1
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Sperschneider J, Yildirir G, Rizzi YS, Malar C M, Mayrand Nicol A, Sorwar E, Villeneuve-Laroche M, Chen ECH, Iwasaki W, Brauer EK, Bosnich W, Gutjahr C, Corradi N. Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host-plant interactions. Nat Microbiol 2023; 8:2142-2153. [PMID: 37884816 DOI: 10.1038/s41564-023-01495-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are prominent root symbionts that can carry thousands of nuclei deriving from two parental strains in a large syncytium. These co-existing genomes can also vary in abundance with changing environmental conditions. Here we assemble the nuclear genomes of all four publicly available AMF heterokaryons using PacBio high-fidelity and Hi-C sequencing. We find that the two co-existing genomes of these strains are phylogenetically related but differ in structure, content and epigenetics. We confirm that AMF heterokaryon genomes vary in relative abundance across conditions and show this can lead to nucleus-specific differences in expression during interactions with plants. Population analyses also reveal signatures of genetic exchange indicative of past events of sexual reproduction in these strains. This work uncovers the origin and contribution of two nuclear genomes in AMF heterokaryons and opens avenues for the improvement and environmental application of these strains.
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Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Yanina S Rizzi
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mathu Malar C
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Essam Sorwar
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Eric C H Chen
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Elizabeth K Brauer
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
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2
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James TY. Sex Without Sexes: Can the Cost of Finding a Mate Explain Diversity in Fungal Mating Systems? Integr Comp Biol 2023; 63:922-935. [PMID: 37218718 DOI: 10.1093/icb/icad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023] Open
Abstract
Eukaryotes have evolved myriad ways of uniting gametes during sexual reproduction. A repeated pattern is the convergent evolution of a mating system with the fusion of larger gametes with smaller gametes (anisogamy) from that of fusion between morphologically identical gametes (isogamy). In anisogamous species, sexes are defined as individuals that produce only one gamete type. Although sexes abound throughout Eukarya, in fungi there are no biological sexes, because even in anisogamous species, individuals are hermaphroditic and produce both gamete types. For this reason, the term mating types is preferred over sexes, and, thus defined, only individuals of differing mating types can mate (homoallelic incompatibility). In anisogamous fungal species, there is scant evidence that there are more than two mating types, and this may be linked to genetic constraints, such as the use of mating types to determine the inheritance of cytoplasmic genomes. However, the mushroom fungi (Agaricomycetes) stand out as having both large numbers of mating types within a species, which will allow nearly all individuals to be compatible with each other, and reciprocal exchange of nuclei during mating, which will avoid cytoplasmic mixing and cyto-nuclear conflicts. Although the limitation of mating types to two in most fungi is consistent with the cyto-nuclear conflicts model, there are many facets of the Agaricomycete life cycle that also suggest they will demand a high outbreeding efficiency. Specifically, they are mostly obligately sexual and outcrossing, inhabit complex competitive niches, and display broadcast spore dispersal. Subsequently, the Agaricomycete individual pays a high cost to being choosy when encountering a mate. Here, I discuss the costs of mate finding and choice and demonstrate how most fungi have multiple ways of reducing these costs, which can explain why mating types are mostly limited to two per species. Nevertheless, it is perplexing that fungi have not evolved multiple mating types on more occasions nor evolved sexes. The few exceptions to these rules suggest that it is dictated by both molecular and evolutionary constraints.
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Affiliation(s)
- Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Gryganskyi AP, Golan J, Muszewska A, Idnurm A, Dolatabadi S, Mondo SJ, Kutovenko VB, Kutovenko VO, Gajdeczka MT, Anishchenko IM, Pawlowska J, Tran NV, Ebersberger I, Voigt K, Wang Y, Chang Y, Pawlowska TE, Heitman J, Vilgalys R, Bonito G, Benny GL, Smith ME, Reynolds N, James TY, Grigoriev IV, Spatafora JW, Stajich JE. Sequencing the Genomes of the First Terrestrial Fungal Lineages: What Have We Learned? Microorganisms 2023; 11:1830. [PMID: 37513002 PMCID: PMC10386755 DOI: 10.3390/microorganisms11071830] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/13/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades-primarily plant-associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.
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Affiliation(s)
- Andrii P. Gryganskyi
- Division of Biological & Nanoscale Technologies, UES, Inc., Dayton, OH 45432, USA
| | - Jacob Golan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Anna Muszewska
- Institute of Biochemistry & Biophysics, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Somayeh Dolatabadi
- Biology Department, Hakim Sabzevari University, Sabzevar 96179-76487, Iran;
| | - Stephen J. Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
| | - Vira B. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | - Volodymyr O. Kutovenko
- Department of Agrobiology, National University of Life & Environmental Sciences, 03041 Kyiv, Ukraine; (V.B.K.)
| | | | - Iryna M. Anishchenko
- MG Kholodny Institute of Botany, National Academy of Sciences, 01030 Kyiv, Ukraine;
| | - Julia Pawlowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological & Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland;
| | - Ngoc Vinh Tran
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Ingo Ebersberger
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Kerstin Voigt
- Leibniz Institute for Natural Product Research & Infection Biology, 07745 Jena, Germany; (I.E.); (K.V.)
| | - Yan Wang
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada;
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Ying Chang
- Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore;
| | - Teresa E. Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Joseph Heitman
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, NC 27708, USA;
| | - Gregory Bonito
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA;
| | - Gerald L. Benny
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Matthew E. Smith
- Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA; (N.V.T.); (G.L.B.); (M.E.S.)
| | - Nicole Reynolds
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA; (T.E.P.); (N.R.)
| | - Timothy Y. James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (S.J.M.); (I.V.G.)
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Joseph W. Spatafora
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
| | - Jason E. Stajich
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 93106, USA;
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4
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Li H, Xu J, Wang S, Wang P, Rao W, Hou B, Zhang Y. Genetic Differentiation and Widespread Mitochondrial Heteroplasmy among Geographic Populations of the Gourmet Mushroom Thelephora ganbajun from Yunnan, China. Genes (Basel) 2022; 13:genes13050854. [PMID: 35627240 PMCID: PMC9141859 DOI: 10.3390/genes13050854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022] Open
Abstract
The mitochondrial genomes are generally considered non-recombining and homoplasmic in nature. However, our previous study provided the first evidence of extensive and stable mitochondrial heteroplasmy in natural populations of the basidiomycete fungus Thelephora ganbajun from Yunnan province, China. The heteroplasmy was characterized by the presence of two types of introns residing at adjacent but different sites in the cytochrome oxidase subunits I (cox1) gene within an individual strain. However, the frequencies of these two introns among isolates from different geographical populations and the implications for the genetic structure in natural populations have not been investigated. In this study, we analyzed DNA sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster among 489 specimens from 30 geographic locations from Yunnan and compared that variation with distribution patterns of the two signature introns in the cox1 gene that are indicative of heteroplasmy in this species. In our samples, evidence for gene flow, abundant genetic diversity, and genotypic uniqueness among geographic samples in Yunnan were revealed by ITS sequence variation. While there was insignificant positive correlation between geographic distance and genetic differentiation among the geographic samples based on ITS sequences, a moderate significant correlation was found between ITS sequence variation, geographical distance of sampling sites, and distribution patterns of the two heteroplasmic introns in the cox1 gene. Interestingly, there was a significantly negative correlation between the copy numbers of the two co-existing introns. We discussed the implications of our results for a better understanding of the spread of stable mitochondrial heteroplasmy, mito-nuclear interactions, and conservation of this important gourmet mushroom.
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Affiliation(s)
- Haixia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Shaojuan Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Pengfei Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
| | - Wanqin Rao
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Bin Hou
- School of Life Science, Yunnan University, Kunming 650032, China; (W.R.); (B.H.)
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650032, China; (H.L.); (J.X.); (S.W.); (P.W.)
- Correspondence:
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5
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van de Peppel LJJ, Nieuwenhuis M, Auxier B, Grum-Grzhimaylo AA, Cárdenas ME, de Beer ZW, Lodge DJ, Smith ME, Kuyper TW, Franco-Molano AE, Baroni TJ, Aanen DK. Ancestral predisposition toward a domesticated lifestyle in the termite-cultivated fungus Termitomyces. Curr Biol 2021; 31:4413-4421.e5. [PMID: 34403645 DOI: 10.1016/j.cub.2021.07.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/22/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022]
Abstract
The ancestor of termites relied on gut symbionts for degradation of plant material, an association that persists in all termite families.1,2 However, the single-lineage Macrotermitinae has additionally acquired a fungal symbiont that complements digestion of food outside the termite gut.3 Phylogenetic analysis has shown that fungi grown by these termites form a clade-the genus Termitomyces-but the events leading toward domestication remain unclear.4 To address this, we reconstructed the lifestyle of the common ancestor of Termitomyces using a combination of ecological data with a phylogenomic analysis of 21 related non-domesticated species and 25 species of Termitomyces. We show that the closely related genera Blastosporella and Arthromyces also contain insect-associated species. Furthermore, the genus Arthromyces produces asexual spores on the mycelium, which may facilitate insect dispersal when growing on aggregated subterranean fecal pellets of a plant-feeding insect. The sister-group relationship between Arthromyces and Termitomyces implies that insect association and asexual sporulation, present in both genera, preceded the domestication of Termitomyces and did not follow domestication as has been proposed previously. Specialization of the common ancestor of these two genera on an insect-fecal substrate is further supported by similar carbohydrate-degrading profiles between Arthromyces and Termitomyces. We describe a set of traits that may have predisposed the ancestor of Termitomyces toward domestication, with each trait found scattered in related taxa outside of the termite-domesticated clade. This pattern indicates that the origin of the termite-fungus symbiosis may not have required large-scale changes of the fungal partner.
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Affiliation(s)
- Lennart J J van de Peppel
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands.
| | - Mathijs Nieuwenhuis
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | - Benjamin Auxier
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands
| | - Alexey A Grum-Grzhimaylo
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Martha E Cárdenas
- Laboratorio de Micología y Fitopatología-LAMFU, Universidad de Los Andes, Carrera 1 # 10A-12, Bogotá, Colombia
| | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - D Jean Lodge
- Department of Plant Pathology, 2105 Miller Plant Sciences Building, University of Georgia, Athens, GA 30606, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Thomas W Kuyper
- Soil Biology Group, Wageningen University & Research, Box 47, 6700AA Wageningen, the Netherlands
| | - Ana E Franco-Molano
- Laboratorio de Taxonomía y Ecología de Hongos (TEHO), Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Timothy J Baroni
- Department of Biological Sciences, State University of New York, College at Cortland, PO Box 2000, Cortland, NY 13045, USA
| | - Duur K Aanen
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands.
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6
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Ku YS, Wang Z, Duan S, Lam HM. Rhizospheric Communication through Mobile Genetic Element Transfers for the Regulation of Microbe-Plant Interactions. BIOLOGY 2021; 10:biology10060477. [PMID: 34071379 PMCID: PMC8227670 DOI: 10.3390/biology10060477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Simple Summary Rhizosphere, where microbes and plants coexist, is a hotspot of mobile genetic element (MGE) transfers. It was suggested that ancient MGE transfers drove the evolution of both microbes and plants. On the other hand, recurrent MGE transfers regulate microbe-plant interaction and the adaptation of microbes and plants to the environment. The studies of MGE transfers in the rhizosphere provide useful information for the research on pathogenic/ beneficial microbe-plant interaction. In addition, MGE transfers between microbes and the influence by plant root exudates on such transfers provide useful information for the research on bioremediation. Abstract The transfer of mobile genetic elements (MGEs) has been known as a strategy adopted by organisms for survival and adaptation to the environment. The rhizosphere, where microbes and plants coexist, is a hotspot of MGE transfers. In this review, we discuss the classic mechanisms as well as novel mechanisms of MGE transfers in the rhizosphere. Both intra-kingdom and cross-kingdom MGE transfers will be addressed. MGE transfers could be ancient events which drove evolution or recurrent events which regulate adaptations. Recent findings on MGE transfers between plant and its interacting microbes suggest gene regulations brought forth by such transfers for symbiosis or defense mechanisms. In the natural environment, factors such as temperature and soil composition constantly influence the interactions among different parties in the rhizosphere. In this review, we will also address the effects of various environmental factors on MGE transfers in the rhizosphere. Besides environmental factors, plant root exudates also play a role in the regulation of MGE transfer among microbes in the rhizosphere. The potential use of microbes and plants for bioremediation will be discussed.
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7
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Baluška F, Miller WB, Reber AS. Biomolecular Basis of Cellular Consciousness via Subcellular Nanobrains. Int J Mol Sci 2021; 22:ijms22052545. [PMID: 33802617 PMCID: PMC7961929 DOI: 10.3390/ijms22052545] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cells emerged at the very beginning of life on Earth and, in fact, are coterminous with life. They are enclosed within an excitable plasma membrane, which defines the outside and inside domains via their specific biophysical properties. Unicellular organisms, such as diverse protists and algae, still live a cellular life. However, fungi, plants, and animals evolved a multicellular existence. Recently, we have developed the cellular basis of consciousness (CBC) model, which proposes that all biological awareness, sentience and consciousness are grounded in general cell biology. Here we discuss the biomolecular structures and processes that allow for and maintain this cellular consciousness from an evolutionary perspective.
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Affiliation(s)
- František Baluška
- Institute of Cellular and Molecular Botany, University of Bonn, 53115 Bonn, Germany
- Correspondence:
| | | | - Arthur S. Reber
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada;
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Mateus ID, Rojas EC, Savary R, Dupuis C, Masclaux FG, Aletti C, Sanders IR. Coexistence of genetically different Rhizophagus irregularis isolates induces genes involved in a putative fungal mating response. THE ISME JOURNAL 2020; 14:2381-2394. [PMID: 32514118 PMCID: PMC7490403 DOI: 10.1038/s41396-020-0694-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/16/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are of great ecological importance because of their effects on plant growth. Closely related genotypes of the same AMF species coexist in plant roots. However, almost nothing is known about the molecular interactions occurring during such coexistence. We compared in planta AMF gene transcription in single and coinoculation treatments with two genetically different isolates of Rhizophagus irregularis in symbiosis independently on three genetically different cassava genotypes. Remarkably few genes were specifically upregulated when the two fungi coexisted. Strikingly, almost all of the genes with an identifiable putative function were known to be involved in mating in other fungal species. Several genes were consistent across host plant genotypes but more upregulated genes involved in putative mating were observed in host genotype (COL2215) compared with the two other host genotypes. The AMF genes that we observed to be specifically upregulated during coexistence were either involved in the mating pheromone response, in meiosis, sexual sporulation or were homologs of MAT-locus genes known in other fungal species. We did not observe the upregulation of the expected homeodomain genes contained in a putative AMF MAT-locus, but observed upregulation of HMG-box genes similar to those known to be involved in mating in Mucoromycotina species. Finally, we demonstrated that coexistence between the two fungal genotypes in the coinoculation treatments explained the number of putative mating response genes activated in the different plant host genotypes. This study demonstrates experimentally the activation of genes involved in a putative mating response and represents an important step towards the understanding of coexistence and sexual reproduction in these important plant symbionts.
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Affiliation(s)
- Ivan D Mateus
- Department of Ecology and Evolution, University of Lausanne, Biophore building, 1015, Lausanne, Switzerland.
| | - Edward C Rojas
- Department of Ecology and Evolution, University of Lausanne, Biophore building, 1015, Lausanne, Switzerland
| | - Romain Savary
- Department of Ecology and Evolution, University of Lausanne, Biophore building, 1015, Lausanne, Switzerland
| | - Cindy Dupuis
- Department of Ecology and Evolution, University of Lausanne, Biophore building, 1015, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Biophore building, 1015, Lausanne, Switzerland
| | - Consolée Aletti
- Department of Ecology and Evolution, University of Lausanne, Biophore building, 1015, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Biophore building, 1015, Lausanne, Switzerland.
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9
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Masclaux FG, Wyss T, Pagni M, Rosikiewicz P, Sanders IR. Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data. PLoS One 2019; 14:e0226497. [PMID: 31881076 PMCID: PMC6934306 DOI: 10.1371/journal.pone.0226497] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants. Recently, studies of the AMF Rhizophagus irregularis recorded within-isolate genetic variation that does not completely match the proposed homokaryon or heterokaryon state (where heterokaryons comprise a population of two distinct nucleus genotypes). We re-analysed published data showing that bi-allelic sites (and their frequencies), detected in proposed homo- and heterokaryote R. irregularis isolates, were similar across independent studies using different techniques. This indicated that observed within-fungus genetic variation was not an artefact of sequencing and that such within- fungus genetic variation possibly exists. We then looked to see if bi-allelic transcripts from three R. irregularis isolates matched those observed in the genome as this would give a strong indication of whether bi-allelic sites recorded in the genome were reliable variants. In putative homokaryon isolates, very few bi-allelic transcripts matched those in the genome. In a putative heterokaryon, a large number of bi-allelic transcripts matched those in the genome. Bi-allelic transcripts also occurred in the same frequency in the putative heterokaryon as predicted from allele frequency in the genome. Our results indicate that while within-fungus genome variation in putative homokaryon and heterokaryon AMF was highly similar in 2 independent studies, there was little support that this variation is transcribed in homokaryons. In contrast, within-fungus variation thought to be segregated among two nucleus genotypes in a heterokaryon isolate was indeed transcribed in a way that is proportional to that seen in the genome.
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Affiliation(s)
- Frédéric G. Masclaux
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, Switzerland
| | - Tania Wyss
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Marco Pagni
- Vital-IT Group, Swiss Institute of Bioinformatics, Switzerland
| | - Pawel Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Switzerland
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10
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Kokkoris V, Hart M. In vitro Propagation of Arbuscular Mycorrhizal Fungi May Drive Fungal Evolution. Front Microbiol 2019; 10:2420. [PMID: 31695689 PMCID: PMC6817466 DOI: 10.3389/fmicb.2019.02420] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 10/07/2019] [Indexed: 12/17/2022] Open
Abstract
Transformed root cultures (TRC) are used to mass produce arbuscular mycorrhizal (AM) fungal propagules in vitro. These propagules are then used in research, agriculture, and ecological restoration. There are many examples from other microbial systems that long-term in vitro propagation leads to domesticated strains that differ genetically and functionally. Here, we discuss potential consequences of in TRC propagation on AM fungal traits, and how this may affect their functionality. We examine weather domestication of AM fungi has already happened and finally, we explore whether it is possible to overcome TRC-induced domestication.
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11
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Evolutionary history and genetic diversity study of heat-shock protein 60 of Rhizophagus irregularis. J Genet 2019. [DOI: 10.1007/s12041-019-1096-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Ding C, Meng M, Jiang Y, Hou L. Improvement of the quality of soy sauce by reducing enzyme activity in Aspergillus oryzae. Food Chem 2019; 292:81-89. [PMID: 31054696 DOI: 10.1016/j.foodchem.2019.04.052] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 04/02/2019] [Accepted: 04/13/2019] [Indexed: 10/27/2022]
Abstract
How to effectively increase or decrease the ability of A. oryzae to produce enzymes was the key to improve the quality of soy sauce. However, multi-core property of A. oryzae resulted in genetic instability of the new strain. Here, A. oryzae 3.042-3 which can stably produce mononuclear spores was constructed based on A. oryzae 3.042. A. oryzae 3.042-3-c obtained by transformation of the fragment of cis-CreA into A. oryzae 3.042-3 exhibited genetic stability. The fragment containing the cis-acting and the promoter CreA from A. oryzae was connected to chromosome VII in A. oryzae 3.042-3-c. Compared with A. oryzae 3.042-3, the cellulase activity of A. oryzae 3.042-3-c was reduced by 50.5% and the pectinase activity was decreased by 10.0%. At the end of the soy sauce fermentation, the salt-free solid content of A. oryzae 3.042-3-c was higher 58.9% than that of A. oryzae 3.042-3. The kinds and contents of the flavor components of the soy sauce from the fermentation by A. oryzae 3.042-3-c were higher than those of the A. oryzae 3.042 and A. oryzae 3.042-3, especially in alcohols and esters. HEMF was only found in the soy sauce from A. oryzae 3.042-3-c. The results indicated that the new strain A. oryzae 3.042-3-c could improve the quality of soy sauce from the low-salt solid fermentation by decreasing enzyme activity of cellulase and pectinase.
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Affiliation(s)
- Chengfang Ding
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, No. 29, 13th Avenue, Tianjin Economic and Technological, Tianjin 300457, China
| | - Meng Meng
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, No. 29, 13th Avenue, Tianjin Economic and Technological, Tianjin 300457, China
| | - Yuyang Jiang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, No. 29, 13th Avenue, Tianjin Economic and Technological, Tianjin 300457, China
| | - Lihua Hou
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, No. 29, 13th Avenue, Tianjin Economic and Technological, Tianjin 300457, China.
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13
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Scott TW, Kiers ET, Cooper GA, dos Santos M, West SA. Evolutionary maintenance of genomic diversity within arbuscular mycorrhizal fungi. Ecol Evol 2019; 9:2425-2435. [PMID: 30891190 PMCID: PMC6405528 DOI: 10.1002/ece3.4834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/12/2023] Open
Abstract
Most organisms are built from a single genome. In striking contrast, arbuscular mycorrhizal fungi appear to maintain genomic variation within an individual fungal network. Arbuscular mycorrhizal fungi dwell in the soil, form mutualistic networks with plants, and bear multiple, potentially genetically diverse nuclei within a network. We explore, from a theoretical perspective, why such genetic diversity might be maintained within individuals. We consider selection acting within and between individual fungal networks. We show that genetic diversity could provide a benefit at the level of the individual, by improving growth in variable environments, and that this can stabilize genetic diversity even in the presence of nuclear conflict. Arbuscular mycorrhizal fungi complicate our understanding of organismality, but our findings offer a way of understanding such biological anomalies.
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Affiliation(s)
| | - E. Toby Kiers
- Institute of Ecological Sciences, Faculty of Earth and Life SciencesVrije UniversiteitAmsterdamThe Netherlands
| | | | - Miguel dos Santos
- Department of ZoologyUniversity of OxfordOxfordUK
- Department of Social Psychology and Social Neuroscience, Institute of PsychologyUniversity of BernBernSwitzerland
| | - Stuart A. West
- Department of ZoologyUniversity of OxfordOxfordUK
- Magdalen CollegeOxfordUK
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14
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15
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Sanders IR. Sex, plasticity, and biologically significant variation in one Glomeromycotina species. THE NEW PHYTOLOGIST 2018; 220:968-970. [PMID: 29480929 DOI: 10.1111/nph.15049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Ian R Sanders
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
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16
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Bruns TD, Corradi N, Redecker D, Taylor JW, Öpik M. Glomeromycotina: what is a species and why should we care? THE NEW PHYTOLOGIST 2018; 220:963-967. [PMID: 29165821 DOI: 10.1111/nph.14913] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A workshop at the recent International Conference on Mycorrhiza was focused on species recognition in Glomeromycotina and parts of their basic biology that define species. The workshop was motivated by the paradigm-shifting evidence derived from genomic data for sex and for the lack of heterokaryosis, and by published exchanges in Science that were based on different species concepts and have led to differing views of dispersal and endemism in these fungi. Although a lively discussion ensued, there was general agreement that species recognition in the group is in need of more attention, and that many basic assumptions about the biology of these important fungi including sexual or clonal reproduction, similarity or dissimilarity of nuclei within an individual, and species boundaries need to be re-examined and scrutinized with current techniques.
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Affiliation(s)
- Thomas D Bruns
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Dirk Redecker
- Agroécologie, Université de Bourgogne Franche-Comté, INRA, CNRS, AgroSup Dijon, F-21000, Dijon, France
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Maarja Öpik
- University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
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17
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Baluška F, Lyons S. Energide-cell body as smallest unit of eukaryotic life. ANNALS OF BOTANY 2018; 122:741-745. [PMID: 29474513 PMCID: PMC6215040 DOI: 10.1093/aob/mcy022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/01/2018] [Indexed: 06/08/2023]
Abstract
Background The evolutionary origin of the eukaryotic nucleus is obscure and controversial. Currently preferred are autogenic concepts; ideas of a symbiotic origin are mostly discarded and forgotten. Here we briefly discuss these issues and propose a new version of the symbiotic and archaeal origin of the eukaryotic nucleus. Scope and Conclusions The nucleus of eukaryotic cells forms via its perinuclear microtubules, the primary eukaryotic unit known also as the Energide-cell body. As for all other endosymbiotic organelles, new Energides are generated only from other Energides. While the Energide cannot be generated de novo, it can use its secretory apparatus to generate de novo the cell periphery apparatus. We suggest that Virchow's tenet Omnis cellula e cellula should be updated as Omnis Energide e Energide to reflect the status of the Energide as the primary unit of the eukaryotic cell, and life. In addition, the plasma membrane provides feedback to the Energide and renders it protection via the plasma membrane-derived endosomal network. New discoveries suggest archaeal origins of both the Energide and its host cell.
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18
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Beaudet D, Chen ECH, Mathieu S, Yildirir G, Ndikumana S, Dalpé Y, Séguin S, Farinelli L, Stajich JE, Corradi N. Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi. DNA Res 2018; 25:217-227. [PMID: 29211832 PMCID: PMC5909441 DOI: 10.1093/dnares/dsx051] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/09/2017] [Indexed: 11/24/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish symbioses with the vast majority of land plants. To date, generation of AMF coding information has been limited to model genera that grow well axenically; Rhizoglomus and Gigaspora. Meanwhile, data on the functional gene repertoire of most AMF families is non-existent. Here, we provide primary large-scale transcriptome data from eight poorly studied AMF species (Acaulospora morrowiae, Diversispora versiforme, Scutellospora calospora, Racocetra castanea, Paraglomus brasilianum, Ambispora leptoticha, Claroideoglomus claroideum and Funneliformis mosseae) using ultra-low input ribonucleic acid (RNA)-seq approaches. Our analyses reveals that quiescent spores of many AMF species harbour a diverse functional diversity and solidify known evolutionary relationships within the group. Our findings demonstrate that RNA-seq data obtained from low-input RNA are reliable in comparison to conventional RNA-seq experiments. Thus, our methodology can potentially be used to deepen our understanding of fungal microbial function and phylogeny using minute amounts of RNA material.
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Affiliation(s)
- Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Stephanie Mathieu
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada
| | - Sylvie Séguin
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada
| | - Laurent Farinelli
- Fasteris SA, Chemin du Pont-du-Centenaire 109, Geneva 1228, Switzerland
| | - Jason E Stajich
- Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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19
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Maeda T, Kobayashi Y, Kameoka H, Okuma N, Takeda N, Yamaguchi K, Bino T, Shigenobu S, Kawaguchi M. Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis. Commun Biol 2018; 1:87. [PMID: 30271968 PMCID: PMC6123716 DOI: 10.1038/s42003-018-0094-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 06/12/2018] [Indexed: 01/21/2023] Open
Abstract
Arbuscular mycorrhizal fungus (AMF) species are some of the most widespread symbionts of land plants. Our much improved reference genome assembly of a model AMF, Rhizophagus irregularis DAOM-181602 (total contigs = 210), facilitated a discovery of repetitive elements with unusual characteristics. R. irregularis has only ten or 11 copies of complete 45S rDNAs, whereas the general eukaryotic genome has tens to thousands of rDNA copies. R. irregularis rDNAs are highly heterogeneous and lack a tandem repeat structure. These findings provide evidence for the hypothesis that rDNA heterogeneity depends on the lack of tandem repeat structures. RNA-Seq analysis confirmed that all rDNA variants are actively transcribed. Observed rDNA/rRNA polymorphisms may modulate translation by using different ribosomes depending on biotic and abiotic interactions. The non-tandem repeat structure and intragenomic heterogeneity of AMF rDNA/rRNA may facilitate successful adaptation to various environmental conditions, increasing host compatibility of these symbiotic fungi.
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Affiliation(s)
- Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Yuuki Kobayashi
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Nao Okuma
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan
| | - Naoya Takeda
- School of Science and Technology, Kwansei Gakuin University, Gakuen, Mita, Hyogo, 669-1337, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Takahiro Bino
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan
| | - Shuji Shigenobu
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan.
- Functional Genomics Facility, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan.
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji Nishigonaka, Okazaki, Aichi, 444-8585, Japan.
- The Graduate University for Advanced Studies [SOKENDAI], Hayama, Miura, Kanagawa, 240-0193, Japan.
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20
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Egan CP, Rummel A, Kokkoris V, Klironomos J, Lekberg Y, Hart M. Using mock communities of arbuscular mycorrhizal fungi to evaluate fidelity associated with Illumina sequencing. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Thomsen CN, Hart MM. Using invasion theory to predict the fate of arbuscular mycorrhizal fungal inoculants. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1746-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Sbrana C, Strani P, Pepe A, de Novais CB, Giovannetti M. Divergence of Funneliformis mosseae populations over 20 years of laboratory cultivation, as revealed by vegetative incompatibility and molecular analysis. MYCORRHIZA 2018; 28:329-341. [PMID: 29574495 DOI: 10.1007/s00572-018-0830-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are widespread, important plant symbionts. They absorb and translocate mineral nutrients from the soil to host plants through an extensive extraradical mycelium, consisting of indefinitely large networks of nonseptate, multinucleated hyphae which may be interconnected by hyphal fusions (anastomoses). This work investigated whether different lineages of the same isolate may lose the ability to establish successful anastomoses, becoming vegetatively incompatible, when grown separately. The occurrence of hyphal incompatibility among five lineages of Funneliformis mosseae, originated from the same ancestor isolate and grown in vivo for more than 20 years in different European locations, was assessed by systematic detection of anastomosis frequency and cytological studies. Anastomosis frequencies ranged from 60 to 80% within the same lineage and from 17 to 44% among different lineages. The consistent detection of protoplasm continuity and nuclei in perfect fusions showed active protoplasm flow both within and between lineages. In pairings between different lineages, post-fusion incompatible reactions occurred in 6-48% of hyphal contacts and pre-fusion incompatibility in 2-17%. Molecular fingerprinting profiles showed genetic divergence among lineages, with overall Jaccard similarity indices ranging from 0.85 to 0.95. Here, phenotypic divergence among the five F. mosseae lineages was demonstrated by the reduction of their ability to form anastomosis and the detection of high levels of vegetative incompatibility. Our data suggest that potential genetic divergence may occur in AMF over only 20 years and represent the basis for detailed studies on the relationship between genes regulating anastomosis formation and hyphal compatibility in AMF.
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Affiliation(s)
- Cristiana Sbrana
- CNR-Institute of Agricultural Biology and Biotechnology, UOS Pisa, Pisa, Italy.
| | - Patrizia Strani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alessandra Pepe
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Candido Barreto de Novais
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Forestry Institute, Federal Rural University of Rio de Janeiro, Seropédica, Brazil
| | - Manuela Giovannetti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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23
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Blanco-Meneses M, Carbone I, Ristaino JB. Population structure and migration of the Tobacco Blue Mold Pathogen, Peronospora tabacina, into North America and Europe. Mol Ecol 2018; 27:737-751. [PMID: 29218863 DOI: 10.1111/mec.14453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/13/2017] [Accepted: 11/08/2017] [Indexed: 11/28/2022]
Abstract
Tobacco blue mold, caused by Peronospora tabacina, is an oomycete plant pathogen that causes yearly epidemics in tobacco (Nicotiana tabacum) in the United States and Europe. The genetic structure of P. tabacina was examined to understand genetic diversity, population structure and patterns of migration. Two nuclear loci, Igs2 and Ypt1, and one mitochondrial locus, cox2, were amplified, cloned and sequenced from fifty-four isolates of P. tabacina from the United States, Central America-Caribbean-Mexico (CCAM), Europe and the Middle East (EULE). Cloned sequences from the three genes showed high genetic variability across all populations. Nucleotide diversity and the population mean mutation parameter per site (Watterson's theta) were higher in EULE and CCAM and lower in U.S. POPULATIONS Neutrality tests were significant and the equilibrium model of neutral evolution was rejected, indicating an excess of recent mutations or rare alleles. Hudson's Snn tests were performed to examine population subdivision and gene flow among populations. An isolation-with-migration analysis (IM) supported the hypothesis of long-distance migration of P. tabacina from the Caribbean region, Florida and Texas into other states in the United States. Within the European populations, the model documented migration from North Central Europe into western Europe and Lebanon, and migration from western Europe into Lebanon. The migration patterns observed support historical observations about the first disease introductions and movement in Europe. The models developed are applicable to other aerial dispersed emerging pathogens and document that high-evolutionary-risk plant pathogens can move over long distances to cause disease due to their large effective population size, population expansion and dispersal.
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Affiliation(s)
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Jean B Ristaino
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
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24
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Koyama A, Pietrangelo O, Sanderson L, Antunes PM. An empirical investigation of the possibility of adaptability of arbuscular mycorrhizal fungi to new hosts. MYCORRHIZA 2017; 27:553-563. [PMID: 28536847 DOI: 10.1007/s00572-017-0776-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
Little is known about the adaptive capacity of arbuscular mycorrhizal (AM) fungi to novel hosts. Here we assessed the possibility of two heterospecific AM fungal isolates to adaptively change, in terms of host biomass response, as a function of host plant identity, over the course of a growing season. First, we produced pure inocula of Rhizophagus clarus and Rhizophagus intraradices, each starting from a single spore. Second, we "trained" each isolate individually in a community with two plants, sudangrass (Sorgum bicolour subsp. drummondii) and leek (Aliium ampeloprasum var. porrum), using a dual-compartment system to allow the establishment of a common mycorrhizal network between the two hosts. Third, we conducted a greenhouse experiment to reciprocally test each "trained" clone, obtained from each compartment, either with the same (home), or the other host (away) under two contrasting phosphorus levels. Overall, results did not support adaptive responses of the AM fungi to their hosts (i.e., greater host biomass under "home" relative to "away" conditions), but the opposite (i.e., greater host biomass under "away" relative to "home" conditions) was more frequently observed. These changes in AM fungal symbiotic functioning open the possibility for relatively rapid genetic change of arbuscular mycorrhizal fungi in response to new hosts, which represents one step forward from in vitro experiments.
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Affiliation(s)
- Akihiro Koyama
- Department of Biology, Algoma University, Queen Street East, Sault Ste. Marie, Ontario, P6A 2G4, Canada
| | - Olivia Pietrangelo
- Department of Biology, Algoma University, Queen Street East, Sault Ste. Marie, Ontario, P6A 2G4, Canada
| | - Laura Sanderson
- Department of Biology, Algoma University, Queen Street East, Sault Ste. Marie, Ontario, P6A 2G4, Canada
| | - Pedro M Antunes
- Department of Biology, Algoma University, Queen Street East, Sault Ste. Marie, Ontario, P6A 2G4, Canada.
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25
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He XL, Li Q, Peng WH, Zhou J, Cao XL, Wang D, Huang ZQ, Tan W, Li Y, Gan BC. Intra- and inter-isolate variation of ribosomal and protein-coding genes in Pleurotus: implications for molecular identification and phylogeny on fungal groups. BMC Microbiol 2017. [PMID: 28651582 PMCID: PMC5485676 DOI: 10.1186/s12866-017-1046-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), and elongation factor 1-alpha (EF1α) are often used in fungal taxonomy and phylogenetic analysis. As we know, an ideal molecular marker used in molecular identification and phylogenetic studies is homogeneous within species, and interspecific variation exceeds intraspecific variation. However, during our process of performing ITS, RPB2, and EF1α sequencing on the Pleurotus spp., we found that intra-isolate sequence polymorphism might be present in these genes because direct sequencing of PCR products failed in some isolates. Therefore, we detected intra- and inter-isolate variation of the three genes in Pleurotus by polymerase chain reaction amplification and cloning in this study. Results Results showed that intra-isolate variation of ITS was not uncommon but the polymorphic level in each isolate was relatively low in Pleurotus; intra-isolate variations of EF1α and RPB2 sequences were present in an unexpectedly high amount. The polymorphism level differed significantly between ITS, RPB2, and EF1α in the same individual, and the intra-isolate heterogeneity level of each gene varied between isolates within the same species. Intra-isolate and intraspecific variation of ITS in the tested isolates was less than interspecific variation, and intra-isolate and intraspecific variation of RPB2 was probably equal with interspecific divergence. Meanwhile, intra-isolate and intraspecific variation of EF1α could exceed interspecific divergence. These findings suggested that RPB2 and EF1α are not desirable barcoding candidates for Pleurotus. We also discussed the reason why rDNA and protein-coding genes showed variants within a single isolate in Pleurotus, but must be addressed in further research. Conclusions Our study demonstrated that intra-isolate variation of ribosomal and protein-coding genes are likely widespread in fungi. This has implications for studies on fungal evolution, taxonomy, phylogenetics, and population genetics. More extensive sampling of these genes and other candidates will be required to ensure reliability as phylogenetic markers and DNA barcodes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1046-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao-Lan He
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Qian Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.,Jilin Agricultural University, Changchun, 130118, China.,Mianyang Institute of Agricultural Sciences, Mianyang, 621023, China
| | - Wei-Hong Peng
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jie Zhou
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Xue-Lian Cao
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Di Wang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Zhong-Qian Huang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Wei Tan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Yu Li
- Jilin Agricultural University, Changchun, 130118, China
| | - Bing-Cheng Gan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
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26
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Koch AM, Antunes PM, Maherali H, Hart MM, Klironomos JN. Evolutionary asymmetry in the arbuscular mycorrhizal symbiosis: conservatism in fungal morphology does not predict host plant growth. THE NEW PHYTOLOGIST 2017; 214:1330-1337. [PMID: 28186629 DOI: 10.1111/nph.14465] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/24/2016] [Indexed: 05/19/2023]
Abstract
Although arbuscular mycorrhizal (AM) fungi are obligate symbionts that can influence plant growth, the magnitude and direction of these effects are highly variable within fungal genera and even among isolates within species, as well as among plant taxa. To determine whether variability in AM fungal morphology and growth is correlated with AM fungal effects on plant growth, we established a common garden experiment with 56 AM fungal isolates comprising 17 genera and six families growing with three plant host species. Arbuscular mycorrhizal fungal morphology and growth was highly conserved among isolates of the same species and among species within a family. By contrast, plant growth response to fungal inoculation was highly variable, with the majority of variation occurring among different isolates of the same AM fungal species. Our findings show that host performance cannot be predicted from AM fungal morphology and growth traits. Divergent effects on plant growth among isolates within an AM fungal species may be caused by coevolution between co-occurring fungal and plant populations.
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Affiliation(s)
- Alexander M Koch
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Pedro M Antunes
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6B 2G4, Canada
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - John N Klironomos
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
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Corradi N, Brachmann A. Fungal Mating in the Most Widespread Plant Symbionts? TRENDS IN PLANT SCIENCE 2017; 22:175-183. [PMID: 27876487 DOI: 10.1016/j.tplants.2016.10.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/26/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are relevant plant symbionts whose hyphae and spores carry hundreds of coexisting nuclei with supposedly divergent genomes but no sign of sexual reproduction. This unusual biology suggested that conventional fungal mating is not amendable to optimize strains for plant growth, but recent evidence of sexual-related nuclear inheritance in these organisms is now challenging this widespread notion. Here, we outline our knowledge of AMF genetics within a historical context, and discuss how past and new information in this area changed our understanding of AMF biology. We also highlight the mating-related processes in AMF, and propose new research avenues and approaches that could lead to a better application of these organisms for agricultural and environmental practices.
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Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, Canada.
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
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28
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Douhan GW, Rizzo DM. Amplified Fragment Length Microsatellites (AFLM) might be used to develop microsatellite markers in organisms with limited amounts of DNA applied to Arbuscular Mycorrhizal (AM) fungi. Mycologia 2017. [DOI: 10.1080/15572536.2004.11833123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - David M. Rizzo
- Department of Plant Pathology, University of California at Davis, Davis, California 95616
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29
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Redecker D, Raab P. Phylogeny of the Glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832618] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Philipp Raab
- Institute of Botany, University of Basel, Hebelstaße 1, CH-4056 Basel, Switzerland
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Kamel L, Keller-Pearson M, Roux C, Ané JM. Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics. THE NEW PHYTOLOGIST 2017; 213:531-536. [PMID: 27780291 DOI: 10.1111/nph.14263] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/27/2016] [Indexed: 06/06/2023]
Abstract
531 I. 531 II. 532 III. 532 IV. 534 V. 534 535 References 535 SUMMARY: Arbuscular mycorrhizal (AM) fungi associate with the vast majority of land plants, providing mutual nutritional benefits and protecting hosts against biotic and abiotic stresses. Significant progress was made recently in our understanding of the genomic organization, the obligate requirements, and the sexual nature of these fungi through the release and subsequent mining of genome sequences. Genomic and genetic approaches also improved our understanding of the signal repertoire used by AM fungi and their plant hosts to recognize each other for the initiation and maintenance of this association. Evolutionary and bioinformatic analyses of host and nonhost plant genomes represent novel ways with which to decipher host mechanisms controlling these associations and shed light on the stepwise acquisition of this genetic toolkit during plant evolution. Mining fungal and plant genomes along with evolutionary and genetic approaches will improve understanding of these symbiotic associations and, in the long term, their usefulness in agricultural settings.
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Affiliation(s)
- Laurent Kamel
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, BP 42617, 31326, Castanet-Tolosan, France
- Agronutrition SA, rue Pierre et Marie Curie Immeuble Biostep, 31670, Labège, France
| | - Michelle Keller-Pearson
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, BP 42617, 31326, Castanet-Tolosan, France
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin - Madison, Madison, WI, 53706, USA
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31
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Ma L, Song B, Curran T, Phong N, Dressaire E, Roper M. Defining individual size in the model filamentous fungus Neurospora crassa. Proc Biol Sci 2016; 283:20152470. [PMID: 26962146 DOI: 10.1098/rspb.2015.2470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
It is challenging to apply the tenets of individuality to filamentous fungi: a fungal mycelium can contain millions of genetically diverse but totipotent nuclei, each capable of founding new mycelia. Moreover, a single mycelium can potentially stretch over kilometres, and it is unlikely that its distant parts share resources or have the same fitness. Here, we directly measure how a single mycelium of the model ascomycete Neurospora crassa is patterned into reproductive units (RUs), meaning subpopulations of nuclei that propagate together as spores, and function as reproductive individuals. The density of RUs is sensitive to the geometry of growth; we detected 50-fold smaller RUs when mycelia had expanding frontiers than when they were constrained to grow in one direction only. RUs fragmented further when the mycelial network was perturbed. In mycelia with expanding frontiers, RU composition was strongly influenced by the distribution of genotypes early in development. Our results provide a concept of fungal individuality that is directly connected to reproductive potential, and therefore to theories of how fungal individuals adapt and evolve over time. Our data show that the size of reproductive individuals is a dynamic and environment-dependent property, even within apparently totally connected fungal mycelia.
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Affiliation(s)
- Linda Ma
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA 90095-1555, USA
| | - Boya Song
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA 90095-1555, USA
| | - Thomas Curran
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA 90095-1555, USA
| | - Nhu Phong
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA 90095-1555, USA
| | - Emilie Dressaire
- Department of Mechanical and Aerospace Engineering, New York University Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Marcus Roper
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA 90095-1555, USA Department of Biomathematics, University of California Los Angeles, Los Angeles, CA 90095-1555, USA
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Wyss T, Masclaux FG, Rosikiewicz P, Pagni M, Sanders IR. Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis. THE ISME JOURNAL 2016; 10:2514-26. [PMID: 26953600 PMCID: PMC5030683 DOI: 10.1038/ismej.2016.29] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 12/15/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi are symbionts of most plants, increasing plant growth and diversity. The model AM fungus Rhizophagus irregularis (isolate DAOM 197198) exhibits low within-fungus polymorphism. In contrast, another study reported high within-fungus variability. Experiments with other R. irregularis isolates suggest that within-fungus genetic variation can affect the fungal phenotype and plant growth, highlighting the biological importance of such variation. We investigated whether there is evidence of differing levels of within-fungus polymorphism in an R. irregularis population. We genotyped 20 isolates using restriction site-associated DNA sequencing and developed novel approaches for characterizing polymorphism among haploid nuclei. All isolates exhibited higher within-isolate poly-allelic single-nucleotide polymorphism (SNP) densities than DAOM 197198 in repeated and non-repeated sites mapped to the reference genome. Poly-allelic SNPs were independently confirmed. Allele frequencies within isolates deviated from diploids or tetraploids, or that expected for a strict dikaryote. Phylogeny based on poly-allelic sites was robust and mirrored the standard phylogeny. This indicates that within-fungus genetic variation is maintained in AM fungal populations. Our results predict a heterokaryotic state in the population, considerable differences in copy number variation among isolates and divergence among the copies, or aneuploidy in some isolates. The variation may be a combination of all of these hypotheses. Within-isolate genetic variation in R. irregularis leads to large differences in plant growth. Therefore, characterizing genomic variation within AM fungal populations is of major ecological importance.
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Affiliation(s)
- Tania Wyss
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frédéric G Masclaux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pawel Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marco Pagni
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Thiéry O, Vasar M, Jairus T, Davison J, Roux C, Kivistik PA, Metspalu A, Milani L, Saks Ü, Moora M, Zobel M, Öpik M. Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions ofRhizophagus irregularisandGigaspora margaritais high and isolate-dependent. Mol Ecol 2016; 25:2816-32. [DOI: 10.1111/mec.13655] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/29/2016] [Accepted: 04/14/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Odile Thiéry
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Martti Vasar
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Teele Jairus
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - John Davison
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales; UPS; CNRS 24 chemin de Borde Rouge-Auzeville; BP 42617; Université de Toulouse; 31326 Castanet-Tolosan France
| | - Paula-Ann Kivistik
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Andres Metspalu
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Lili Milani
- Estonian Genome Center; University of Tartu; 23b Riia St. 51010 Tartu Estonia
| | - Ülle Saks
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Mari Moora
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Martin Zobel
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
| | - Maarja Öpik
- Department of Botany; University of Tartu; 40 Lai St. 51005 Tartu Estonia
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Nadimi M, Daubois L, Hijri M. Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi. Mol Phylogenet Evol 2016; 98:74-83. [DOI: 10.1016/j.ympev.2016.01.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 12/16/2015] [Accepted: 01/14/2016] [Indexed: 11/29/2022]
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35
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Ropars J, Toro KS, Noel J, Pelin A, Charron P, Farinelli L, Marton T, Krüger M, Fuchs J, Brachmann A, Corradi N. Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi. Nat Microbiol 2016; 1:16033. [PMID: 27572831 DOI: 10.1038/nmicrobiol.2016.33] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
Sexual reproduction is ubiquitous among eukaryotes, and fully asexual lineages are extremely rare. Prominent among ancient asexual lineages are the arbuscular mycorrhizal fungi (AMF), a group of plant symbionts with a multinucleate cytoplasm. Genomic divergence among co-existing nuclei was proposed to drive the evolutionary success of AMF in the absence of sex(1), but this hypothesis has been contradicted by recent genome analyses that failed to find significant genetic diversity within an AMF isolate(2,3). Here, we set out to resolve issues surrounding the genome organization and sexual potential of AMF by exploring the genomes of five isolates of Rhizophagus irregularis, a model AMF. We find that genetic diversity in this species varies among isolates and is structured in a homo-dikaryon-like manner usually linked with the existence of a sexual life cycle. We also identify a putative AMF mating-type locus, containing two genes with structural and evolutionary similarities with the mating-type locus of some Dikarya. Our analyses suggest that this locus may be multi-allelic and that AMF could be heterothallic and bipolar. These findings reconcile opposing views on the genome organization of these ubiquitous plant symbionts and open avenues for strain improvement and environmental application of these organisms.
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Affiliation(s)
- Jeanne Ropars
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Jessica Noel
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Philippe Charron
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Laurent Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, PO Box 28, CH-1228 Plan-les-Ouates, Switzerland
| | - Timea Marton
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Manuela Krüger
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.,Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Andreas Brachmann
- LMU Munich, Faculty of Biology, Genetics, D-82152 Planegg-Martinsried, Germany
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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Rodriguez A, Sanders IR. CIENCIA Y TECNOLOGÍA COLOMBO-SUIZA AYUDA A ALIMENTAR EL PLANETA: DE LA REVOLUCIÓN VERDE A LA REVOLUCIÓN MICROBIANA. ACTA BIOLÓGICA COLOMBIANA 2016. [DOI: 10.15446/abc.v21n1supl.50856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
<p>Por milenios los agricultores han mejorado sus cultivos utilizando la variación genética y seleccionando las mejores variedades. Hoy nos enfrentamos a un reto sin precedentes: alimentar la creciente población mundial. Así, aumentar los rendimientos de cultivos de importancia global, para la seguridad alimentaria, como la yuca, es crucial. Esta raíz tropical alimenta aproximadamente 1.000 millones de personas en alrededor de 105 países en el mundo y sus productos son la tercera fuente de calorías más importante para los países del trópico (FAO, 2005). Esta planta es altamente dependiente de la asociación con hongos formadores de micorrizas arbusculares (HFMA). Estos hongos ayudan a la planta a obtener fósforo del suelo, un nutriente limitante principalmente en los suelos del trópico. Recientemente mostramos que la inoculación de cultivos de yuca con Rhizophagus irregularis incrementó los rendimientos en dos localidades diferentes de Colombia (Ceballos <em>et al</em>., 2013). Más aún, conseguimos enormes diferencias en la productividad de la yuca, utilizando diferentes líneas genéticamente mejoradas del hongo R. irregularis, en condiciones de campo (Ceballos <em>et al</em>., 2014). Es improbable observar cambios tan dramáticos, en campo, en la producción de yuca, con un ciclo de mejoramiento de la planta. Así, combinando la agronomía con la biología y la genética, proponemos un cambio en el paradigma del mejoramiento vegetal, que pueda contribuir a resolver el problema de hambruna en el mundo.</p><p>Abstract<br /><br /></p><p>For millennia farmers have been improving crops by using their natural genetic variation, selecting the best varieties. Today we face an unprecedented challenge to feed the growing global human population that can only be achieved with major changes in how we combine science and technology with agronomy. Cassava is globally important, annually feeding almost a billion people in 105 countries. It is an important crop for subsistence farming throughout tropical and subtropical regions for smallholder farmers, but especially in sub-Saharan Africa. Cassava is highly dependant on arbuscular mycorrhizal fungi to survive. Mycorrhizal fungi form symbioses with all our major crops. They help plants obtain phosphate from the soil; an essential nutrient that limits cassava production in the tropics. Our Colombian-swiss group have shown a significant effect of Rhizophagus irregularis inoculation on yield of<br />cassava in field conditions in two locations in Colombia. Further, huge differences in the productivity of cassava can be achieved by inoculating it with genetically different lines of R. irregularis. The variation in cassava growth we observed is so large that it would be very unlikely in one generation of plant breeding to see similar variation in cassava growth. By combining agronomy with biology and genetics, we propose a shift in the paradigm of plant breeding that could help to solve the problem of hunger in the world.</p><p> </p>
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Tang N, San Clemente H, Roy S, Bécard G, Zhao B, Roux C. A Survey of the Gene Repertoire of Gigaspora rosea Unravels Conserved Features among Glomeromycota for Obligate Biotrophy. Front Microbiol 2016; 7:233. [PMID: 26973612 PMCID: PMC4771724 DOI: 10.3389/fmicb.2016.00233] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/15/2016] [Indexed: 01/22/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi are a diverse group of soil fungi (Glomeromycota) that form the most ancient mutualistic association termed AM symbiosis with a majority of land plants, improving their nutrition uptake and resistance to stresses. In contrast to their great ecological implications, the knowledge of the molecular biological mechanisms involved is still scant, partly due to the limited genomic resources available. Here, we describe the gene repertoire of a new AM fungus Gigaspora rosea (Diversisporales). Among the 86332 non-redundant virtual transcripts assembled, 15346 presented similarities with proteins in the Refseq database and 10175 were assigned with GO terms. KOG and Interpro domain annotations clearly showed an enrichment of genes involved in signal transduction in G. rosea. KEGG pathway analysis indicates that most primary metabolic processes are active in G. rosea. However, as for Rhizophagus irregularis, several metabolic genes were not found, including the fatty acid synthase (FAS) gene. This finding supports the hypothesis that AM fungi depend on the lipids produced by their hosts. Furthermore, the presence of a large number of transporters and 100s of secreted proteins, together with the reduced number of plant cell wall degrading enzymes could be interpreted as an evolutionary adaptation to its mutualistic obligate biotrophy. The detection of meiosis-related genes suggests that G. rosea might use a cryptic sexual process. Lastly, a phylogeny of basal fungi clearly shows Glomeromycota as a sister clade to Mucoromycotina, not only to the Mucorales or Mortierellales. The characterization of the gene repertoire from an AM fungal species belonging to the order of Diversisporales and its comparison with the gene sets of R. irregularis (Glomerales) and Gigaspora margarita (Diversisporales), reveal that AM fungi share several features linked to mutualistic obligate biotrophy. This work contributes to lay the foundation for forthcoming studies into the genomics of Diversisporales, and also illuminates the utility of comparing gene repertoires of species from Diversisporales and other clades of Glomeromycota to gain more insights into the genetics and evolution of this fungal group.
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Affiliation(s)
- Nianwu Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Hélène San Clemente
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Sébastien Roy
- AGRONUTRITION Laboratoire de BiotechnologiesToulouse, France
| | - Guillaume Bécard
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Christophe Roux
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
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Campos C, Cardoso H, Nogales A, Svensson J, Lopez-Ráez JA, Pozo MJ, Nobre T, Schneider C, Arnholdt-Schmitt B. Intra and Inter-Spore Variability in Rhizophagus irregularis AOX Gene. PLoS One 2015; 10:e0142339. [PMID: 26540237 PMCID: PMC4634980 DOI: 10.1371/journal.pone.0142339] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/20/2015] [Indexed: 12/03/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF symbiosis improves nutrient uptake and buffers the plant against a diversity of stresses. Rhizophagus irregularis is one of the most widespread AMF species in the world, and its application in agricultural systems for yield improvement has increased over the last years. Still, from the inoculum production perspective, a lack of consistency of inoculum quality is referred to, which partially may be due to a high genetic variability of the fungus. The alternative oxidase (AOX) is an enzyme of the alternative respiratory chain already described in different taxa, including various fungi, which decreases the damage caused by oxidative stress. Nevertheless, virtually nothing is known on the involvement of AMF AOX on symbiosis establishment, as well on the existence of AOX variability that could affect AMF effectiveness and consequently plant performance. Here, we report the isolation and characterisation of the AOX gene of R. irregularis (RiAOX), and show that it is highly expressed during early phases of the symbiosis with plant roots. Phylogenetic analysis clustered RiAOX sequence with ancient fungi, and multiple sequence alignment revealed the lack of several regulatory motifs which are present in plant AOX. The analysis of RiAOX polymorphisms in single spores of three different isolates showed a reduced variability in one spore relatively to a group of spores. A high number of polymorphisms occurred in introns; nevertheless, some putative amino acid changes resulting from non-synonymous variants were found, offering a basis for selective pressure to occur within the populations. Given the AOX relatedness with stress responses, differences in gene variants amongst R. irregularis isolates are likely to be related with its origin and environmental constraints and might have a potential impact on inoculum production.
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Affiliation(s)
- Catarina Campos
- EU Marie Curie Chair, ICAAM—Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de Évora, Núcleo da Mitra, Évora, Portugal
| | - Hélia Cardoso
- EU Marie Curie Chair, ICAAM—Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de Évora, Núcleo da Mitra, Évora, Portugal
| | - Amaia Nogales
- EU Marie Curie Chair, ICAAM—Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de Évora, Núcleo da Mitra, Évora, Portugal
| | | | - Juan Antonio Lopez-Ráez
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Granada, Spain
| | - María José Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas (EEZ-CSIC), Granada, Spain
| | - Tânia Nobre
- EU Marie Curie Chair, ICAAM—Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de Évora, Núcleo da Mitra, Évora, Portugal
| | | | - Birgit Arnholdt-Schmitt
- EU Marie Curie Chair, ICAAM—Instituto de Ciências Agrárias e Ambientais Mediterrânicas, IIFA-Instituto de Formação e Investigação Avançada, Universidade de Évora, Núcleo da Mitra, Évora, Portugal
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39
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Kooij PW, Aanen DK, Schiøtt M, Boomsma JJ. Evolutionarily advanced ant farmers rear polyploid fungal crops. J Evol Biol 2015; 28:1911-24. [PMID: 26265100 PMCID: PMC5014177 DOI: 10.1111/jeb.12718] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 07/28/2015] [Indexed: 12/25/2022]
Abstract
Innovative evolutionary developments are often related to gene or genome duplications. The crop fungi of attine fungus-growing ants are suspected to have enhanced genetic variation reminiscent of polyploidy, but this has never been quantified with cytological data and genetic markers. We estimated the number of nuclei per fungal cell for 42 symbionts reared by 14 species of Panamanian fungus-growing ants. This showed that domesticated symbionts of higher attine ants are polykaryotic with 7-17 nuclei per cell, whereas nonspecialized crops of lower attines are dikaryotic similar to most free-living basidiomycete fungi. We then investigated how putative higher genetic diversity is distributed across polykaryotic mycelia, using microsatellite loci and evaluating models assuming that all nuclei are either heterogeneously haploid or homogeneously polyploid. Genetic variation in the polykaryotic symbionts of the basal higher attine genera Trachymyrmex and Sericomyrmex was only slightly enhanced, but the evolutionarily derived crop fungi of Atta and Acromyrmex leaf-cutting ants had much higher genetic variation. Our opposite ploidy models indicated that the symbionts of Trachymyrmex and Sericomyrmex are likely to be lowly and facultatively polyploid (just over two haplotypes on average), whereas Atta and Acromyrmex symbionts are highly and obligatorily polyploid (ca. 5-7 haplotypes on average). This stepwise transition appears analogous to ploidy variation in plants and fungi domesticated by humans and in fungi domesticated by termites and plants, where gene or genome duplications were typically associated with selection for higher productivity, but allopolyploid chimerism was incompatible with sexual reproduction.
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Affiliation(s)
- P W Kooij
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - D K Aanen
- Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - M Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - J J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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40
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Ropars J, Corradi N. Homokaryotic vs heterokaryotic mycelium in arbuscular mycorrhizal fungi: different techniques, different results? THE NEW PHYTOLOGIST 2015; 208:638-641. [PMID: 25952991 DOI: 10.1111/nph.13448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Jeanne Ropars
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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41
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Hartfield M. Evolutionary genetic consequences of facultative sex and outcrossing. J Evol Biol 2015; 29:5-22. [DOI: 10.1111/jeb.12770] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023]
Affiliation(s)
- M. Hartfield
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto ON Canada
- Bioinformatics Research Centre; University of Aarhus; Aarhus Denmark
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42
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Abstract
Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305-E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest.
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43
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Young JPW. Genome diversity in arbuscular mycorrhizal fungi. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:113-119. [PMID: 26190590 DOI: 10.1016/j.pbi.2015.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/28/2015] [Accepted: 06/06/2015] [Indexed: 06/04/2023]
Abstract
Arbuscular mycorrhizal fungi (Glomeromycota) are the most widespread and important symbionts of plants. They cannot be cultured without plants, are apparently asexual, and have multiple nuclei in a common cytoplasm. There is evidence for genetic variation among nuclei, and for segregation of this variation during growth, but these findings remain contentious. Recently, two papers have reported whole genome sequences for a strain of Rhizophagus irregularis; both suggest that genetic variation among nuclei is low. Genome assembly is very incomplete, though, so significant nuclear diversity cannot be excluded. While the diversity of nuclear genomes remains unresolved, multiple complete mitochondrial genomes are now available; there is virtually no variation within isolates, but significant variation between them.
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Affiliation(s)
- J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK.
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44
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Boon E, Halary S, Bapteste E, Hijri M. Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm. Genome Biol Evol 2015; 7:505-21. [PMID: 25573960 PMCID: PMC4350173 DOI: 10.1093/gbe/evv002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2015] [Indexed: 11/12/2022] Open
Abstract
Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.
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Affiliation(s)
- Eva Boon
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada
| | - Sébastien Halary
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada
| | - Eric Bapteste
- CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, France
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada
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45
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Beaudet D, de la Providencia IE, Labridy M, Roy-Bolduc A, Daubois L, Hijri M. Intraisolate mitochondrial genetic polymorphism and gene variants coexpression in arbuscular mycorrhizal fungi. Genome Biol Evol 2014; 7:218-27. [PMID: 25527836 PMCID: PMC4316628 DOI: 10.1093/gbe/evu275] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2014] [Indexed: 11/13/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are multinucleated and coenocytic organisms, in which the extent of the intraisolate nuclear genetic variation has been a source of debate. Conversely, their mitochondrial genomes (mtDNAs) have appeared to be homogeneous within isolates in all next generation sequencing (NGS)-based studies. Although several lines of evidence have challenged mtDNA homogeneity in AMF, extensive survey to investigate intraisolate allelic diversity has not previously been undertaken. In this study, we used a conventional polymerase chain reaction -based approach on selected mitochondrial regions with a high-fidelity DNA polymerase, followed by cloning and Sanger sequencing. Two isolates of Rhizophagus irregularis were used, one cultivated in vitro for several generations (DAOM-197198) and the other recently isolated from the field (DAOM-242422). At different loci in both isolates, we found intraisolate allelic variation within the mtDNA and in a single copy nuclear marker, which highlighted the presence of several nonsynonymous mutations in protein coding genes. We confirmed that some of this variation persisted in the transcriptome, giving rise to at least four distinct nad4 transcripts in DAOM-197198. We also detected the presence of numerous mitochondrial DNA copies within nuclear genomes (numts), providing insights to understand this important evolutionary process in AMF. Our study reveals that genetic variation in Glomeromycota is higher than what had been previously assumed and also suggests that it could have been grossly underestimated in most NGS-based AMF studies, both in mitochondrial and nuclear genomes, due to the presence of low-level mutations.
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Affiliation(s)
- Denis Beaudet
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Ivan Enrique de la Providencia
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Manuel Labridy
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Alice Roy-Bolduc
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Laurence Daubois
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada
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46
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Jansa J, Erb A, Oberholzer HR, Smilauer P, Egli S. Soil and geography are more important determinants of indigenous arbuscular mycorrhizal communities than management practices in Swiss agricultural soils. Mol Ecol 2014; 23:2118-35. [PMID: 24611988 DOI: 10.1111/mec.12706] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/20/2014] [Accepted: 02/21/2014] [Indexed: 11/29/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are ubiquitous soil fungi, forming mutualistic symbiosis with a majority of terrestrial plant species. They are abundant in nearly all soils, less diverse than soil prokaryotes and other intensively studied soil organisms and thus are promising candidates for universal indicators of land management legacies and soil quality degradation. However, insufficient data on how the composition of indigenous AMF varies along soil and landscape gradients have hampered the definition of baselines and effect thresholds to date. Here, indigenous AMF communities in 154 agricultural soils collected across Switzerland were profiled by quantitative real-time PCR with taxon-specific markers for six widespread AMF species. To identify the key determinants of AMF community composition, the profiles were related to soil properties, land management and site geography. Our results indicate a number of well-supported dependencies between abundances of certain AMF taxa and soil properties such as pH, soil fertility and texture, and a surprising lack of effect of available soil phosphorus on the AMF community profiles. Site geography, especially the altitude and large geographical distance, strongly affected AMF communities. Unexpected was the apparent lack of a strong land management effect on the AMF communities as compared to the other predictors, which could be due to the rarity of highly intensive and unsustainable land management in Swiss agriculture. In spite of the extensive coverage of large geographical and soil gradients, we did not identify any taxon suitable as an indicator of land use among the six taxa we studied.
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Affiliation(s)
- Jan Jansa
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Praha 4 - Krč, Czech Republic; Department of Environmental Systems Science, ETH Zurich, Eschikon 33, 8315, Lindau (ZH), Switzerland
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47
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Angelard C, Tanner CJ, Fontanillas P, Niculita-Hirzel H, Masclaux F, Sanders IR. Rapid genotypic change and plasticity in arbuscular mycorrhizal fungi is caused by a host shift and enhanced by segregation. THE ISME JOURNAL 2014; 8:284-94. [PMID: 24030596 PMCID: PMC3906815 DOI: 10.1038/ismej.2013.154] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/22/2013] [Accepted: 08/05/2013] [Indexed: 11/09/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are among the most abundant symbionts of plants, improving plant productivity and diversity. They are thought to mostly grow vegetatively, a trait assumed to limit adaptability. However, AMF can also harbor genetically different nuclei (nucleotypes). It has been shown that one AMF can produce genotypically novel offspring with proportions of different nucleotypes. We hypothesized that (1) AMF respond rapidly to a change of environment (plant host) through changes in the frequency of nucleotypes; (2) genotypically novel offspring exhibit different genetic responses to environmental change than the parent; and (3) genotypically novel offspring exhibit a wide range of phenotypic plasticity to a change of environment. We subjected AMF parents and offspring to a host shift. We observed rapid and large genotypic changes in all AMF lines that were not random. Genotypic and phenotypic responses were different among offspring and their parents. Even though growing vegetatively, AMF offspring display a broad range of genotypic and phenotypic changes in response to host shift. We conclude that AMF have the ability to rapidly produce variable progeny, increasing their probability to produce offspring with different fitness than their parents and, consequently, their potential adaptability to new environmental conditions. Such genotypic and phenotypic flexibility could be a fast alternative to sexual reproduction and is likely to be a key to the ecological success of AMF.
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Affiliation(s)
- Caroline Angelard
- Department of Ecology and Evolution,
University of Lausanne, Lausanne, Switzerland
| | | | | | | | - Frédéric Masclaux
- Department of Ecology and Evolution,
University of Lausanne, Lausanne, Switzerland
- Vital-IT Group, Swiss Institute for
Bioinformatics, University of Lausanne, Lausanne,
Switzerland
| | - Ian R Sanders
- Department of Ecology and Evolution,
University of Lausanne, Lausanne, Switzerland
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48
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Abstract
Gene transfer has been identified as a prevalent and pervasive phenomenon and an important source of genomic innovation in bacteria. The role of gene transfer in microbial eukaryotes seems to be of a reduced magnitude but in some cases can drive important evolutionary innovations, such as new functions that underpin the colonization of different niches. The aim of this review is to summarize published cases that support the hypothesis that horizontal gene transfer (HGT) has played a role in the evolution of phytopathogenic traits in fungi and oomycetes. Our survey of the literature identifies 46 proposed cases of transfer of genes that have a putative or experimentally demonstrable phytopathogenic function. When considering the life-cycle steps through which a pathogen must progress, the majority of the HGTs identified are associated with invading, degrading, and manipulating the host. Taken together, these data suggest HGT has played a role in shaping how fungi and oomycetes colonize plant hosts.
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Affiliation(s)
- Darren Soanes
- Biosciences, University of Exeter, Exeter, EX4 4QD, United Kingdom;
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49
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Lin K, Limpens E, Zhang Z, Ivanov S, Saunders DGO, Mu D, Pang E, Cao H, Cha H, Lin T, Zhou Q, Shang Y, Li Y, Sharma T, van Velzen R, de Ruijter N, Aanen DK, Win J, Kamoun S, Bisseling T, Geurts R, Huang S. Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus. PLoS Genet 2014; 10:e1004078. [PMID: 24415955 PMCID: PMC3886924 DOI: 10.1371/journal.pgen.1004078] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/18/2013] [Indexed: 12/03/2022] Open
Abstract
Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.
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Affiliation(s)
- Kui Lin
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Erik Limpens
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Sergey Ivanov
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | | | - Desheng Mu
- Novome Biotech Inc., Zhongguancun Life Science Park, Beijing, China
| | - Erli Pang
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Huifen Cao
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hwangho Cha
- Laboratory of Computational Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Qian Zhou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Yi Shang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Ying Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
| | - Trupti Sharma
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Norbert de Ruijter
- Laboratory of Cell Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Duur K. Aanen
- Laboratory of Genetics, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Ton Bisseling
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
- College of Science, King Saud University, Riyadh, Saudi Arabia
| | - René Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Beijing, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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50
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Riley R, Charron P, Idnurm A, Farinelli L, Dalpé Y, Martin F, Corradi N. Extreme diversification of the mating type-high-mobility group (MATA-HMG) gene family in a plant-associated arbuscular mycorrhizal fungus. THE NEW PHYTOLOGIST 2014; 201:254-268. [PMID: 24033097 DOI: 10.1111/nph.12462] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/22/2013] [Indexed: 06/02/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are important plant symbionts that have long been considered evolutionary anomalies because of their apparent long-term lack of sexuality, but recent explorations of available DNA sequence have challenged this notion by revealing the presence of homologues of fungal mating type-high-mobility group (MATA-HMG) and core meiotic genes in these organisms. To obtain more insights into the sexual potential of AMF, homologues of MATA-HMGs were sought in the transcriptome of three AMF isolates, and their functional and evolutionary trajectories were studied in genetically divergent strains of Rhizophagus irregularis using conventional and quantitative PCR procedures. Our analyses revealed the presence of at least 76 homologues of MATA-HMGs in R. irregularis isolates. None of these was found to be surrounded by genes generally found near other known fungal mating type loci, but here we report the presence of a 9-kb-long region in the AMF R. irregularis harbouring a total of four tandem-repeated MATA-HMGs; a feature that highlights a potentially elevated intragenomic diversity in this AMF species. The present study provides intriguing insights into the genome evolution of R. irregularis, and represents a stepping stone for understanding the potential of these fungi to undergo cryptic sex.
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Affiliation(s)
- Rohan Riley
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Philippe Charron
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Alexander Idnurm
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Laurent Farinelli
- FASTERIS S.A., Ch. du Pont-du-Centenaire 109, PO Box 28, CH-1228, Plan-les-Ouates, Switzerland
| | - Yolande Dalpé
- Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Francis Martin
- UMR INRA-UHP 'Interaction Arbres/Micro-Organismes', Centre INRA de Nancy, Champenoux, France
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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