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      A Novel NAC Transcription Factor From Eucalyptus, EgNAC141, Positively Regulates Lignin Biosynthesis and Increases Lignin Deposition

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          Abstract

          Wood formation is a complicated process under the control of a large set of transcription factors. NAC transcription factors are considered “master switches” in this process. However, few NAC members have been cloned and characterized in Eucalyptus, which is one of the most economically important woody plants. Here, we reported an NAC transcription factor from Eucalyptus grandis, EgNAC141, which has no Arabidopsis orthologs associated with xylogenesis-related processes. EgNAC141 was predominantly expressed in lignin-rich tissues, such as the stem and xylem. Overexpression of EgNAC141 in Arabidopsis resulted in stronger lignification, larger xylem, and higher lignin content. The expression of lignin biosynthetic genes in transgenic plants was significantly higher compared with wild-type plants. The transient expression of EgNAC141 activated the expression of Arabidopsis lignin biosynthetic genes in a dual-luciferase assay. Overall, these results showed that EgNAC141 is a positive regulator of lignin biosynthesis and may help us understand the regulatory mechanism of wood formation.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                08 April 2021
                2021
                : 12
                : 642090
                Affiliations
                [1] 1School of Life Sciences, Southwest University , Chongqing, China
                [2] 2Chongqing Three Gorges University College of Public Administration , Chongqing, China
                [3] 3College of Life Sciences, Shandong Normal University (SDNU) , Jinan, China
                [4] 4School of Life Sciences, Jinggangshan University , Ji’an, China
                Author notes

                Edited by: Juan Guiamet, National University of La Plata, Argentina

                Reviewed by: Steven Grant Hussey, University of Pretoria, South Africa; Xiaoli Jin, Zhejiang University, China

                *Correspondence: Jianjun Zeng, 764178121@ 123456qq.com

                This article was submitted to Plant Biotechnology, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2021.642090
                8061705
                5118dd93-954b-495f-bc96-b281feeea39e
                Copyright © 2021 Sun, Jiang, Jiang, Wang, Zhang and Zeng.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 15 December 2020
                : 05 March 2021
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 40, Pages: 10, Words: 0
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                eucalyptus,nac transcription factor,lignin biosynthesis,wood formation,secondary cell wall

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