scholarly journals Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. Gaud (ramie)

2020 ◽  
Author(s):  
Jiyong Xie ◽  
Jiaqi Li ◽  
Yucheng Jie ◽  
Deyu Xie ◽  
Di Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
De Novo ◽  
Fiber Quality ◽  
Histological Study ◽  
Raw Material ◽  
Acid Oxidase ◽  
Phloem Tissue ◽  
Bast Fiber ◽  
Boehmeria Nivea

Abstract Background: Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie.Results: In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed and de novo transcriptome was assembled. Unigenes and differentially expressed genes (DEGs) in these three samples were identified. The analysis of DEGs by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed clear differences in gene expression between ER and FER. Some unigenes involved in secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, the ethylene respond factors (ERFs) in the ethylene signaling pathway were up-regulated in FER, and ent-kaurenoic acid oxidase (KAO) and GA 20-oxidase (GA20ox) for gibberellins biosynthesis were up-regulated while GA 2-oxidase (GA2ox) for gibberellin inactivation was down-regulated in FER.Conclusions: Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.

scholarly journals Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. Gaud (ramie)

2019 ◽  
Author(s):  
Jiyong Xie ◽  
Jiaqi Li ◽  
Yucheng Jie ◽  
Deyu Xie ◽  
Di Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Developmental Stages ◽  
De Novo ◽  
Fiber Quality ◽  
Histological Study ◽  
Raw Material ◽  
Phloem Tissue ◽  
Bast Fiber ◽  
Boehmeria Nivea

Abstract Background: Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie. Results: In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs) in these three samples. The de novo transcriptome was assembled and unigenes were identified. The DEGs among TB, ER and FER were analyzed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) studies revealed clear differences in gene expression between ER and FER. Some unigenes for secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, ethylene activating pathway and gibberellins biosynthesis showed distinct regulation and coincided with the developmental stages of the samples. Conclusions: Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and the phytohormon ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.

scholarly journals Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. Gaud (ramie)

2019 ◽  
Author(s):  
Jiyong Xie ◽  
Jiaqi Li ◽  
Yucheng Jie ◽  
Deyu Xie ◽  
Di Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Developmental Stages ◽  
De Novo ◽  
Fiber Quality ◽  
Histological Study ◽  
Raw Material ◽  
Phloem Tissue ◽  
Bast Fiber ◽  
Boehmeria Nivea

Abstract Background: Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie.Results: In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs) in these three samples. The de novo transcriptome was assembled and unigenes were identified. The DEGs among TB, ER and FER were analyzed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) studies revealed clear differences in gene expression between ER and FER. Some unigenes for secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, ethylene activating pathway and gibberellins biosynthesis showed distinct regulation and coincided with the developmental stages of the samples. Conclusions: Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and the phytohormon ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.

scholarly journals Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. Gaud (ramie)

2019 ◽  
Author(s):  
Jiyong Xie ◽  
Jiaqi Li ◽  
Yucheng Jie ◽  
Deyu Xie ◽  
Di Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
De Novo ◽  
Fiber Quality ◽  
Histological Study ◽  
Raw Material ◽  
Phloem Tissue ◽  
Cell Wall Modification ◽  
Bast Fiber ◽  
Boehmeria Nivea

Abstract Background: Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie is the raw material for fiber and primarily includes the entire phloem tissue of the plant stem. Therefore, identifying the molecular regulation of phloem development is important for the understanding of bast fiber biosynthesis and improvement in fiber quality in ramie. Results: In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed to identify differentially expressed genes (DEGs) among these three samples. The de novo transcriptome was assembled and unigenes were identified. The DEGs among TB, ER and FER were analyzed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) studies revealed clear differences in gene expression between ER and FER. Some unigenes for secondary cell wall biosynthesis were up-regulated in both ER and FER, and other cell wall components or cell wall modification related genes showed differential expression between ER and FER. In addition, ethylene activating pathway and gibberellins biosynthesis varied among samples in a stage dependent pattern. Conclusions: Both morphological study and gene expression analysis supported a burst of phloem and vascular development processes during the fiber maturation in the ramie stem. Two types of phytohormons, ethylene and gibberellin, might be involved in. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.

scholarly journals Transcriptome analysis of Pará rubber tree (H. brasiliensis) seedlings under ethylene stimulation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yoshimi Nakano ◽  
Nobutaka Mitsuda ◽  
Kohei Ide ◽  
Teppei Mori ◽  
Farida Rosana Mira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Natural Rubber ◽  
Management Practices ◽  
Rubber Tree ◽  
Raw Material ◽  
Tree Seedlings ◽  
Cell Wall Formation ◽  
Wall Formation ◽  
Ethephon Treatment

Abstract Background Natural rubber (cis-1,4-polyioprene, NR) is an indispensable industrial raw material obtained from the Pará rubber tree (H. brasiliensis). Natural rubber cannot be replaced by synthetic rubber compounds because of the superior resilience, elasticity, abrasion resistance, efficient heat dispersion, and impact resistance of NR. In NR production, latex is harvested by periodical tapping of the trunk bark. Ethylene enhances and prolongs latex flow and latex regeneration. Ethephon, which is an ethylene-releasing compound, applied to the trunk before tapping usually results in a 1.5- to 2-fold increase in latex yield. However, intense mechanical damage to bark tissues by excessive tapping and/or over-stimulation with ethephon induces severe oxidative stress in laticifer cells, which often causes tapping panel dryness (TPD) syndrome. To enhance NR production without causing TPD, an improved understanding of the molecular mechanism of the ethylene response in the Pará rubber tree is required. Therefore, we investigated gene expression in response to ethephon treatment using Pará rubber tree seedlings as a model system. Results After ethephon treatment, 3270 genes showed significant differences in expression compared with the mock treatment. Genes associated with carotenoids, flavonoids, and abscisic acid biosynthesis were significantly upregulated by ethephon treatment, which might contribute to an increase in latex flow. Genes associated with secondary cell wall formation were downregulated, which might be because of the reduced sugar supply. Given that sucrose is an important molecule for NR production, a trade-off may arise between NR production and cell wall formation for plant growth and for wound healing at the tapping panel. Conclusions Dynamic changes in gene expression occur specifically in response to ethephon treatment. Certain genes identified may potentially contribute to latex production or TPD suppression. These data provide valuable information to understand the mechanism of ethylene stimulation, and will contribute to improved management practices and/or molecular breeding to attain higher yields of latex from Pará rubber trees.

scholarly journals Cell wall gene expression in two sub-species of flax

2017 ◽  
Vol 1 (2) ◽  
pp. 192-195 ◽  
Author(s):  
Dmitry Galinousky ◽  
Tsimafei Padvitski
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Linum Usitatissimum ◽  
Fiber Quality ◽  
Cellulose Synthase ◽  
Expression Level ◽  
Fiber Flax ◽  
Linum Usitatissimum L ◽  
Lower Expression ◽  
Dehiscent Flax

Abstract In this work, we attempted to elucidate mechanisms of flax fiber biogenesis by measuring, using qPCR, expression of the cellwall related genes (cellulose synthase, cellulose synthase-like and chitinase-like genes) in stems of two contrasting fiber quality subspecies of flax (Linum usitatissimum L.). We studied elongatum Vav. et Ell. (cultivar Blakit, Belarus) and crepitans Boenn. (dehiscent flax) subspecies, which are differed in the height of plants, width of stems etc. Amongst all measured genes chitinase- like Ctl19 and Ctl21 genes showed drastic difference in expression between stems of the two flax varieties, showing higher expression level in the fiber flax versus the dehiscent flax. In contrast, cellulose synthase-like CslG4 gene had lower expression levels in the stem of fiber flax than in dehiscent flax. We suggest that hemicellulose composition and cellulose - non-cellulose glycan organisation can vary between stalk cells of different flax subspecies.

New insights on Laminaria digitata ultrastructure through combined conventional chemical fixation and cryofixation

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Christos Katsaros ◽  
Sophie Le Panse ◽  
Gillian Milne ◽  
Carl J. Carrano ◽  
Frithjof Christian Küpper
Keyword(s):  
Cell Wall ◽  
General Structure ◽  
Raw Material ◽  
Rocky Shores ◽  
Chemical Fixation ◽  
Laminaria Digitata ◽  
Vegetative Cells ◽  
Biological Studies ◽  
New Findings ◽  
Wide Range

Abstract The objective of the present study is to examine the fine structure of vegetative cells of Laminaria digitata using both chemical fixation and cryofixation. Laminaria digitata was chosen due to its importance as a model organism in a wide range of biological studies, as a keystone species on rocky shores of the North Atlantic, its use of iodide as a unique inorganic antioxidant, and its significance as a raw material for the production of alginate. Details of the fine structural features of vegetative cells are described, with particular emphasis on the differences between the two methods used, i.e. conventional chemical fixation and freeze-fixation. The general structure of the cells was similar to that already described, with minor differences between the different cell types. An intense activity of the Golgi system was found associated with the thick external cell wall, with large dictyosomes from which numerous vesicles and cisternae are released. An interesting type of cisternae was found in the cryofixed material, which was not visible with the chemical fixation. These are elongated structures, in sections appearing tubule-like, close to the external cell wall or to young internal walls. An increased number of these structures was observed near the plasmodesmata of the pit fields. They are similar to the “flat cisternae” found associated with the forming cytokinetic diaphragm of brown algae. Their possible role is discussed. The new findings of this work underline the importance of such combined studies which reveal new data not known until now using the old conventional methods. The main conclusion of the present study is that cryofixation is the method of choice for studying Laminaria cytology by transmission electron microscopy.

scholarly journals AAV-Mediated CRISPRi and RNAi Based Gene Silencing in Mouse Hippocampal Neurons

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 324
Author(s):  
Matthias Deutsch ◽  
Anne Günther ◽  
Rodrigo Lerchundi ◽  
Christine R. Rose ◽  
Sabine Balfanz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Hippocampal Neurons ◽  
De Novo ◽  
Protein Biosynthesis ◽  
Physiological Role ◽  
High Specificity ◽  
Hcn Channels ◽  
Proliferating Cells ◽  
Neuronal Tissues

Uncovering the physiological role of individual proteins that are part of the intricate process of cellular signaling is often a complex and challenging task. A straightforward strategy of studying a protein’s function is by manipulating the expression rate of its gene. In recent years, the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9-based technology was established as a powerful gene-editing tool for generating sequence specific changes in proliferating cells. However, obtaining homogeneous populations of transgenic post-mitotic neurons by CRISPR/Cas9 turned out to be challenging. These constraints can be partially overcome by CRISPR interference (CRISPRi), which mediates the inhibition of gene expression by competing with the transcription machinery for promoter binding and, thus, transcription initiation. Notably, CRISPR/Cas is only one of several described approaches for the manipulation of gene expression. Here, we targeted neurons with recombinant Adeno-associated viruses to induce either CRISPRi or RNA interference (RNAi), a well-established method for impairing de novo protein biosynthesis by using cellular regulatory mechanisms that induce the degradation of pre-existing mRNA. We specifically targeted hyperpolarization-activated and cyclic nucleotide-gated (HCN) channels, which are widely expressed in neuronal tissues and play essential physiological roles in maintaining biophysical characteristics in neurons. Both of the strategies reduced the expression levels of three HCN isoforms (HCN1, 2, and 4) with high specificity. Furthermore, detailed analysis revealed that the knock-down of just a single HCN isoform (HCN4) in hippocampal neurons did not affect basic electrical parameters of transduced neurons, whereas substantial changes emerged in HCN-current specific properties.

scholarly journals Malpigmentation of Common Sole (Solea solea) during Metamorphosis Is Associated with Differential Synaptic-Related Gene Expression

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2273
Author(s):  
Menelaos Kavouras ◽  
Emmanouil E. Malandrakis ◽  
Ewout Blom ◽  
Kyriaki Tsilika ◽  
Theodoros Danis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
De Novo ◽  
Close Association ◽  
Ionic Channels ◽  
Long Term Potentiation ◽  
General Term ◽  
The Difference ◽  
Common Sole

In farmed flatfish, such as common sole, color disturbances are common. Dyschromia is a general term that includes the color defects on the blind and ocular sides of the fish. The purpose was to examine the difference in gene expression between normal pigmented and juveniles who present ambicoloration. The analysis was carried out with next-generation sequencing techniques and de novo assembly of the transcriptome. Transcripts that showed significant differences (FDR < 0.05) in the expression between the two groups, were related to those of zebrafish (Danio rerio), functionally identified, and classified into categories of the gene ontology. The results revealed that ambicolorated juveniles exhibit a divergent function, mainly of the central nervous system at the synaptic level, as well as the ionic channels. The close association of chromophore cells with the growth of nerve cells and the nervous system was recorded. The pathway, glutamate binding–activation of AMPA and NMDA receptors–long-term stimulation of postsynaptic potential–LTP (long term potentiation)–plasticity of synapses, appears to be affected. In addition, the development of synapses also seems to be affected by the interaction of the LGI (leucine-rich glioma inactivated) protein family with the ADAM (a disintegrin and metalloprotease) ones.

scholarly journals Microtubule Dynamics Plays a Vital Role in Plant Adaptation and Tolerance to Salt Stress

2021 ◽  
Vol 22 (11) ◽  
pp. 5957
Author(s):  
Hyun Jin Chun ◽  
Dongwon Baek ◽  
Byung Jun Jin ◽  
Hyun Min Cho ◽  
Mi Suk Park ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Salt Stress ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Related Gene ◽  
Plant Adaptation ◽  
Salt Stress Response ◽  
Network Analyses ◽  
Cell Wall Biogenesis

Although recent studies suggest that the plant cytoskeleton is associated with plant stress responses, such as salt, cold, and drought, the molecular mechanism underlying microtubule function in plant salt stress response remains unclear. We performed a comparative proteomic analysis between control suspension-cultured cells (A0) and salt-adapted cells (A120) established from Arabidopsis root callus to investigate plant adaptation mechanisms to long-term salt stress. We identified 50 differentially expressed proteins (45 up- and 5 down-regulated proteins) in A120 cells compared with A0 cells. Gene ontology enrichment and protein network analyses indicated that differentially expressed proteins in A120 cells were strongly associated with cell structure-associated clusters, including cytoskeleton and cell wall biogenesis. Gene expression analysis revealed that expressions of cytoskeleton-related genes, such as FBA8, TUB3, TUB4, TUB7, TUB9, and ACT7, and a cell wall biogenesis-related gene, CCoAOMT1, were induced in salt-adapted A120 cells. Moreover, the loss-of-function mutant of Arabidopsis TUB9 gene, tub9, showed a hypersensitive phenotype to salt stress. Consistent overexpression of Arabidopsis TUB9 gene in rice transgenic plants enhanced tolerance to salt stress. Our results suggest that microtubules play crucial roles in plant adaptation and tolerance to salt stress. The modulation of microtubule-related gene expression can be an effective strategy for developing salt-tolerant crops.

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