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)

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 ◽  
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 De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

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 Leishmania infection induces a limited differential gene expression in the sand fly midgut

2020 ◽  
Author(s):  
Iliano V. Coutinho-Abreu ◽  
Tiago D. Serafim ◽  
Claudio Meneses ◽  
Shaden Kamhawi ◽  
Fabiano Oliveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Early Time ◽  
Differentially Expressed ◽  
Sand Fly ◽  
Leishmania Infection ◽  
Lutzomyia Longipalpis ◽  
Late Time ◽  
Time Points

Abstract Background: Phlebotomine sand flies are the vectors of Leishmania worldwide. To develop in the sand fly midgut, Leishmania multiplies and undergoes multiple stage differentiations leading to the infective form, the metacyclic promastigotes. To gain a better understanding of the influence of Leishmania infection on midgut gene expression, we performed RNA-Seq comparing uninfected and Leishmania infantum -infected Lutzomyia longipalpis midguts at seven time points which cover the various Leishmania developmental stages including early time points when blood digestion is taking place, and late time points when the parasites are undergoing metacyclogenesis. Results: Out of over 13,841 transcripts assembled de novo , only 113 sand fly transcripts, about 1%, were differentially expressed. Further, we observed a low overlap of differentially expressed sand fly transcripts across different time points suggesting that each Leishmania stage influences midgut gene expression in a specific manner. Two main patterns of sand fly gene expression modulation were noted. At early time points (days 1-4), more transcripts were down-regulated by Leishmania infection at large fold changes (> -32 fold). Among the down-regulated genes, the transcription factor Forkhead/HNF-3 and hormone degradation enzymes were differentially regulated on day 4 and appear to be the upstream regulators of nutrient transport, digestive enzymes, and peritrophic matrix proteins. Conversely, at later time points (days 6 onwards), most of the differentially expressed transcripts were up-regulated by small fold changes (< 32 fold). The molecular function of these genes has been associated with the metabolism of lipids and detoxification of xenobiotics. Conclusion: Overall, it appears that Leishmania modulates sand fly gene expression early on in order to overcome the barriers imposed by the midgut, yet it behaves like a commensal at later time points, where a massive number of parasites in the anterior midgut results only in modest changes in midgut gene expression.

scholarly journals Multi-responses of O-methyltransferase genes to salt stress and fiber development of Gossypium species

2020 ◽  
Author(s):  
Abdul Hafeez ◽  
Qún Gě ◽  
Qí Zhāng ◽  
Jùnwén Lǐ ◽  
Jǔwǔ Gōng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Salt Stress ◽  
Plant Cell Wall ◽  
Developmental Stages ◽  
Fiber Quality ◽  
Regulatory Elements ◽  
Fiber Development ◽  
Specific Expression ◽  
Salt Stress Response ◽  
Quality Formation

Abstract Background: O-methyltransferases (OMTs) are an important group of enzymes that catalyze the transfer of a methyl group from S-adenosyl-L-methionine to their acceptor substrates. OMTs are divided into several groups according to their structural features. In Gossypium species, they are involved in phenolics and flavonoid pathways. Phenolics defend the cellulose fiber from dreadful external conditions of biotic and abiotic stresses, promoting strength and growth of plant cell wall. Results: An OMT gene family, containing a total of 192 members, has been identified and characterized in three main Gossypium species, G. hirsutum, G. arboreum and G. raimondii. Cis-regulatory elements analysis suggested important roles of OMT genes in growth, development, and defense against stresses. Transcriptome data of different fiber developmental stages in Chromosome Substitution Segment Lines (CSSLs), Recombination Inbred Lines (RILs) with excellent fiber quality, and standard genetic cotton cultivar TM-1 demonstrate that up-regulation of OMT genes at different fiber developmental stages, and abiotic stress treatments have some significant correlations with fiber quality formation, and with salt stress response. Quantitative RT-PCR results revealed that GhOMT10_Dt and GhOMT70_At genes had a specific expression in response to salt stress while GhOMT49_At, GhOMT49_Dt, and GhOMT48_At in fiber elongation and secondary cell wall stages. Conclusions: Our results indicate that O-methyltransferase genes have multi-responses to salt stress and fiber development in Gossypium species and that they may contribute to salt tolerance or fiber quality formation in Gossypium.

scholarly journals Phenylpropanoid Biosynthesis Gene Expression Precedes Lignin Accumulation During Shoot Development in Lowland and Upland Switchgrass Genotypes

2021 ◽  
Vol 12 ◽  
Author(s):  
Prasenjit Saha ◽  
Fan Lin ◽  
Sandra Thibivilliers ◽  
Yi Xiong ◽  
Chongle Pan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Developmental Stages ◽  
Lignin Biosynthesis ◽  
Biomass Composition ◽  
Cell Wall Component ◽  
Cell Wall Digestibility ◽  
Gini Correlation ◽  
Biosynthesis Gene ◽  
Phenylpropanoid Biosynthesis

Efficient conversion of lignocellulosic biomass into biofuels is influenced by biomass composition and structure. Lignin and other cell wall phenylpropanoids, such as para-coumaric acid (pCA) and ferulic acid (FA), reduce cell wall sugar accessibility and hamper biochemical fuel production. Toward identifying the timing and key parameters of cell wall recalcitrance across different switchgrass genotypes, this study measured cell wall composition and lignin biosynthesis gene expression in three switchgrass genotypes, A4 and AP13, representing the lowland ecotype, and VS16, representing the upland ecotype, at three developmental stages [Vegetative 3 (V3), Elongation 4 (E4), and Reproductive 3 (R3)] and three segments (S1–S3) of the E4 stage under greenhouse conditions. A decrease in cell wall digestibility and an increase in phenylpropanoids occur across development. Compared with AP13 and A4, VS16 has significantly less lignin and greater cell wall digestibility at the V3 and E4 stages; however, differences among genotypes diminish by the R3 stage. Gini correlation analysis across all genotypes revealed that lignin and pCA, but also pectin monosaccharide components, show the greatest negative correlations with digestibility. Lignin and pCA accumulation is delayed compared with expression of phenylpropanoid biosynthesis genes, while FA accumulation coincides with expression of these genes. The different cell wall component accumulation profiles and gene expression correlations may have implications for system biology approaches to identify additional gene products with cell wall component synthesis and regulation functions.

scholarly journals Immunohistochemical analyses on two distinct internodes of stinging nettle show different distribution of polysaccharides and proteins in the cell walls of bast fibers

PROTOPLASMA ◽  
2021 ◽  
Author(s):  
Claudia Faleri ◽  
Xuan Xu ◽  
Lavinia Mareri ◽  
Jean-Francois Hausman ◽  
Giampiero Cai ◽  
...  
Keyword(s):  
Cell Wall ◽  
Cell Walls ◽  
Vascular Tissue ◽  
Developmental Stages ◽  
Cell Wall Polysaccharides ◽  
Stinging Nettle ◽  
Bast Fiber ◽  
Bast Fibers ◽  
Biochemical Approach ◽  
Immunohistochemical Analyses

AbstractStinging nettle is a perennial herbaceous species holding value as a multi-purpose plant. Indeed, its leaves and roots are phytofactories providing functional ingredients of medicinal interest and its stems produce silky and resistant extraxylary fibers (a.k.a. bast fibers) valued in the biocomposite sector. Similarly to what is reported in other fiber crops, the stem of nettle contains both lignified and hypolignified fibers in the core and cortex, respectively, and it is therefore a useful model for cell wall research. Indeed, data on nettle stem tissues can be compared to those obtained in other models, such as hemp and flax, to support hypotheses on the differentiation and development of bast fibers. The suitability of the nettle stem as model for cell wall-related research was already validated using a transcriptomics and biochemical approach focused on internodes at different developmental stages sampled at the top, middle, and bottom of the stem. We here sought to complement and enrich these data by providing immunohistochemical and ultrastructural details on young and older stem internodes. Antibodies recognizing non-cellulosic polysaccharides (galactans, arabinans, rhamnogalacturonans) and arabinogalactan proteins were here investigated with the goal of understanding whether their distribution changes in the stem tissues in relation to the bast fiber and vascular tissue development. The results obtained indicate that the occurrence and distribution of cell wall polysaccharides and proteins differ between young and older internodes and that these changes are particularly evident in the bast fibers.

scholarly journals Developmental Transcriptional Model Describing Regulated Genes, Qtls And Pathways During The Primary And Secondary Cell Walls Of Pima Fibers

2016 ◽  
Author(s):  
Magdy S. Alabady ◽  
Bulak A. Arpat
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Fiber Quality ◽  
Time Frame ◽  
Developmental Time ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Time Points ◽  
Cotton Genotypes

AbstractGossypium barbadense L. (Egyptian and Pima) produces single celled fiber trichomes that are the longest and richest in cellulosic contents in the plant kingdom. Developmental dissection of fiber at the transcriptional level is crucial to unveiling the genetic mechanisms underpinning fiber morphogenesis. We profiled the transcriptome of developing Pima fibers, as well as genes associated with consensus fiber quality QTLs, at seven developmental time points covering both primary (PCW) and secondary (SCW) cell wall stages. A total of 2,934 genes were differentially expressed at only one (45.19%) or at multiple (54.81%) developmental time points. Based on the coincidence between gene expression dynamics and the time frame of fiber developmental stages, five stage-specific expression profiles were identified. As a link between fiber QTLs and gene expression, 5 potential developmentally regulated QTLs (drQTLs) corresponding to different fiber developmental stages were identified. Genes in the ubiquitin proteolytic pathway, particularly QTL associated genes, appeared to be involved in regulating the transition stage between PCW and SCW; a stage that is crucial to both fiber length and strength in the extra-long staple cotton genotypes. In this respect, Yeast-two-hybrids identified interactions between UBC9 and genes involved in cell and organ elongation, polar cell expansion, microtubule cytoskeleton dynamics and organization, and basic amino acids transportation during the SCW/SCW transition. Altogether, these results were integrated into a proposed model linking fiber developmental stages with the Pima fiber traits.

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