapped to sequences in MSGI 1.0. We identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index (MSGI 1.0) assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a cellulosic feedstock. Examination of 2 different tissue types at different developmental stages (Elongating vs. post-elongation stem internodes) in two alfalfa genotypes (708 and 773) with divergent cell wall composition in stems.
2011-04-21 | E-GEOD-26757 | biostudies-arrayexpress
Project description:Transcriptome analysis during the growth and development of asparagus stems
| PRJNA1061188 | ENA
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. Hybridizations were performed to compare gravistimulated poplar stems (basal region) after 45 min of inclination and untreated control stems. Two biological replicates were done. Two hybridizations with a dye swap for each tree pair were done, making a total of four hybridizations.
2013-04-12 | E-GEOD-44981 | biostudies-arrayexpress
Project description:In the autumn, stems of woody perennials such as forest trees undergo a transition from active growth to dormancy. We used microarray transcriptomic profiling in combination with a proteomics analysis to elucidate processes that occur during this growth-to-dormancy transition in a conifer, white spruce (Picea glauca [Moench] Voss). Several differentially expressed genes were likely associated with the developmental transition that occurs during growth cessation in the cambial zone and the concomitant completion of cell maturation in vascular tissues. Genes encoding for cell wall and membrane biosynthetic enzymes showed transcript abundance patterns consistent with completion of cell maturation, and also of cell wall and membrane modifications potentially enabling cells to withstand the harsh conditions of winter. Several differentially expressed genes were identified that encoded putative regulators of cambial activity, cell development, and of the photoperiodic pathway. Reconfiguration of carbon allocation figured centrally in the tree’s overwintering preparations. For example, genes associated with carbon-based defenses such as terpenoids were downregulated, while many genes associated with proteinbased defenses and other stress mitigation mechanisms were upregulated. Several of these correspond to proteins that were accumulated during the growth-to-dormancy transition, emphasizing the importance of stress protection in the tree’s adaptive response to overwintering. Two year old white spruce (Picea glauca [Moench] Voss) seedlings were used for all experiments, which were conducted as described by El Kayal et al. (2011). Using a complete randomized block design, seedlings were grown in growth chambers under long days (LD; 16h day / 8h night, 20°C, 50 to 60% RH) for 8-10 weeks. Shortly before seedlings were to begin bud formation, the photoperiod was changed to short days (SD; 8h day / 16h night, 20°C, 50 to 60% RH) to induce rapid and synchronous bud formation. This was designated Day 0. Lignified whole stems representing the current year’s growth (microarrays, microscopy) or previous year’s growth (protein analyses) were sampled at 0, 3, 7, 14, 28 and 70 d (10 wk) SD, and immediately frozen in liquid nitrogen. Remaining plants were maintained in SD for an additional 8-15 wk, and then transferred to low temperatures (LT, 2 - 4°C) for 3 to 4 weeks with continuing SD prior to harvest. These are referred to as LT samples.
2011-10-16 | E-GEOD-31090 | biostudies-arrayexpress