1
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Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 2024; 384:eadj4503. [PMID: 38662846 PMCID: PMC11298794 DOI: 10.1126/science.adj4503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.
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Affiliation(s)
- Dana A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 Research Campus Drive, Kannapolis, NC 28081, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - John F. Wolters
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Chao Liu
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Yonglin Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Jacek Kominek
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hayley R. Stoneman
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jenna VanDenAvond
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Caroline R. Miller
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Emily J. Ubbelohde
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kelly V. Buh
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Martin Jarzyna
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Max A. B. Haase
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Neža Čadež
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - Jeremy H. DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
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2
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Castel B, El Mahboubi K, Jacquet C, Delaux PM. Immunobiodiversity: Conserved and specific immunity across land plants and beyond. MOLECULAR PLANT 2024; 17:92-111. [PMID: 38102829 DOI: 10.1016/j.molp.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Angiosperms represent most plants that humans cultivate, grow, and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature, and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defense pathways. Exploring diversity at the genomic and functional levels demonstrates the conservation of these pathways across land plants, some of which are beyond plants. On basis of the conserved mechanisms, lineage-specific variations have occurred, leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species by integration of wild immune receptors or engineering of novel forms of receptors for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.
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Affiliation(s)
- Baptiste Castel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Karima El Mahboubi
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Christophe Jacquet
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France.
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3
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Cittadino GM, Andrews J, Purewal H, Estanislao Acuña Avila P, Arnone JT. Functional Clustering of Metabolically Related Genes Is Conserved across Dikarya. J Fungi (Basel) 2023; 9:jof9050523. [PMID: 37233234 DOI: 10.3390/jof9050523] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/08/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Transcriptional regulation is vital for organismal survival, with many layers and mechanisms collaborating to balance gene expression. One layer of this regulation is genome organization, specifically the clustering of functionally related, co-expressed genes along the chromosomes. Spatial organization allows for position effects to stabilize RNA expression and balance transcription, which can be advantageous for a number of reasons, including reductions in stochastic influences between the gene products. The organization of co-regulated gene families into functional clusters occurs extensively in Ascomycota fungi. However, this is less characterized within the related Basidiomycota fungi despite the many uses and applications for the species within this clade. This review will provide insight into the prevalence, purpose, and significance of the clustering of functionally related genes across Dikarya, including foundational studies from Ascomycetes and the current state of our understanding throughout representative Basidiomycete species.
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Affiliation(s)
- Gina M Cittadino
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Johnathan Andrews
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Harpreet Purewal
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | | | - James T Arnone
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
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4
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Gupta YK, Marcelino-Guimarães FC, Lorrain C, Farmer A, Haridas S, Ferreira EGC, Lopes-Caitar VS, Oliveira LS, Morin E, Widdison S, Cameron C, Inoue Y, Thor K, Robinson K, Drula E, Henrissat B, LaButti K, Bini AMR, Paget E, Singan V, Daum C, Dorme C, van Hoek M, Janssen A, Chandat L, Tarriotte Y, Richardson J, Melo BDVA, Wittenberg AHJ, Schneiders H, Peyrard S, Zanardo LG, Holtman VC, Coulombier-Chauvel F, Link TI, Balmer D, Müller AN, Kind S, Bohnert S, Wirtz L, Chen C, Yan M, Ng V, Gautier P, Meyer MC, Voegele RT, Liu Q, Grigoriev IV, Conrath U, Brommonschenkel SH, Loehrer M, Schaffrath U, Sirven C, Scalliet G, Duplessis S, van Esse HP. Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nat Commun 2023; 14:1835. [PMID: 37005409 PMCID: PMC10067951 DOI: 10.1038/s41467-023-37551-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/22/2023] [Indexed: 04/04/2023] Open
Abstract
With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world's most economically damaging agricultural diseases. Despite P. pachyrhizi's impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.
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Affiliation(s)
- Yogesh K Gupta
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Cécile Lorrain
- Pathogen Evolutionary Ecology, ETH Zürich, Zürich, Switzerland
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Everton Geraldo Capote Ferreira
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Valéria S Lopes-Caitar
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Liliane Santana Oliveira
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | | | | | - Connor Cameron
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Yoshihiro Inoue
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kathrin Thor
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kelly Robinson
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Elodie Drula
- AFMB, Aix-Marseille Univ., INRAE, Marseille, France
- Biodiversité et Biotechnologie Fongiques, INRAE, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aline Mara Rudsit Bini
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | - Eric Paget
- Bayer SAS, Crop Science Division, Lyon, France
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tobias I Link
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | - André N Müller
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Sabine Kind
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Stefan Bohnert
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Louisa Wirtz
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Maurício Conrado Meyer
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | | | - Qingli Liu
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Uwe Conrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | - Marco Loehrer
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | | | | | - H Peter van Esse
- 2Blades, Evanston, Illinois, USA.
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
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5
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Wint R, Salamov A, Grigoriev IV. Kingdom-Wide Analysis of Fungal Transcriptomes and tRNAs Reveals Conserved Patterns of Adaptive Evolution. Mol Biol Evol 2022; 39:6513383. [PMID: 35060603 PMCID: PMC8826637 DOI: 10.1093/molbev/msab372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.
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Affiliation(s)
- Rhondene Wint
- Molecular and Cell Biology Unit, Quantitative and Systems Biology Program, University of California Merced, Merced, CA, 95343, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720 US
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6
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Boekhout T, Aime MC, Begerow D, Gabaldón T, Heitman J, Kemler M, Khayhan K, Lachance MA, Louis EJ, Sun S, Vu D, Yurkov A. The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks. FUNGAL DIVERS 2021; 109:27-55. [PMID: 34720775 PMCID: PMC8550739 DOI: 10.1007/s13225-021-00475-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.
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Affiliation(s)
- Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - M. Catherine Aime
- Dept Botany and Plant Pathology, College of Agriculture, Purdue University, West Lafayette, IN 47907 USA
| | - Dominik Begerow
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC–CNS), Jordi Girona, 29, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Martin Kemler
- Evolution of Plants and Fungi, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Kantarawee Khayhan
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, University of Phayao, Phayao, 56000 Thailand
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada
| | - Edward J. Louis
- Department of Genetics and Genome Biology, Genetic Architecture of Complex Traits, University of Leicester, Leicester, LE1 7RH UK
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710 USA
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Andrey Yurkov
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Brunswick, Germany
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7
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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8
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Merényi Z, Prasanna AN, Wang Z, Kovács K, Hegedüs B, Bálint B, Papp B, Townsend JP, Nagy LG. Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi. Mol Biol Evol 2020; 37:2228-2240. [PMID: 32191325 PMCID: PMC7403615 DOI: 10.1093/molbev/msaa077] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Convergent evolution is pervasive in nature, but it is poorly understood how various constraints and natural selection limit the diversity of evolvable phenotypes. Here, we analyze the transcriptome across fruiting body development to understand the independent evolution of complex multicellularity in the two largest clades of fungi-the Agarico- and Pezizomycotina. Despite >650 My of divergence between these clades, we find that very similar sets of genes have convergently been co-opted for complex multicellularity, followed by expansions of their gene families by duplications. Over 82% of shared multicellularity-related gene families were expanding in both clades, indicating a high prevalence of convergence also at the gene family level. This convergence is coupled with a rich inferred repertoire of multicellularity-related genes in the most recent common ancestor of the Agarico- and Pezizomycotina, consistent with the hypothesis that the coding capacity of ancestral fungal genomes might have promoted the repeated evolution of complex multicellularity. We interpret this repertoire as an indication of evolutionary predisposition of fungal ancestors for evolving complex multicellular fruiting bodies. Our work suggests that evolutionary convergence may happen not only when organisms are closely related or are under similar selection pressures, but also when ancestral genomic repertoires render certain evolutionary trajectories more likely than others, even across large phylogenetic distances.
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Affiliation(s)
- Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Arun N Prasanna
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT
| | - Károly Kovács
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
- Hungarian Centre of Excellence for Molecular Medicine, Metabolic Systems Biology Lab, Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
- Hungarian Centre of Excellence for Molecular Medicine, Metabolic Systems Biology Lab, Szeged, Hungary
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University, New Haven, CT
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Szeged, Hungary
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9
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Wang B, Liang X, Gleason ML, Hsiang T, Zhang R, Sun G. A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi. BMC Genomics 2020; 21:321. [PMID: 32326892 PMCID: PMC7181583 DOI: 10.1186/s12864-020-6732-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/14/2020] [Indexed: 11/19/2022] Open
Abstract
Background The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface-dwelling extremophile, based on long-read DNA sequencing technology, to assess possible mechanisms associated with genome compaction. Results At 18.99 million bases (Mb), P. fructicola possesses one of the smallest known genomes sequence among filamentous fungi. The genome is highly compact relative to other fungi, with substantial reductions in repeat content, ribosomal DNA copies, tRNA gene quantity, and intron sizes, as well as intergenic lengths and the size of gene families. Transposons take up just 0.05% of the entire genome, and no full-length transposon was found. We concluded that reduced genome sizes in filamentous fungi such as P. fructicola, Taphrina deformans and Pneumocystis jirovecii occurred through reduction in ribosomal DNA copy number and reduced intron sizes. These dual mechanisms contrast with genome reduction in the yeast fungus Saccharomyces cerevisiae, whose small and compact genome is associated solely with intron loss. Conclusions Our results reveal a unique genomic compaction architecture of filamentous fungi inhabiting plant surfaces, and broaden the understanding of the mechanisms associated with compaction of fungal genomes.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.,MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
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10
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Prasanna AN, Gerber D, Kijpornyongpan T, Aime MC, Doyle VP, Nagy LG. Model Choice, Missing Data, and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships. Syst Biol 2020; 69:17-37. [PMID: 31062852 DOI: 10.1093/sysbio/syz029] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 11/12/2022] Open
Abstract
Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic data sets. Relationships between Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and allies (Ustilaginomycotina), and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene tree-based analyses of various phylogenomic data sets to examine the contribution of several potential sources of bias. We evaluate the contribution of biological causes (hard polytomy, incomplete lineage sorting) versus unmodeled evolutionary processes and factors that exacerbate their effects (e.g., fast-evolving sites and long-branch taxa) to inferences of basal Basidiomycota relationships. Bayesian Markov Chain Monte Carlo and likelihood mapping analyses reject the hard polytomy with confidence. In concatenated analyses, fast-evolving sites and oversimplified models of amino acid substitution favored the grouping of smuts with mushroom-forming fungi, often leading to maximal bootstrap support in both concatenation and coalescent analyses. On the contrary, the most conserved data subsets grouped rusts and allies with mushroom-forming fungi, although this relationship proved labile, sensitive to model choice, to different data subsets and to missing data. Excluding putative long-branch taxa, genes with high proportions of missing data and/or with strong signal failed to reveal a consistent trend toward one or the other topology, suggesting that additional sources of conflict are at play. While concatenated analyses yielded strong but conflicting support, individual gene trees mostly provided poor support for any resolution of rusts, smuts, and mushroom-forming fungi, suggesting that the true Basidiomycota tree might be in a part of tree space that is difficult to access using both concatenation and gene tree-based approaches. Inference-based assessments of absolute model fit strongly reject best-fit models for the vast majority of genes, indicating a poor fit of even the most commonly used models. While this is consistent with previous assessments of site-homogenous models of amino acid evolution, this does not appear to be the sole source of confounding signal. Our analyses suggest that topologies uniting smuts with mushroom-forming fungi can arise as a result of inappropriate modeling of amino acid sites that might be prone to systematic bias. We speculate that improved models of sequence evolution could shed more light on basal splits in the Basidiomycota, which, for now, remain unresolved despite the use of whole genome data.
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Affiliation(s)
- Arun N Prasanna
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary
| | - Daniel Gerber
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary.,Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1097, Hungary
| | | | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70803, USA
| | - Laszlo G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged 6726, Hungary
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11
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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12
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Sen D, Paul K, Saha C, Mukherjee G, Nag M, Ghosh S, Das A, Seal A, Tripathy S. A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1-a comparative genomics viewpoint. DNA Res 2019; 26:131-146. [PMID: 30615101 PMCID: PMC6476726 DOI: 10.1093/dnares/dsy044] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 12/05/2018] [Indexed: 01/30/2023] Open
Abstract
Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides. JGTA-S1 is a haploid yeast possessing several genes potentially facilitating its endophytic lifestyle such as those responsible for solubilizing phosphate and producing phytohormones. An intact mating-locus in JGTA-S1 raised the possibility of a yet unknown sexual reproductive cycle in Rhodotorula yeasts. Additionally, JGTA-S1 had functional anti-freezing genes and was also unique in lacking a functional nitrate-assimilation pathway—a feature that is associated with obligate biotrophs. Nitrogen-fixing endobacteria were found within JGTA-S1 that may circumvent this defective N-metabolism. JGTA-S1 genome data coupled with experimental evidence give us an insight into the nature of its beneficial interaction with plants.
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Affiliation(s)
- Diya Sen
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Karnelia Paul
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Chinmay Saha
- Department of Endocrinology & Metabolism, Institute of Post Graduate Medical Education & Research and SSKM Hospital, Kolkata, West Bengal, India
| | - Gairik Mukherjee
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Mayurakshi Nag
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Samrat Ghosh
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Abhishek Das
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
| | - Anindita Seal
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, India
| | - Sucheta Tripathy
- Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research, New Delhi, India
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13
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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14
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Nguyen HDT, Sultana T, Kesanakurti P, Hambleton S. Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat. IMA Fungus 2019; 10:11. [PMID: 32355611 PMCID: PMC7184893 DOI: 10.1186/s43008-019-0011-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022] Open
Abstract
Tilletia species cause diseases on grass hosts with some causing bunt diseases on wheat (Triticum). Two of the four species infecting wheat have restricted distributions globally and are subject to quarantine regulations to prevent their spread to new areas. Tilletia indica causes Karnal bunt and is regulated by many countries while the non-regulated T. walkeri is morphologically similar and very closely related phylogenetically, but infects ryegrass (Lolium) and not wheat. Tilletia controversa causes dwarf bunt of wheat (DB) and is also regulated by some countries, while the closely related but non-regulated species, T. caries and T. laevis, both cause common bunt of wheat (CB). Historically, diagnostic methods have relied on cryptic morphology to differentiate these species in subsamples from grain shipments. Of the DNA-based methods published so far, most have focused on sequence variation among tested strains at a single gene locus. To facilitate the development of additional molecular assays for diagnostics, we generated whole genome data for multiple strains of the two regulated wheat pathogens and their closest relatives. Depending on the species, the genomes were assembled into 907 to 4633 scaffolds ranging from 24 Mb to 30 Mb with 7842 to 9952 gene models predicted. Phylogenomic analyses confirmed the placement of Tilletia in the Exobasidiomycetes and showed that T. indica and T. walkeri were in one clade whereas T. controversa, T. caries and T. laevis grouped in a separate clade. Single copy and species-specific genes were identified by orthologous group analysis. Unique species-specific genes were identified and evaluated as suitable markers to differentiate the quarantine and non-quarantine species. After further analyses and manual inspection, primers and probes for the optimum candidate genes were designed and tested in silico, for validation in future wet-lab studies.
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Affiliation(s)
- Hai D. T. Nguyen
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6 Canada
| | - Tahera Sultana
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6 Canada
- Present Address: Research Farm – Vineland, London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Avenue N., Vineland Station, Ontario L0R 2E0 Canada
| | - Prasad Kesanakurti
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6 Canada
- Present Address: NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 Canada
| | - Sarah Hambleton
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6 Canada
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15
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Bewick AJ, Hofmeister BT, Powers RA, Mondo SJ, Grigoriev IV, James TY, Stajich JE, Schmitz RJ. Diversity of cytosine methylation across the fungal tree of life. Nat Ecol Evol 2019; 3:479-490. [PMID: 30778188 PMCID: PMC6533610 DOI: 10.1038/s41559-019-0810-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/13/2019] [Indexed: 12/22/2022]
Abstract
The generation of thousands of fungal genomes is leading to a better understanding of genes and genomic organization within the kingdom. However, the epigenome, which includes DNA and chromatin modifications, remains poorly investigated in fungi. Large comparative studies in animals and plants have deepened our understanding of epigenomic variation, particularly of the modified base 5-methylcytosine (5mC), but taxonomic sampling of disparate groups is needed to develop unifying explanations for 5mC variation. Here we utilize the largest phylogenetic resolution of 5mC methyltransferases (5mC MTases) and genome evolution to better understand levels and patterns of 5mC across fungi. We show that extant 5mC MTase genotypes are descendent from ancestral maintenance and de novo genotypes, whereas the 5mC MTases DIM-2 and RID are more recently derived, and that 5mC levels are correlated with 5mC MTase genotype and transposon content. Our survey also revealed that fungi lack canonical gene body methylation, which distinguishes fungal epigenomes from certain insect and plant species. However, some fungal species possess independently derived clusters of contiguous 5mC encompassing many genes. In some cases, DNA repair pathways and the N6-methyladenine (6mA) DNA modification negatively coevolved with 5mC pathways, which additionally contributed to interspecific epigenomic variation across fungi.
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Affiliation(s)
- Adam J Bewick
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | | | - Rob A Powers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
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16
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Bergeron MJ, Feau N, Stewart D, Tanguay P, Hamelin RC. Genome-enhanced detection and identification of fungal pathogens responsible for pine and poplar rust diseases. PLoS One 2019; 14:e0210952. [PMID: 30726264 PMCID: PMC6364900 DOI: 10.1371/journal.pone.0210952] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/06/2019] [Indexed: 01/19/2023] Open
Abstract
Biosurveillance is a proactive approach that may help to limit the spread of invasive fungal pathogens of trees, such as rust fungi which have caused some of the world's most damaging diseases of pines and poplars. Most of these fungi have a complex life cycle, with up to five spore stages, which is completed on two different hosts. They have a biotrophic lifestyle and may be propagated by asymptomatic plant material, complicating their detection and identification. A bioinformatics approach, based on whole genome comparison, was used to identify genome regions that are unique to the white pine blister rust fungus, Cronartium ribicola, the poplar leaf rust fungi Melampsora medusae and Melampsora larici-populina or to members of either the Cronartium and Melampsora genera. Species- and genus-specific real-time PCR assays, targeting these unique regions, were designed with the aim of detecting each of these five taxonomic groups. In total, twelve assays were developed and tested over a wide range of samples, including different spore types, different infected plant parts on the pycnio-aecial or uredinio-telial host, and captured insect vectors. One hundred percent detection accuracy was achieved for the three targeted species and two genera with either a single assay or a combination of two assays. This proof of concept experiment on pine and poplar leaf rust fungi demonstrates that the genome-enhanced detection and identification approach can be translated into effective real-time PCR assays to monitor tree fungal pathogens.
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Affiliation(s)
- Marie-Josée Bergeron
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, Québec, Canada
| | - Nicolas Feau
- Forest Sciences Centre, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Don Stewart
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, Québec, Canada
| | - Philippe Tanguay
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, Québec, Canada
| | - Richard C. Hamelin
- Forest Sciences Centre, Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologie Intégrative des Systèmes, Université Laval, Québec, Québec, Canada
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Kijpornyongpan T, Mondo SJ, Barry K, Sandor L, Lee J, Lipzen A, Pangilinan J, LaButti K, Hainaut M, Henrissat B, Grigoriev IV, Spatafora JW, Aime MC. Broad Genomic Sampling Reveals a Smut Pathogenic Ancestry of the Fungal Clade Ustilaginomycotina. Mol Biol Evol 2018; 35:1840-1854. [DOI: 10.1093/molbev/msy072] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Juna Lee
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | | | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN
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Abstract
The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.
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Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi. Sci Rep 2018; 8:6321. [PMID: 29679020 PMCID: PMC5910433 DOI: 10.1038/s41598-018-24686-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/06/2018] [Indexed: 01/09/2023] Open
Abstract
Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.
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Abstract
The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.
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21
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The only known white blister rust on a basal angiosperm is a member of the genus Albugo. ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-017-0353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Mishra B, Choi YJ, Thines M. Phylogenomics of Bartheletia paradoxa reveals its basal position in Agaricomycotina and that the early evolutionary history of basidiomycetes was rapid and probably not strictly bifurcating. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1349-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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23
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24
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Dupont PY, Cox MP. Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi. G3 (BETHESDA, MD.) 2017; 7:1301-1314. [PMID: 28235827 PMCID: PMC5386878 DOI: 10.1534/g3.116.038448] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/17/2017] [Indexed: 12/26/2022]
Abstract
Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported.
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Affiliation(s)
- Pierre-Yves Dupont
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
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25
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Castanera R, Borgognone A, Pisabarro AG, Ramírez L. Biology, dynamics, and applications of transposable elements in basidiomycete fungi. Appl Microbiol Biotechnol 2017; 101:1337-1350. [PMID: 28074220 DOI: 10.1007/s00253-017-8097-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/20/2016] [Accepted: 01/02/2017] [Indexed: 11/25/2022]
Abstract
The phylum Basidiomycota includes filamentous fungi and yeast species with different ecological and genomic characteristics. Transposable elements (TEs) are abundant components of most eukaryotic genomes, and their transition from being genomic parasites to key drivers of genomic architecture, functionality, and evolution is a subject receiving much attention. In light of the abundant genomic information released during the last decade, the aims of this mini-review are to discuss the dynamics and impact of TEs in basidiomycete fungi. To do this, we surveyed and explored data from 75 genomes, which encompass the phylogenetic diversity of the phylum Basidiomycota. We describe annotation approaches and analyze TE distribution in the context of species phylogeny and genome size. Further, we review the most relevant literature about the role of TEs in species lifestyle, their impact on genome architecture and functionality, and the defense mechanisms evolved to control their proliferation. Finally, we discuss potential applications of TEs that can drive future innovations in fungal research.
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Affiliation(s)
- Raúl Castanera
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Alessandra Borgognone
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Antonio G Pisabarro
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain
| | - Lucía Ramírez
- Genetics and Microbiology Research Group, Department of Agrarian Production, Public University of Navarre, 31006, Pamplona, Spain.
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Phylogenetics and Phylogenomics of Rust Fungi. FUNGAL PHYLOGENETICS AND PHYLOGENOMICS 2017; 100:267-307. [DOI: 10.1016/bs.adgen.2017.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Johns AMB, Love J, Aves SJ. Four Inducible Promoters for Controlled Gene Expression in the Oleaginous Yeast Rhodotorula toruloides. Front Microbiol 2016; 7:1666. [PMID: 27818654 PMCID: PMC5073140 DOI: 10.3389/fmicb.2016.01666] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/05/2016] [Indexed: 01/24/2023] Open
Abstract
Rhodotorula (Rhodosporidium) toruloides is an oleaginous yeast with great biotechnological potential, capable of accumulating lipid up to 70% of its dry biomass, and of carotenoid biosynthesis. However, few molecular genetic tools are available for manipulation of this basidiomycete yeast and its high genomic GC content can make routine cloning difficult. We have developed plasmid vectors for transformation of R. toruloides which include elements for Saccharomyces cerevisiae in-yeast assembly; this method is robust to the assembly of GC-rich DNA and of large plasmids. Using such vectors we screened for controllable promoters, and identified inducible promoters from the genes NAR1, ICL1, CTR3, and MET16. These four promoters have independent induction/repression conditions and exhibit different levels and rates of induction in R. toruloides, making them appropriate for controllable transgene expression in different experimental situations. Nested deletions were used to identify regulatory regions in the four promoters, and to delimit the minimal inducible promoters, which are as small as 200 bp for the NAR1 promoter. The NAR1 promoter shows very tight regulation under repressed conditions as determined both by an EGFP reporter gene and by conditional rescue of a leu2 mutant. These new tools facilitate molecular genetic manipulation and controllable gene expression in R. toruloides.
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Affiliation(s)
| | - John Love
- Department of Biosciences, University of Exeter Exeter, UK
| | - Stephen J Aves
- Department of Biosciences, University of Exeter Exeter, UK
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28
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Novel fungi from an ancient niche: cercosporoid and related sexual morphs on ferns. Persoonia - Molecular Phylogeny and Evolution of Fungi 2016; 37:106-141. [PMID: 28232762 PMCID: PMC5315284 DOI: 10.3767/003158516x690934] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/25/2015] [Indexed: 11/25/2022]
Abstract
The fern flora of the world (Pteridophyta) has direct evolutionary links with the earliest vascular plants that appeared in the late Devonian. Knowing the mycobiota associated to this group of plants is critical for a full understanding of the Fungi. Nevertheless, perhaps because of the minor economic significance of ferns, this niche remains relatively neglected by mycologists. Cercosporoid fungi represent a large assemblage of fungi belonging to the Mycosphaerellaceae and Teratosphaeriaceae (Ascomycota) having cercospora-like asexual morphs. They are well-known pathogens of many important crops, occurring on a wide host range. Here, the results of a taxonomic study of cercosporoid fungi collected on ferns in Brazil are presented. Specimens were obtained from most Brazilian regions and collected over a 7-yr period (2009–2015). Forty-three isolates of cercosporoid and mycosphaerella-like species, collected from 18 host species, representing 201 localities, were studied. This resulted in a total of 21 frond-spotting taxa, which were identified based on morphology, ecology and sequence data of five genomic loci (actin, calmodulin, ITS, LSU and partial translation elongation factor 1-α). One novel genus (Clypeosphaerella) and 15 novel species (Cercospora samambaiae, Clypeosphaerella sticheri, Neoceratosperma alsophilae, N. cyatheae, Paramycosphaerella blechni, Pa. cyatheae, Pa. dicranopteridis-flexuosae, Pa. sticheri, Phaeophleospora pteridivora, Pseudocercospora brackenicola, Ps. paranaensis, Ps. serpocaulonicola, Ps. trichogena, Xenomycosphaerella diplazii and Zasmidium cyatheae) are introduced. Furthermore, 11 new combinations (Clypeosphaerella quasiparkii, Neoceratosperma yunnanensis, Paramycosphaerella aerohyalinosporum, Pa. dicranopteridis, Pa. gleicheniae, Pa. irregularis, Pa. madeirensis, Pa. nabiacense, Pa. parkii, Pa. pseudomarksii and Pa. vietnamensis) are proposed. Finally, nine new host associations are recorded for the following known fungal species: Cercospora coniogrammes, Cercospora sp. Q, Ps. abacopteridicola, Ps. lygodiicola and Ps. thelypteridis.
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Latest Developments in the Research of Rust Fungi and Their Allies (Pucciniomycotina). ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-29137-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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30
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Qhanya LB, Matowane G, Chen W, Sun Y, Letsimo EM, Parvez M, Yu JH, Mashele SS, Syed K. Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens. PLoS One 2015; 10:e0142100. [PMID: 26536121 PMCID: PMC4633277 DOI: 10.1371/journal.pone.0142100] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022] Open
Abstract
Fungi are an exceptional source of diverse and novel cytochrome P450 monooxygenases (P450s), heme-thiolate proteins, with catalytic versatility. Agaricomycotina saprophytes have yielded most of the available information on basidiomycete P450s. This resulted in observing similar P450 family types in basidiomycetes with few differences in P450 families among Agaricomycotina saprophytes. The present study demonstrated the presence of unique P450 family patterns in basidiomycete biotrophic plant pathogens that could possibly have originated from the adaptation of these species to different ecological niches (host influence). Systematic analysis of P450s in basidiomycete biotrophic plant pathogens belonging to three different orders, Agaricomycotina (Armillaria mellea), Pucciniomycotina (Melampsora laricis-populina, M. lini, Mixia osmundae and Puccinia graminis) and Ustilaginomycotina (Ustilago maydis, Sporisorium reilianum and Tilletiaria anomala), revealed the presence of numerous putative P450s ranging from 267 (A. mellea) to 14 (M. osmundae). Analysis of P450 families revealed the presence of 41 new P450 families and 27 new P450 subfamilies in these biotrophic plant pathogens. Order-level comparison of P450 families between biotrophic plant pathogens revealed the presence of unique P450 family patterns in these organisms, possibly reflecting the characteristics of their order. Further comparison of P450 families with basidiomycete non-pathogens confirmed that biotrophic plant pathogens harbour the unique P450 families in their genomes. The CYP63, CYP5037, CYP5136, CYP5137 and CYP5341 P450 families were expanded in A. mellea when compared to other Agaricomycotina saprophytes and the CYP5221 and CYP5233 P450 families in P. graminis and M. laricis-populina. The present study revealed that expansion of these P450 families is due to paralogous evolution of member P450s. The presence of unique P450 families in these organisms serves as evidence of how a host/ecological niche can influence shaping the P450 content of an organism. The present study initiates our understanding of P450 family patterns in basidiomycete biotrophic plant pathogens.
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Affiliation(s)
- Lehlohonolo Benedict Qhanya
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Godfrey Matowane
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Yuxin Sun
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Elizabeth Mpholoseng Letsimo
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Mohammad Parvez
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI, 53706, United States of America
| | - Samson Sitheni Mashele
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
| | - Khajamohiddin Syed
- Unit for Drug Discovery Research, Department of Health Sciences, Faculty of Health and Environmental Sciences, Central University of Technology, Bloemfontein 9300, Free State, South Africa
- * E-mail:
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Nguyen HD, Chabot D, Hirooka Y, Roberson RW, Seifert KA. Basidioascus undulatus: genome, origins, and sexuality. IMA Fungus 2015; 6:215-31. [PMID: 26203425 PMCID: PMC4500085 DOI: 10.5598/imafungus.2015.06.01.14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/13/2015] [Indexed: 11/24/2022] Open
Abstract
Basidioascus undulatus is a soil basidiomycete belonging to the order Geminibasidiales. The taxonomic status of the order was unclear as originally it was only tentatively classified in the class Wallemiomycetes. The fungi in Geminibasidiales have an ambiguously defined sexual cycle. In this study, we sequenced the genome of B. undulatus to gain insights into its sexuality and evolutionary origins. The assembled genome draft was approximately 32 Mb in size, had a median nucleotide coverage of 24X, and contained 6123 predicted genes. Previous morphological descriptions of B. undulatus relied on interpretation of putative sexual structures. In this study, nuclear staining and confocal microscopy showed meiosis occurring in basidia and genome analysis confirmed the existence of genes involved in meiosis and mating. Using 35 protein-coding genes extracted from genomic information, phylogenomic and molecular dating analyses confirmed that B. undulatus indeed belongs to a lineage distantly related to Wallemia while retaining a basal position in Agaricomycotina. These results, combined with differences in septal pore morphology, led us to move the order Geminibasidiales out of the Wallemiomycetes and into the new class Geminibasidiomycetes cl. nov. Finally, the concept of Agaricomycotina is emended to include both Wallemiomycetes and Geminibasidiomycetes.
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Affiliation(s)
- Hai D.T. Nguyen
- Department of Biology, Faculty of Science, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Denise Chabot
- Microscopy Centre, Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Yuuri Hirooka
- Department of Biology, Faculty of Science, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Robert W. Roberson
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-1601, USA
| | - Keith A. Seifert
- Department of Biology, Faculty of Science, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, K1N 6N5, Canada
- Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
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Sharma R, Gassel S, Steiger S, Xia X, Bauer R, Sandmann G, Thines M. The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina. BMC Genomics 2015; 16:233. [PMID: 25887949 PMCID: PMC4393869 DOI: 10.1186/s12864-015-1380-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/21/2015] [Indexed: 11/14/2022] Open
Abstract
Background Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota. Results The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned. Conclusions The current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1380-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
| | - Sören Gassel
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Sabine Steiger
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany.
| | - Robert Bauer
- Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
| | - Gerhard Sandmann
- Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany.
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. .,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
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Struck C. Amino acid uptake in rust fungi. FRONTIERS IN PLANT SCIENCE 2015; 6:40. [PMID: 25699068 PMCID: PMC4318339 DOI: 10.3389/fpls.2015.00040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/15/2015] [Indexed: 05/05/2023]
Abstract
The plant pathogenic rust fungi colonize leaf tissue and feed off their host plants without killing them. Certain economically important species of different genera such as Melampsora, Phakopsora, Puccinia, or Uromyces are extensively studied for resolving the mechanisms of the obligate biotrophy. As obligate parasites rust fungi only can complete their life cycle on living hosts where they grow through the leaf tissue by developing an extended network of intercellular hyphae from which intracellular haustoria are differentiated. Haustoria are involved in key functions of the obligate biotrophic lifestyle: suppressing host defense responses and acquiring nutrients. This review provides a survey of rust fungi nitrogen nutrition with special emphasis on amino acid uptake. A variety of sequences of amino acid transporter genes of rust fungi have been published; however, transport activity of only three in planta highly up-regulated amino acid permeases have been characterized. Functional and immunohistochemical investigations have shown the specificity and localization of these transporters. Sequence data of various genome projects allowed identification of numerous rust amino acid transporter genes. An in silico analysis reveals that these genes can be classified into different transporter families. In addition, genetic and molecular data of amino acid transporters have provided new insights in the corresponding metabolic pathways.
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Affiliation(s)
- Christine Struck
- *Correspondence: Christine Struck, Group Crop Health, Faculty of Agricultural and Environmental Sciences, University of Rostock, Satower Straße 48, 18059 Rostock, Germany e-mail:
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Lo Presti L, Lanver D, Schweizer G, Tanaka S, Liang L, Tollot M, Zuccaro A, Reissmann S, Kahmann R. Fungal effectors and plant susceptibility. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:513-45. [PMID: 25923844 DOI: 10.1146/annurev-arplant-043014-114623] [Citation(s) in RCA: 659] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants can be colonized by fungi that have adopted highly diverse lifestyles, ranging from symbiotic to necrotrophic. Colonization is governed in all systems by hundreds of secreted fungal effector molecules. These effectors suppress plant defense responses and modulate plant physiology to accommodate fungal invaders and provide them with nutrients. Fungal effectors either function in the interaction zone between the fungal hyphae and host or are transferred to plant cells. This review describes the effector repertoires of 84 plant-colonizing fungi. We focus on the mechanisms that allow these fungal effectors to promote virulence or compatibility, discuss common plant nodes that are targeted by effectors, and provide recent insights into effector evolution. In addition, we address the issue of effector uptake in plant cells and highlight open questions and future challenges.
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Affiliation(s)
- Libera Lo Presti
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; , , , , , , , ,
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Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts. Nat Commun 2014; 5:4471. [PMID: 25034666 DOI: 10.1038/ncomms5471] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/19/2014] [Indexed: 01/29/2023] Open
Abstract
Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms arose early in fungal evolution and became dominant independently in multiple clades, most likely via parallel diversification of Zn-cluster transcription factors, a fungal-specific family involved in regulating yeast-filamentous switches. Our results imply that convergent evolution can happen by the repeated deployment of a conserved genetic toolkit for the same function in distinct clades via regulatory evolution. We suggest that this mechanism might be a common source of evolutionary convergence even at large time scales.
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Draft Genome Sequence of a Rare Smut Relative, Tilletiaria anomala UBC 951. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00539-14. [PMID: 24926052 PMCID: PMC4056295 DOI: 10.1128/genomea.00539-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The draft genome sequence of the smut fungus Tilletiaria anomala UBC 951 (Basidiomycota, Ustilaginomycotina) is presented. The sequenced genome size is 18.7 Mb, consisting of 289 scaffolds and a total of 6,810 predicted genes. This is the first genome sequence published for a fungus in the order Georgefisheriales (Exobasidiomycetes).
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Cristancho MA, Botero-Rozo DO, Giraldo W, Tabima J, Riaño-Pachón DM, Escobar C, Rozo Y, Rivera LF, Durán A, Restrepo S, Eilam T, Anikster Y, Gaitán AL. Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales. FRONTIERS IN PLANT SCIENCE 2014; 5:594. [PMID: 25400655 PMCID: PMC4215621 DOI: 10.3389/fpls.2014.00594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 10/11/2014] [Indexed: 05/20/2023]
Abstract
Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.
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Affiliation(s)
- Marco A. Cristancho
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- *Correspondence: Marco A. Cristancho, Department of Plant Pathology, National Center for Coffee Research – CENICAFÉ, Km 4 vía a Manizales, Chinchiná 2427, Colombia e-mail:
| | - David Octavio Botero-Rozo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | - William Giraldo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Javier Tabima
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | | | - Carolina Escobar
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Yomara Rozo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Luis F. Rivera
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Andrés Durán
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | - Tamar Eilam
- Institute for Cereal Crops Improvement, Tel Aviv UniversityTel Aviv, Israel
| | - Yehoshua Anikster
- Institute for Cereal Crops Improvement, Tel Aviv UniversityTel Aviv, Israel
| | - Alvaro L. Gaitán
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
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Pendleton AL, Smith KE, Feau N, Martin FM, Grigoriev IV, Hamelin R, Nelson CD, Burleigh JG, Davis JM. Duplications and losses in gene families of rust pathogens highlight putative effectors. FRONTIERS IN PLANT SCIENCE 2014; 5:299. [PMID: 25018762 PMCID: PMC4071342 DOI: 10.3389/fpls.2014.00299] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/06/2014] [Indexed: 05/20/2023]
Abstract
Rust fungi are a group of fungal pathogens that cause some of the world's most destructive diseases of trees and crops. A shared characteristic among rust fungi is obligate biotrophy, the inability to complete a lifecycle without a host. This dependence on a host species likely affects patterns of gene expansion, contraction, and innovation within rust pathogen genomes. The establishment of disease by biotrophic pathogens is reliant upon effector proteins that are encoded in the fungal genome and secreted from the pathogen into the host's cell apoplast or within the cells. This study uses a comparative genomic approach to elucidate putative effectors and determine their evolutionary histories. We used OrthoMCL to identify nearly 20,000 gene families in proteomes of 16 diverse fungal species, which include 15 basidiomycetes and one ascomycete. We inferred patterns of duplication and loss for each gene family and identified families with distinctive patterns of expansion/contraction associated with the evolution of rust fungal genomes. To recognize potential contributors for the unique features of rust pathogens, we identified families harboring secreted proteins that: (i) arose or expanded in rust pathogens relative to other fungi, or (ii) contracted or were lost in rust fungal genomes. While the origin of rust fungi appears to be associated with considerable gene loss, there are many gene duplications associated with each sampled rust fungal genome. We also highlight two putative effector gene families that have expanded in Cqf that we hypothesize have roles in pathogenicity.
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Affiliation(s)
- Amanda L. Pendleton
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
| | - Katherine E. Smith
- Southern Research Station, Southern Institute of Forest Genetics, USDA Forest ServiceSaucier, MS, USA
| | - Nicolas Feau
- Department of Forest Sciences, University of British ColumbiaVancouver, BC, Canada
| | - Francis M. Martin
- Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, INRA-Nancy, UMR Institut National de la Recherche Agronomique – Université de LorraineChampenoux, France
| | - Igor V. Grigoriev
- US Department of Energy, Joint Genome InstituteWalnut Creek, CA, USA
| | - Richard Hamelin
- Department of Forest Sciences, University of British ColumbiaVancouver, BC, Canada
| | - C. Dana Nelson
- Southern Research Station, Southern Institute of Forest Genetics, USDA Forest ServiceSaucier, MS, USA
| | - J. Gordon Burleigh
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
- Biology Department, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
| | - John M. Davis
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
- School of Forest Resources and Conservation, University of FloridaGainesville, FL, USA
- *Correspondence: John M. Davis, School of Forest Resources and Conservation, University of Florida, 365 Newins-Ziegler Hall, Gainesville, FL 32611, USA e-mail:
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