0
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Transcriptome analysis highlights the influence of temperature on hydrolase and traps in nematode-trapping fungi

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Pine wilt disease caused by Bursaphelenchus xylophilus poses a serious threat to the economic and ecological value of forestry. Nematode trapping fungi trap and kill nematodes using specialized trapping devices, which are highly efficient and non-toxic to the environment, and are very promising for use as biological control agents. In this study, we isolated several nematode-trapping fungi from various regions and screened three for their high nematocidal efficiency. However, the effectiveness of these fungi as nematicides is notably influenced by temperature and exhibits different morphologies in response to temperature fluctuations, which are categorized as “NA,” “thin,” “dense,” and “sparse.” The trend of trap formation with temperature was consistent with the trend of nematocidal efficiency with temperature. Both of which initially increased and then decreased with increasing temperature. Among them, Arthrobotrys cladodes exhibited the highest level of nematocidal activity and trap formation among the tested species. Transcriptome data were collected from A. cladodes with various trap morphologies. Hydrolase activity was significantly enriched according to GO and KEGG enrichment analyses. Eight genes related to hydrolases were found to be consistent with the trend of trap morphology with temperature. Weighted gene co-expression analysis and the Cytoscape network revealed that these 8 genes are associated with either mitosis or autophagy. This suggests that they contribute to the formation of “dense” structures in nematode-trapping fungi. One of these genes is the serine protein hydrolase gene involved in autophagy. This study reveals a potentially critical role for hydrolases in trap formation and nematocidal efficiency. And presents a model where temperature affects trap formation and nematocidal efficiency by influencing the serine protease prb1 involved in the autophagy process.

          Related collections

          Most cited references56

          • Record: found
          • Abstract: found
          • Article: not found

          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.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Fast gapped-read alignment with Bowtie 2.

            As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              WGCNA: an R package for weighted correlation network analysis

              Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at .
                Bookmark

                Author and article information

                Contributors
                URI : http://loop.frontiersin.org/people/2580827/overviewRole: Role: Role: Role: Role: Role: Role: Role: Role: Role:
                URI : http://loop.frontiersin.org/people/2120379/overviewRole:
                URI : http://loop.frontiersin.org/people/1925762/overviewRole:
                Role: Role: Role:
                Role: Role:
                Role: Role: Role:
                URI : http://loop.frontiersin.org/people/1743938/overviewRole: Role: Role: Role:
                URI : http://loop.frontiersin.org/people/326296/overviewRole: Role: Role: Role:
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                07 May 2024
                2024
                : 15
                : 1384459
                Affiliations
                [1] 1Key Laboratory of Alien Forest Pest Detection and Control-Heilongjiang Province, School of Forestry, Northeast Forestry University , Harbin, China
                [2] 2Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration , Shenyang, China
                [3] 3Key Laboratory of Forest Plant Ecology, Ministry of Education, School of Forestry, Northeast Forestry University , Harbin, China
                [4] 4State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University , Harbin, China
                Author notes

                Edited by: Brianna R. Beechler, Oregon State University, United States

                Reviewed by: Zhang Shouke, Zhejiang Agriculture and Forestry University, China

                Yunsheng Wang, Hunan Agricultural University, China

                *Correspondence: Yantao Zhou, zhouyantao2023@ 123456163.com

                These authors have contributed equally to this work

                Article
                10.3389/fmicb.2024.1384459
                11106486
                38774504
                1cd6ae81-b7b5-4691-83f5-a0b69272edb3
                Copyright © 2024 Jia, Xia, Zhang, Liang, Zhuang, Zhou, Li and Wang.

                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
                : 09 February 2024
                : 01 April 2024
                Page count
                Figures: 8, Tables: 0, Equations: 1, References: 56, Pages: 14, Words: 8382
                Funding
                The authors declare that financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Science Foundation of China (31971656).
                Categories
                Microbiology
                Original Research
                Custom metadata
                Microbial Symbioses

                Microbiology & Virology
                nematode-trapping fungi,arthrobotrys cladodes,traps,bursaphelenchus xylophilus,rna-seq

                Comments

                Comment on this article