Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A model system to study secondary growth and bast fibre development: the hemp hypocotyl peeks behind the wall

ABSTRACT: Cannabis sativa L. is an annual herbaceous crop grown for the production of long extraxylary fibers, the bast fibers, rich in cellulose and used both in the textile and biocomposite sectors. Despite being herbaceous, hemp undergoes secondary growth and this is well exemplified by the hypocotyl. The hypocotyl was already shown to be a suitable model to study secondary growth in other herbaceous species, namely Arabidopsis thaliana and it shows an important practical advantage, i.e. elongation and radial thickening are temporally separated. This study focuses on the mechanisms marking the transition from primary to secondary growth in the hemp hypocotyl by analysing the suite of events accompanying vascular tissue and bast fiber development. RNA-Seq transcriptomics, imaging and quantification of phytohormones were carried out on four representative developmental stages (i.e. 6-9-15-20 days after sowing) to provide a first comprehensive profiling of the events associated with primary and secondary growth in hemp. This multidisciplinary approach provides cell wall-related snapshots of the growing hemp hypocotyl and identifies marker genes associated with the young (expansins, β-galactosidases and transcription factors involved in light-related processes) and the older hypocotyl (secondary cell wall biosynthetic genes and transcription factors).

ORGANISM(S): Cannabis sativa

PROVIDER: GSE85144 | GEO | 2016/11/18

SECONDARY ACCESSION(S): PRJNA336328

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptomic profiling of hemp bast fibres at different developmental stages

Project description:Cellulosic phloem fibres, also known as bast fibres, find a wide array of applications in industry, for example as eco-friendly substitutes of glass fibres in the manufacture of biocomposites. Bast fibres are cells characterized by a noteworthy length and by a tertiary cell wall (gelatinous or G-layer) mainly composed of crystalline cellulose. During their differentiation, bast fibres undergo specific developmental stages: the cells initially elongate rapidly by intrusive growth, then they cease elongation and start to thicken. In the light of their importance in fostering a bio-economy, it is desirable to widen our knowledge on the molecular mechanisms underlying the differentiation and maturation of bast fibres. The goal of the present study is to provide a transcriptomic close-up of the key events accompanying bast fibre development. The stages going from rapid elongation to cell wall thickening are here studied in textile hemp (Cannabis sativa L.), a fibre crop of great economic importance.

2017-07-10 | GSE94156 | GEO

Whole transcriptome profiling of bast fibers of ramie

Project description:Ramie fibers extracted from the stem barks have been utilized for thousands years in China, and its biosynthetic mechanism is poorly understood. Here, we have characterized and compared the expression profiling of the barks from the top and middle part of stem where the secondary cellular walls (SCWs) of fiber cell have not initiated growth and was thickening, respectively; resulting in 4,520 differential expression (DE) protein-coding transcripts (PCTs), 1,287 DE long noncoding RNAs (lncRNAs), 88 DE miRNAs and 78 DE circular RNAs (circRNAs). Among the 4,520 DE PCTs, 75 were identified to be the homolog of the Arabidopsis SCW-biosynthetic genes. Overexpression of whole_GLEAN_10014861 (a homolog of SND1) in Arabidopsis caused a significant up-regulation in the expression of AtMYB46 and AtMYB83 that are two key regulators for SCW biosynthesis, thus conferring more fiber cells, along with a remarkable thickening in the SCWs of these cells. Bioinformatic prediction revealed 14 of the 75 homolog targeted by 16 noncoding RNAs (including 8 miRNAs and 8 lncRNAs), and two involved in the competing endogenous RNAs networks, indicating a complex regulatory network for the SCW biosynthesis of bast fiber in ramie. This study provides important insights into the bast fiber biosynthesis of ramie.

2019-05-02 | GSE130587 | GEO

Whole transcriptome profiling of bast fibers of ramie

Project description:Whole transcriptome profiling of bast fibers of ramie

| PRJNA540688 | ENA

Transcription profiling of flax stems and leaves from 4 week old flax plants to identify transcripts enriched in stem and phloem bast fibres

Project description:Stems and leaves from 4 week old flax plants were hybridized to an array of cDNAs from the outer (i.e. phloem enriched) layer of stems of the same age to identify transcripts enriched in stem (and phloem bast fibres).

2007-05-01 | E-MEXP-989 | biostudies-arrayexpress

AtC3H14, a direct target of MYB46, suppress cell elongation and involved in the secondary wall formation.

Project description:Recently, AtC3H14, a CCCH-type zinc finger protein, was identified as one of the direct targets of MYB46, which is known as a master regulator of secondary wall biosynthesis. AtC3H14 and their homologs (i.e., AtC3H15 and PtrC3H14-1 from Arabidopsis and poplar, respectively) are predominantly expressed in the secondary wall forming tissues. Transgenic Arabidopsis plants overexpressing AtC3H14 (i.e., 35S::AtC3H14 plants) produced dwarfing phenotypes. 35S::AtC3H14 plants developed phloem fibers earlier than wild-type and this phenotype was more pronounced in the roots. Interestingly, ectopic secondary wall thickenings were found in both stems and roots. These phenotypic consequences are successively reproduced from the 35S::AtC3H15 and 35S::PtrC3H14-1 plants. Whole transcriptome GeneChip analysis identified that the ‘cell wall’ and ‘extracellular’-related genes are extremely over-represented in the stem tissues of 35S::AtC3H14 plants. These results suggest that AtC3H14 may act as a negative regulator of cell elongation with modification of cell wall reassembly and be involved in the secondary wall formation in Arabidopsis.

2014-12-05 | GSE23801 | GEO

Proteome and differential proteomic analysis of ramie stem bark

Project description:According to a previous study on the microscopic examination of stem barks in ramie, bast fibers from different parts of stem bark showed distinct differences at the developmental level: specifically, the barks in the top part of stem (TPS) did not initiate fiber growth, whereas barks in the middle part of stem (MPS) had a large number of fibers with thickening secondary walls. We have performed the Proteome analysis for the tissues of TPS and MPS, and then carried out the comparison of Proteomic level of proteins between two tissues, thereby to identified differentially Proteomic proteins. These datasets represent the raw UHPLC spectra for Proteome of ramie TPS and MPS.

2022-02-17 | PXD026596 | Pride

Parallel reaction monitoring (PRM) analysis for protein expression

Project description:According to a previous study on the microscopic examination of stem barks in ramie, bast fibers from different parts of stem bark showed distinct differences at the developmental level: specifically, the barks in the top part of stem (TPS) did not initiate fiber growth, whereas barks in the middle part of stem (MPS) had a large number of fibers with thickening secondary walls. We have performed the phosphoproteome analysis for the tissues of TPS and MPS, and then carried out the comparison of phosphorylation level of proteins between two tissues, thereby to identified differentially phosphorylated proteins. These datasets represent the raw UHPLC spectra for phosphoproteome of ramie TPS and MPS.

2022-02-17 | PXD026598 | Pride

Transcriptomics modifications in outer stem tissues of the flax lignified bast fiber mutant1 (lbf1)

Project description:Comparison of whole genome transcriptomics between stem outer tissues from flax lignified bast fiber mutant1 (lbf1) and wild-type

2014-09-11 | GSE61310 | GEO

Transcriptomics modifications in inner stem tissues of the flax lignified bast fiber mutant1 (lbf1)

Project description:Comparison of whole genome transcriptomics between stem inner tissues from flax lignified bast fiber mutant1 (lbf1) and wild-type

2014-09-11 | GSE61309 | GEO

Transcription profiling of Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis

Project description:The aim of this experiment was to understand secondary cell wall formation as it is a major constituent of wood and plant fibres. To identify potential novel genes involved in this process, data has been generated from Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis.

2006-01-01 | E-MEXP-265 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data