Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes
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ABSTRACT:
ORGANISM(S): Paulownia tomentosa
PROVIDER: GSE109323 | GEO | 2021/01/17
REPOSITORIES: GEO
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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:Secondary vascular system (SVS) development resulted from cambial growth is a currently not well understood process. Therefore, more studies are needed to shed more lights on the molecular mechanisms underpinning the cambial activity. The regeneration of SVS from debarked trunk that can mimic the vascular cambium-driven wood formation has developed and could be used to revealed a larger number of differentially expressed genes during the stages of cambium formation and xylem differentiation in Populus tomentosa. We used microarrays to detail the global programme of gene expression in 6 time points during the regeneration of SVS.
2015-07-21 | GSE71094 | 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.
2015-04-07 | GSE53933 | 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:(paper abstract) Wood is a renewable resource that serves as a sustainable raw material for energy, fuels and materials. A basic understanding of the cambial meristem and the origin of wood cells is critical for forest tree molecular breeding to increase the availability of woody raw materials. Gene expression per cell type in the cambium of poplar (Populus trichocarpa x P. deltoïdes cultivar Boelare) was investigated using poplar microarray. Cells were hand microdissected from lyophilized sections of vascular cambial zone sampled in growing poplar. Two cell types were isolated, fusiform cambial cells (FCCs) and ray cambial cells (RCCs). Results showed about one thousand genes differentially expressed per cell type. Microarray expression results were validated by a second cell sampling used for reverse northern dot blot and RT-PCR analysis. RCCs revealed specific photosynthetic competences involving at least 35 genes of the photosystems. RCCs revealed also a marked difference for intercellular transport involving notably aquaporin genes. Distinct classes of cell-wall related genes were detected in RCCs and FCCs. A candidate xyloglucan endotransglycosylase showed to be upregulated and highly expressed in FCCs and an extensin family gene was also very highly expressed in these cells. A candidate polygalacturonase was strikingly expressed specifically in RCCs. A marked expression of cytoskeleton genes was also reported for FCCs where profilin family genes were very highly expressed. Related to cell signaling and regulation, one of the most intriguing result was the observation of LAX1 gene specificity in FCCs whereas PIN genes were expressed in both cell types.
2008-06-30 | E-MEXP-794 | biostudies-arrayexpress
Project description:We sequenced mRNA from dormant, reactivating, and actively growing C. lanceolata vascular cambium using tangential cryosections to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for cambium development and wood formation in the conifer. Examination of mRNA levels in dormant, reactivating, and actively growing C. lanceolata vascular cambium, respectively
2014-03-31 | E-GEOD-37152 | biostudies-arrayexpress
Project description:We sequenced mRNA from dormant, reactivating, and actively growing C. lanceolata vascular cambium using tangential cryosections to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for cambium development and wood formation in the conifer.
2014-03-31 | GSE37152 | GEO
Project description:Genome-wide identification and profiling of microRNAs in Paulownia tomentosa cambial tissues in response to seasonal changes
| PRJNA430425 | ENA
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:Transcriptome of Populus tomentosa tension wood xylem
| PRJNA239548 | ENA