23
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

      research-article
      1 , 2 , 3 , 4 , 1 , 5 , 1 , 3 , 3 , 6 , 1 , 3 , 3 , 1 , 3 , 7 , 8 , 1 , 9 , 3 , 2 , 3 , 3 , 4 , 7 , 1 , 1 , 3 , 3 , 3 , 1 , 9 , 10 , 10 , 3 , 11 , 8 , 2 , 12 , 12 , 13 , 14 , 15 , 16 , 3 , 17 , 18 , 19 , 12 , 20 , 21 , 4 , 22 , 23 , 3 , 19 , 5 , 2 , 1 , 24 ,
      Nature Communications
      Nature Publishing Group UK
      Microbial ecology, Evolutionary developmental biology

      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

          Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

          Abstract

          Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

          Related collections

          Most cited references85

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          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.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

              S Altschul (1997)
              The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
                Bookmark

                Author and article information

                Contributors
                francis.martin@inrae.fr
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                12 October 2020
                12 October 2020
                2020
                : 11
                : 5125
                Affiliations
                [1 ]GRID grid.29172.3f, ISNI 0000 0001 2194 6418, Université de Lorraine, Institut national de recherche pour l’agriculture, l’alimentation et l’ environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, ; 54280 Champenoux, France
                [2 ]GRID grid.418331.c, ISNI 0000 0001 2195 9606, Synthetic and Systems Biology Unit, Biological Research Centre, ; 6726 Szeged, Hungary
                [3 ]GRID grid.184769.5, ISNI 0000 0001 2231 4551, US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, ; Berkeley, CA USA
                [4 ]GRID grid.463764.4, ISNI 0000 0004 1798 275X, INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, ; 13009 Marseille, France
                [5 ]GRID grid.254277.1, ISNI 0000 0004 0486 8069, Biology Department, , Clark University, Lasry Center for Bioscience, ; 950 Main Street, Worcester, MA 01610 USA
                [6 ]GRID grid.17088.36, ISNI 0000 0001 2150 1785, Plant Soil and Microbial Sciences, Michigan State University, ; East Lansing, MI 48824 USA
                [7 ]GRID grid.451303.0, ISNI 0000 0001 2218 3491, Chemical & Biological Processes Development Group, Pacific Northwest National Laboratory, ; Richland, WA USA
                [8 ]GRID grid.418704.e, ISNI 0000 0004 0368 8584, Westerdijk Fungal Biodiversity Institute, ; Uppsalalaan 8, 3584 CT Utrecht, Netherlands
                [9 ]GRID grid.7605.4, ISNI 0000 0001 2336 6580, Department of Life Sciences and Systems Biology, , University of Torino, ; Viale Mattioli 25, 10125 Torino, Italy
                [10 ]GRID grid.419754.a, ISNI 0000 0001 2259 5533, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, ; Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
                [11 ]GRID grid.7489.2, ISNI 0000 0004 1937 0511, The Jacob Blaustein Institutes for Desert Research, Bergman Campus, Ben-Gurion University of The Negev, ; Beer-Sheva, Israel
                [12 ]GRID grid.418800.5, ISNI 0000 0004 0555 4846, Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, ; Videnska 1083, 14220 Praha 4, Czech Republic
                [13 ]GRID grid.4391.f, ISNI 0000 0001 2112 1969, Department Botany & Plant Pathology, , Oregon State University, ; Corvallis, OR USA
                [14 ]GRID grid.10939.32, ISNI 0000 0001 0943 7661, Natural History Museum, , University of Tartu, ; 14a Ravila, 50411 Tartu, Estonia
                [15 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Department of Forest Sciences, , University of Helsinki, ; Helsinki, Finland
                [16 ]GRID grid.263518.b, ISNI 0000 0001 1507 4692, Institute of Mountain Science, Faculty of Agriculture, Shinshu University, Minami-minowa, Kami-ina, ; Nagano, 399-4598 Japan
                [17 ]GRID grid.415444.4, Department of Key Laboratory, The 2nd Affiliated Hospital of Kunming Medical University, ; 374 Dian Mian Road, Kunming, 650101 Yunnan China
                [18 ]GRID grid.25073.33, ISNI 0000 0004 1936 8227, Department of Biology, , McMaster University, ; 1280 Main St. West, Hamilton, ON L8S 4K1 Canada
                [19 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Plant and Microbial Biology, , University of California – Berkeley, ; Berkeley, CA USA
                [20 ]GRID grid.26009.3d, ISNI 0000 0004 1936 7961, Department of Biology, , Duke University, ; Durham, NC 27708 USA
                [21 ]Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse, France
                [22 ]GRID grid.463764.4, ISNI 0000 0004 1798 275X, Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Univ., ; 13009 Marseille, France
                [23 ]GRID grid.412125.1, ISNI 0000 0001 0619 1117, Department of Biological Sciences, , King Abdulaziz University, ; Jeddah, Saudi Arabia
                [24 ]Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Tsinghua East Road Haidian District, Beijing, China
                Author information
                http://orcid.org/0000-0002-0620-5547
                http://orcid.org/0000-0002-2571-0274
                http://orcid.org/0000-0002-5236-7918
                http://orcid.org/0000-0002-5838-1972
                http://orcid.org/0000-0001-7712-7024
                http://orcid.org/0000-0003-0685-7307
                http://orcid.org/0000-0003-0121-1806
                http://orcid.org/0000-0002-8556-845X
                http://orcid.org/0000-0003-2915-2780
                http://orcid.org/0000-0002-8983-2721
                http://orcid.org/0000-0001-8299-3605
                http://orcid.org/0000-0002-3434-8588
                http://orcid.org/0000-0002-3136-8903
                Article
                18795
                10.1038/s41467-020-18795-w
                7550596
                33046698
                3f593a8c-1207-4485-9ccf-20aa06a09e87
                © The Author(s) 2020

                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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 22 January 2020
                : 16 September 2020
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                microbial ecology,evolutionary developmental biology
                Uncategorized
                microbial ecology, evolutionary developmental biology

                Comments

                Comment on this article