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      Function of MYB8 in larch under PEG simulated drought stress

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          Abstract

          Larch, a prominent afforestation, and timber species in northeastern China, faces growth limitations due to drought. To further investigate the mechanism of larch’s drought resistance, we conducted full-length sequencing on embryonic callus subjected to PEG-simulated drought stress. The sequencing results revealed that the differentially expressed genes (DEGs) primarily played roles in cellular activities and cell components, with molecular functions such as binding, catalytic activity, and transport activity. Furthermore, the DEGs showed significant enrichment in pathways related to protein processing, starch and sucrose metabolism, benzose-glucuronic acid interconversion, phenylpropyl biology, flavonoid biosynthesis, as well as nitrogen metabolism and alanine, aspartic acid, and glutamic acid metabolism. Consequently, the transcription factor T_transcript_77027, which is involved in multiple pathways, was selected as a candidate gene for subsequent drought stress resistance tests. Under PEG-simulated drought stress, the LoMYB8 gene was induced and showed significantly upregulated expression compared to the control. Physiological indices demonstrated an improved drought resistance in the transgenic plants. After 48 h of PEG stress, the transcriptome sequencing results of the transiently transformed LoMYB8 plants and control plants exhibited that genes were significantly enriched in biological process, cellular component and molecular function. Function analyses indicated for the enrichment of multiple KEGG pathways, including energy synthesis, metabolic pathways, antioxidant pathways, and other relevant processes. The pathways annotated by the differential metabolites mainly encompassed signal transduction, carbohydrate metabolism, amino acid metabolism, and flavonoid metabolism.

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Pfam: the protein families database

            Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures.
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              KEGG for linking genomes to life and the environment

              KEGG (http://www.genome.jp/kegg/) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes to life through the process of PATHWAY mapping, which is to map, for example, a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes to the environment, such as for the analysis of drug-target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies of various biological objects, including molecules, cells, organisms, diseases and drugs, as well as relationships among them. KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps. In addition, smaller pathway modules are defined and stored in KEGG MODULE that also contains other functional units and complexes. The KEGG resource is being expanded to suit the needs for practical applications. KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers.
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                Author and article information

                Contributors
                hanguozhang1@sina.com
                109477986@qq.com
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                17 May 2024
                17 May 2024
                2024
                : 14
                : 11290
                Affiliations
                [1 ]GRID grid.412246.7, ISNI 0000 0004 1789 9091, State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), ; Harbin, China
                [2 ]Forestry Research Institute in Heilongjiang Province, Harbin, China
                [3 ]State Administration of Forestry and Grassland, Harbin Research Institute of Forestry Machinery, ( https://ror.org/03f2n3n81) Harbin, China
                [4 ]College of Forestry and Landscape Architecture, South China Agricultural University, ( https://ror.org/05v9jqt67) Guangzhou, China
                [5 ]GRID grid.216566.0, ISNI 0000 0001 2104 9346, State Key Laboratory of Tree Genetics and Breeding (Chinese Academy of Forestry), ; Beijing, China
                Article
                61510
                10.1038/s41598-024-61510-8
                11101485
                38760385
                dae1ad67-c281-42d4-8e02-eba515462b36
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 8 March 2024
                : 7 May 2024
                Funding
                Funded by: Heilongjiang Touyan Innovation Team Program
                Award ID: Tree Genetics and Breeding Innovation Team
                Award ID: Tree Genetics and Breeding Innovation Team
                Award ID: Tree Genetics and Breeding Innovation Team
                Award ID: Tree Genetics and Breeding Innovation Team
                Award ID: Tree Genetics and Breeding Innovation Team
                Award ID: Tree Genetics and Breeding Innovation Team
                Award ID: Tree Genetics and Breeding Innovation Team
                Award ID: Tree Genetics and Breeding Innovation Team
                Award ID: Tree Genetics and Breeding Innovation Team
                Award Recipient :
                Funded by: National Natural Science Foundation of China
                Award ID: Grant No. 31700595
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100018537, National Science and Technology Major Project;
                Award ID: 2018ZX08020003-001-001
                Award ID: 2018ZX08020003-001-001
                Award Recipient :
                Funded by: Fundamental Research Funds for the Central Universities
                Award ID: 2572019BA13
                Award Recipient :
                Categories
                Article
                Custom metadata
                © Springer Nature Limited 2024

                Uncategorized
                larix spp.,myb,peg stress,transient genetic transformation,drought,gene expression analysis,genomic analysis

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