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      Cell wall composition and transcriptomics in stem tissues of stinging nettle ( Urtica dioica L.): Spotlight on a neglected fibre crop

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          Abstract

          Stinging nettle ( Urtica dioica L.) produces silky cellulosic fibres, as well as bioactive molecules. To improve the knowledge on nettle and enhance its opportunities of exploitation, a draft transcriptome of the “clone 13” (a fibre clone) is here presented. The transcriptome of whole internodes sampled at the top and middle of the stem is then compared with the core and cortical tissues sampled at the bottom. Young internodes show an enrichment in genes involved in the biosynthesis of phytohormones (auxins and jasmonic acid) and secondary metabolites (flavonoids). The core of internodes collected at the bottom of the stem is enriched in genes partaking in different aspects of secondary cell wall formation (cellulose, hemicellulose, lignin biosynthesis), while the cortical tissues reveal the presence of a C starvation signal probably due to the UDP‐glucose demand necessary for the thickening phase of bast fibres. Cell wall analysis indicates a difference in rhamnogalacturonan structure/composition of mature bast fibres, as evidenced by the higher levels of galactose measured, as well as the occurrence of more water‐soluble pectins in elongating internodes. The targeted quantification of phenolics shows that the middle internode and the cortical tissues at the bottom have higher contents than top internodes. Ultrastructural analyses reveal the presence of a gelatinous layer in bast fibres with a lamellar structure. The data presented will be an important resource and reference for future molecular studies on a neglected fibre crop.

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          Cluster analysis and display of genome-wide expression patterns.

          A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data. Thus patterns seen in genome-wide expression experiments can be interpreted as indications of the status of cellular processes. Also, coexpression of genes of known function with poorly characterized or novel genes may provide a simple means of gaining leads to the functions of many genes for which information is not available currently.
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            A battery of transcription factors involved in the regulation of secondary cell wall biosynthesis in Arabidopsis.

            SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) is a master transcriptional switch activating the developmental program of secondary wall biosynthesis. Here, we demonstrate that a battery of SND1-regulated transcription factors is required for normal secondary wall biosynthesis in Arabidopsis thaliana. The expression of 11 SND1-regulated transcription factors, namely, SND2, SND3, MYB103, MYB85, MYB52, MYB54, MYB69, MYB42, MYB43, MYB20, and KNAT7 (a Knotted1-like homeodomain protein), was developmentally associated with cells undergoing secondary wall thickening. Of these, dominant repression of SND2, SND3, MYB103, MYB85, MYB52, MYB54, and KNAT7 significantly reduced secondary wall thickening in fiber cells. Overexpression of SND2, SND3, and MYB103 increased secondary wall thickening in fibers, and overexpression of MYB85 led to ectopic deposition of lignin in epidermal and cortical cells in stems. Furthermore, SND2, SND3, MYB103, MYB85, MYB52, and MYB54 were able to induce secondary wall biosynthetic genes. Direct target analysis using the estrogen-inducible system revealed that MYB46, SND3, MYB103, and KNAT7 were direct targets of SND1 and also of its close homologs, NST1, NST2, and vessel-specific VND6 and VND7. Together, these results demonstrate that a transcriptional network consisting of SND1 and its downstream targets is involved in regulating secondary wall biosynthesis in fibers and that NST1, NST2, VND6, and VND7 are functional homologs of SND1 that regulate the same downstream targets in different cell types.
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              New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants.

              The aromatic amino acids phenylalanine, tyrosine, and tryptophan in plants are not only essential components of protein synthesis, but also serve as precursors for a wide range of secondary metabolites that are important for plant growth as well as for human nutrition and health. The aromatic amino acids are synthesized via the shikimate pathway followed by the branched aromatic amino acids biosynthesis pathway, with chorismate serving as a major intermediate branch point metabolite. Yet, the regulation and coordination of synthesis of these amino acids are still far from being understood. Recent studies on these pathways identified a number of alternative cross-regulated biosynthesis routes with unique evolutionary origins. Although the major route of Phe and Tyr biosynthesis in plants occurs via the intermediate metabolite arogenate, recent studies suggest that plants can also synthesize phenylalanine via the intermediate metabolite phenylpyruvate (PPY), similarly to many microorganisms. Recent studies also identified a number of transcription factors regulating the expression of genes encoding enzymes of the shikimate and aromatic amino acids pathways as well as of multiple secondary metabolites derived from them in Arabidopsis and in other plant species.
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                Author and article information

                Contributors
                gea.guerriero@list.lu
                Journal
                Plant Direct
                Plant Direct
                10.1002/(ISSN)2475-4455
                PLD3
                Plant Direct
                John Wiley and Sons Inc. (Hoboken )
                2475-4455
                12 August 2019
                August 2019
                : 3
                : 8 ( doiID: 10.1002/pld3.2019.3.issue-8 )
                : e00151
                Affiliations
                [ 1 ] Environmental Research and Innovation (ERIN) Department Luxembourg Institute of Science and Technology (LIST) Esch/Alzette Luxembourg
                [ 2 ] Department of Life Sciences University of Siena Siena Italy
                [ 3 ] Trees and Timber Institute‐National Research Council of Italy (CNR‐IVALSA) Follonica Italy
                [ 4 ] Institute of Biometeorology (IBIMET) National Research Council Bologna Italy
                [ 5 ]Present address: Unité de Recherche Résistance Induite et BioProtection des Plantes UFR Sciences Exactes et Naturelles SFR Condorcet FR CNRS 3417 Université de Reims‐Champagne‐Ardenne Reims Cedex 2 France
                Author notes
                [*] [* ] Correspondence

                Gea Guerriero, Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, Esch/Alzette L‐4362, Luxembourg.

                Email: gea.guerriero@ 123456list.lu

                Article
                PLD3151
                10.1002/pld3.151
                6689792
                31417976
                52186f39-aad4-498a-9a05-cdd07a5810d6
                © 2019 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 15 May 2019
                : 18 June 2019
                : 21 June 2019
                Page count
                Figures: 5, Tables: 1, Pages: 17, Words: 14857
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                pld3151
                August 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.7 mode:remove_FC converted:12.08.2019

                bast fibres,electron microscopy,immunohistochemistry,rna‐seq cell wall composition,urtica dioica l.

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