Expression values from 6 time points during the regeneration of secondary vascular System (SVS)
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus sp. Populus tomentosa
PROVIDER: GSE71094 | GEO | 2015/07/21
SECONDARY ACCESSION(S): PRJNA290339
REPOSITORIES: GEO
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Project description:Analysis of Paulownia tomentosa cambial tissues at gene expression level. The hypothesis tested in the present study was that miRNAs can regulate the development of the vascular cambium.The results provide new insights into the important regulatory functions of miRNAs in vascular cambium development and wood formation in conifers.
2021-01-17 | GSE109323 | GEO
Project description:Regeneration is a common strategy for plants to repair their damaged body plans after attack from other organisms or physical assaults. Trees with bark girdling on a large scale will grow new bark within one month and this bark regeneration after girdling system has been proven to be an efficient method to study secondary vascular development as well as plant tissue regeneration in vivo. We herein show the molecular features of differentiating xylem cell fate switch process during secondary vascular tissue (SVT) regeneration in Populus. Based on our data, we propose a working model to illustrate the molecular dynamics underlying xylem cell fate switch process during SVT regeneration, which is significant to understand the pattern formation during the SVTs regeneration and also would shed light on the mechanisms of tissue regeneration in plants. Specific regenerated tissues of Populus at different stages were isolated by tangential cryo-sectioning. Total RNA from cryo-sections representing different regenerating tissues was extracted for Affymetrix Poplar Whole Genome Array hybridization. Five samples (two replicates for each sample) were used for gene expression analysis: differentiating xylem (diX, Stage 0), dedifferentiating xylem cells (deX, Stage I), regenerated phloem (rPh, Stage II), differentiating regenerated cambium (diC, Stage II) and regenerated cambium (rC, Stage III). In addition, one pooled genomic DNA sample from cryo-sections of differentiating xylem from two trees was isolated for DNA hybridization to produce a new CDF file that was used to mask out some potentially cross-hybridizing probesets from the standard Affymetrix Poplar Genome Array. Supplementary file: poplar.cdf
2012-07-25 | E-GEOD-25309 | biostudies-arrayexpress
Project description:Wood is formed by the differentiation of cells from the vascular cambium and it is an important source for pulp, paper and bioenergy production. However there is little information about the vascular cambium at the molecular level, particularly in response to seasonality in tropical regions. We used three different molecular approaches: transcripts, proteome and metabolome to characterize the seasonal alterations in the primary metabolism of the eucalyptus cambial zone. Based on 2-DE analysis, 71 proteins were differentially expressed.
2016-07-26 | PXD003504 | Pride
Project description:Vascular cambium is a secondary meristem which produces xylem (wood) inwards and phloem (bark) outwards. The activity of cambium leads to expansion in the diameters in plants, that is, secondary growth, and thus contributes to biomass increase. The regulation of cambium development is at multilevel including phytohormones and peptide-receptor kinase (CLE41/44-PXY) signalling pathways. However, only limited progress has been made on the transcriptional regulation level. To construct the transcriptional network that regulates cambium development, we performed a genome wide transcript profiling in sorted procambial and cambial cells in Arabidopsis roots. More than 500 genes were identified as cambium abundant genes via comparison against transcriptomes of other Arabidopsis root cell types. We then investigated the roles of almost all the cambial transcription factors (TFs) and some of their homologous genes during secondary growth. Many of the candidate TFs were highly expressed in cambium based on the promoter GUS fusion and in situ hybridization. An unbiased transcriptional regulatory network was constructed using transcript profiling data collected from inducible overexpression lines for selected candidate TFs and a few major nodes were identified in the network including WOX4 and KNAT1. Moreover, the severity of mutant phenotypes was predicted based on the network. Next, we used the predication as a guide and generated over 70 double mutants within the same or among different TF families to explore the genetic interactions of candidate genes. Phenotype characterization on the secondary growth of the mutants and the overexpression lines identified promoters and inhibitors of cambium activity. The phenotypic data also suggested the redundancy within and among TF families because the phenotypes could be enhanced when additional TFs were mutated. We also found that combinations of certain overexpression lines and mutants led to pronounced increase of cell proliferation or xylem differentiation and in the extreme case the formation of ectopic cambium. We herein propose that cambium development is orchestrated by a wide network at the transcriptional level, where each TF has a different contribution to cell proliferation and differentiation.
2019-03-31 | GSE125244 | GEO
Project description:Water transport is required for photosynthesis; thus plant vascular development must proceed such that water demands can be met during formation of new organs. Precise regulation of the balance between cell proliferation and differentiation in the cambial meristem defines formation of xylem and phloem, which constitute the vascular tissues. The TDIF-PXY/TDR signalling pathway is central to this process1. Peptide ligand, TDIF, encoded by CLE41 and CLE44 2, activates PXY/TDR receptors to maintain proliferative cambium. Cambium cells differentiate to xylem or phloem in the absence of active TDIF-PXY/TDR complexes. Vascular development is stimulated by light. After gemination, light induces the establishment of photoautotrophic growth via photosynthesis. Consequently, the differentiation of vascular cells must occur to favour the transport of water and minerals from the soil to the green tissues and newly developing organs. Plants perceive light through the action of photoreceptors, which modulate the activity of the transcription factors that orchestrate development. Despite the association between light signalling and vascular development, molecular mechanisms linking the two are unknown. Our work shows that vascular differentiation is inhibited in the dark by a mechanism that depends on PIF transcription factors. The dark accumulation of PIFs is necessary for CLE44 induction and thus maintenance of undifferentiated vasculature. In illuminated environments, PIF inactivation by photoreceptors causes a decrease in CLE44 expression. CLE44 reduction, in turn, leads to reduced PXY/TDR signalling which induces the xylem differentiation required to fulfil the water demands associated with photoautotrophic development.
2022-07-18 | GSE178268 | GEO
Project description:Currently little is known about the genetic mechanisms regulating the vascular cambium or the secondary growth of stems. We show here that the Populus Class I KNOX homeobox gene ARBORKNOX2 (ARK2) regulates both cell division in the cambium region and the differentiation of daughter cells in secondary xylem and phloem. ARK2 is expressed in the shoot apical meristem, and the vascular cambium region, reflecting some overlap in the regulation of these meristems. ARK2 is expressed broadly in the cambium region and in differentiating lignified cells types before becoming progressively restricted to the cambium. Populus overexpressing ARK2 present stem phenotypes with precocious cambium formation, delayed differentiation of cambium daughter cells, a wider cambium region, and ultimately less phloem fibers and secondary xylem. In contrast, Populus expressing RNAi or amicroRNA that target ARK2 transcripts present precocious differentiation of secondary phloem fibers and xylem, and ultimately more secondary xylem tissue and thicker secondary cell walls in phloem fibers and secondary xylem cells. These phenotypes in turn correlate with changes in the expression of genes affecting cell division, auxin, and cell wall synthesis and lignification that indicate that ARK2 primarily affects woody tissue development by regulation of cell differentiation. Notably, wood properties associated with secondary cell wall synthesis are negatively associated with ARK2 expression, including lignin and cellulose content. Together, our results suggest that ARK2 functions primarily by negatively regulating cell differentiation during secondary growth. We propose that ARK2 may identify a co-evolved regulatory module that influences complex wood properties relevant to ecological, industrial, and biofuels applications.
2009-10-01 | GSE15595 | GEO
Project description:MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in the process of plant development. To date, extensive studies of miRNAs have been performed in a few model plants, but few efforts have focused on small RNAs in conifers because of the lack of reference sequences for these enormous genomes. In this study, Solexa sequencing of three small RNA libraries obtained from dormant, reactivating, and active vascular cambium in Chinese fir samples identified 76 known miRNAs from 27 miRNA families and 18 new potential miRNAs, of which 15 novel miRNA precursors were validated by RT-PCR and sequencing. More than half of these novel miRNAs displayed stage-specific expression patterns in the vascular cambium. Furthermore, analyzing the 103 miRNAs and their predicted targets indicated that 30% of miRNAs appeared to negatively regulate their targets, of which 4 target genes involved in the regulation of cambial cell division were validated via RNA ligase-mediated rapid amplification of 5’ cDNA ends (RLM 5’-RACE). Interestingly, miRNA156 and miRNA172 may regulate the phase transition in vascular cambium from dormancy to active growth. These results provide new insights into the important regulatory functions of miRNAs in vascular cambium development and wood formation in conifers. The aim of this study is to investigate the small RNA transcriptome in different stages of vascular cambium development in Cunninghamia lanceolata. We herein conducted our comprehensive analysis of a plant sRNAome during development of the vascular cambium in Chinese fir using cryosectioning to isolate cambial meristem, which allowed a higher cellular resolution for defining small RNA profiles and overcomed the limitations resulting from the mixed samples in many previous investigations. Total RNAs of dormant, reactivating, and active cambial meristem, respectively were isolated using the Concert Plant RNA Reagent (Invitrogen, Carlsbad, CA, USA), and were then treated with RNase-free DNase I (Promega, Madison, WI, USA). Twenty micrograms of total RNAs were used and 16 to 30-nt sRNAs were purified using Novex 15% TBE-¬Urea gel (Invitrogen). Two adaptors were sequentially ligated to the 5' and 3' ends of purified sRNAs. The ligation products were further purified from Novex 10% TBE-Urea gel. Reverse transcriptase SuperScript II (Invitrogen) and high-fidelity DNA polymerase Phusion (New England Biolabs, Ipswich, MA, USA) were used in the following RT-PCR reaction. The amplification products were cut from Novex 6% TBE-Urea gel. The purified DNA fragments were used for sequencing on an Illumina 2G Genome Analyzer at the Beijing Genomics Institute, Shenzhen, China.
2015-04-07 | E-GEOD-53933 | biostudies-arrayexpress
Project description:The goal of this experiment is to assess tissue preferential transcript accumulation and fold difference between two tissues that support secondary vascular growth in three spruces: Picea glauca, Picea sitchensis and Picea mariana. Tissues compared are secondary xylem (wood forming tissue located on the internal side of the cambial meristem) and phelloderm (composite sample of the phloem and phelloderm tissues located on the outer side of the cambial meristem).
2012-02-18 | GSE35922 | GEO
Project description:The goal of this experiment is to assess tissue preferential transcript accumulation and fold difference between two tissues that support secondary vascular growth in three spruces: Picea glauca, Picea sitchensis and Picea mariana. Tissues compared are secondary xylem (wood forming tissue located on the internal side of the cambial meristem) and phelloderm (composite sample of the phloem and phelloderm tissues located on the outer side of the cambial meristem). One-color comparison of 3 spruce species in 2 tissue types: xylem and phelloderm. 20 biological repetitions per tissue for Picea glauca and 15 for Picea sitchensis and Picea mariana, for a total of 100 slides.
2012-02-18 | E-GEOD-35922 | biostudies-arrayexpress
Project description:We take the two year old plant for sampling. Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa newly formed developing xylem and lignified xylem. We used microarrays to detail the global programme of gene expression in newly formed developing xylem and lignified xylem. Populus tomentosa newly formed developing xylem and lignified xylem were taken for RNA extraction and hybridization on Affymetrix microarrays. CB2009304-A and CB2009304-B from newly formed developing xylem, CB2009304-G and CB2009304-H from lignified xylem.
2013-05-16 | E-GEOD-46946 | biostudies-arrayexpress