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Lee SC, Sun S, Heitman J. Unseen sex in ancient virgin fungi. THE NEW PHYTOLOGIST 2014; 201:3-5. [PMID: 24274789 PMCID: PMC4110719 DOI: 10.1111/nph.12564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
| | | | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University
Medical Center, Durham, NC 27710, USA
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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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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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Chi J, Mahé F, Loidl J, Logsdon J, Dunthorn M. Meiosis gene inventory of four ciliates reveals the prevalence of a synaptonemal complex-independent crossover pathway. Mol Biol Evol 2013; 31:660-72. [PMID: 24336924 DOI: 10.1093/molbev/mst258] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To establish which meiosis genes are present in ciliates, and to look for clues as to which recombination pathways may be treaded by them, four genomes were inventoried for 11 meiosis-specific and 40 meiosis-related genes. We found that the set of meiosis genes shared by Tetrahymena thermophila, Paramecium tetraurelia, Ichthyophthirius multifiliis, and Oxytricha trifallax is consistent with the prevalence of a Mus81-dependent class II crossover pathway that is considered secondary in most model eukaryotes. There is little evidence for a canonical class I crossover pathway that requires the formation of a synaptonemal complex (SC). This gene inventory suggests that meiotic processes in ciliates largely depend on mitotic repair proteins for executing meiotic recombination. We propose that class I crossovers and SCs were reduced sometime during the evolution of ciliates. Consistent with this reduction, we provide microscopic evidence for the presence only of degenerate SCs in Stylonychia mytilus. In addition, lower nonsynonymous to synonymous mutation rates of some of the meiosis genes suggest that, in contrast to most other nuclear genes analyzed so far, meiosis genes in ciliates are largely evolving at a slower rate than those genes in fungi and animals.
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Affiliation(s)
- Jingyun Chi
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
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55
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Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A 2013; 110:20117-22. [PMID: 24277808 DOI: 10.1073/pnas.1313452110] [Citation(s) in RCA: 444] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularis genes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.
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Halary S, Daubois L, Terrat Y, Ellenberger S, Wöstemeyer J, Hijri M. Mating type gene homologues and putative sex pheromone-sensing pathway in arbuscular mycorrhizal fungi, a presumably asexual plant root symbiont. PLoS One 2013; 8:e80729. [PMID: 24260466 PMCID: PMC3834313 DOI: 10.1371/journal.pone.0080729] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/05/2013] [Indexed: 12/15/2022] Open
Abstract
The fungal kingdom displays a fascinating diversity of sex-determination systems. Recent advances in genomics provide insights into the molecular mechanisms of sex, mating type determination, and evolution of sexual reproduction in many fungal species in both ancient and modern phylogenetic lineages. All major fungal groups have evolved sexual differentiation and recombination pathways. However, sexuality is unknown in arbuscular mycorrhizal fungi (AMF) of the phylum Glomeromycota, an ecologically vital group of obligate plant root symbionts. AMF are commonly considered an ancient asexual lineage dating back to the Ordovician, approximately 460 M years ago. In this study, we used genomic and transcriptomic surveys of several AMF species to demonstrate the presence of conserved putative sex pheromone-sensing mitogen-activated protein (MAP) kinases, comparable to those described in Ascomycota and Basidiomycota. We also find genes for high mobility group (HMG) transcription factors, homologous to SexM and SexP genes in the Mucorales. The SexM genes show a remarkable sequence diversity among multiple copies in the genome, while only a single SexP sequence was detected in some isolates of Rhizophagus irregularis. In the Mucorales and Microsporidia, the sexM gene is flanked by genes for a triosephosphate transporter (TPT) and a RNA helicase, but we find no evidence for synteny in the vicinity of the Sex locus in AMF. Nonetheless, our results, together with previous observations on meiotic machinery, suggest that AMF could undergo a complete sexual reproduction cycle.
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Affiliation(s)
- Sébastien Halary
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, Québec, Canada
| | - Laurence Daubois
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, Québec, Canada
| | - Yves Terrat
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, Québec, Canada
| | - Sabrina Ellenberger
- Institute of General Microbiology and Microbe Genetics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Johannes Wöstemeyer
- Institute of General Microbiology and Microbe Genetics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montréal, Québec, Canada
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57
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de la Providencia IE, Nadimi M, Beaudet D, Rodriguez Morales G, Hijri M. Detection of a transient mitochondrial DNA heteroplasmy in the progeny of crossed genetically divergent isolates of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2013; 200:211-221. [PMID: 23790215 DOI: 10.1111/nph.12372] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/14/2013] [Indexed: 06/02/2023]
Abstract
Nonself fusion and nuclear genetic exchange have been documented in arbuscular mycorrhizal fungi (AMF), particularly in Rhizophagus irregularis. However, mitochondrial transmission accompanying nonself fusion of genetically divergent isolates remains unknown. Here, we tested the hypothesis that mitochondrial DNA (mtDNA) heteroplasmy occurs in the progeny of spores, obtained by crossing genetically divergent mtDNAs in R. irregularis isolates. Three isolates of geographically distant locations were used to investigate nonself fusions and mtDNA transmission to the progeny. We sequenced two additional mtDNAs of two R. irregularis isolates and developed isolate-specific size-variable markers in intergenic regions of these isolates and those of DAOM-197198. We achieved three crossing combinations in pre-symbiotic and symbiotic phases. Progeny spores per crossing combination were genotyped using isolate-specific markers. We found evidence that nonself recognition occurs between isolates originating from different continents both in pre-symbiotic and symbiotic phases. Genotyping patterns of individual spores from the progeny clearly showed the presence of markers of the two parental mtDNA haplotypes. Our results demonstrate that mtDNA heteroplasmy occurs in the progeny of the crossed isolates. However, this heteroplasmy appears to be a transient stage because all the live progeny spores that were able to germinate showed only one mtDNA haplotype.
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Affiliation(s)
- Ivan Enrique de la Providencia
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Maryam Nadimi
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Denis Beaudet
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Gabriela Rodriguez Morales
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
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Beaudet D, Nadimi M, Iffis B, Hijri M. Rapid mitochondrial genome evolution through invasion of mobile elements in two closely related species of arbuscular mycorrhizal fungi. PLoS One 2013; 8:e60768. [PMID: 23637766 PMCID: PMC3630166 DOI: 10.1371/journal.pone.0060768] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/02/2013] [Indexed: 11/19/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are common and important plant symbionts. They have coenocytic hyphae and form multinucleated spores. The nuclear genome of AMF is polymorphic and its organization is not well understood, which makes the development of reliable molecular markers challenging. In stark contrast, their mitochondrial genome (mtDNA) is homogeneous. To assess the intra- and inter-specific mitochondrial variability in closely related Glomus species, we performed 454 sequencing on total genomic DNA of Glomus sp. isolate DAOM-229456 and we compared its mtDNA with two G. irregulare isolates. We found that the mtDNA of Glomus sp. is homogeneous, identical in gene order and, with respect to the sequences of coding regions, almost identical to G. irregulare. However, certain genomic regions vary substantially, due to insertions/deletions of elements such as introns, mitochondrial plasmid-like DNA polymerase genes and mobile open reading frames. We found no evidence of mitochondrial or cytoplasmic plasmids in Glomus species, and mobile ORFs in Glomus are responsible for the formation of four gene hybrids in atp6, atp9, cox2, and nad3, which are most probably the result of horizontal gene transfer and are expressed at the mRNA level. We found evidence for substantial sequence variation in defined regions of mtDNA, even among closely related isolates with otherwise identical coding gene sequences. This variation makes it possible to design reliable intra- and inter-specific markers.
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Affiliation(s)
- Denis Beaudet
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Maryam Nadimi
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Bachir Iffis
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Mohamed Hijri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
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59
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Riley R, Corradi N. Searching for clues of sexual reproduction in the genomes of arbuscular mycorrhizal fungi. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2012.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Thiéry O, Moora M, Vasar M, Zobel M, Öpik M. Inter- and intrasporal nuclear ribosomal gene sequence variation within one isolate of arbuscular mycorrhizal fungus, Diversispora sp. Symbiosis 2012. [DOI: 10.1007/s13199-012-0212-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Formey D, Molès M, Haouy A, Savelli B, Bouchez O, Bécard G, Roux C. Comparative analysis of mitochondrial genomes of Rhizophagus irregularis - syn. Glomus irregulare - reveals a polymorphism induced by variability generating elements. THE NEW PHYTOLOGIST 2012; 196:1217-1227. [PMID: 22967288 DOI: 10.1111/j.1469-8137.2012.04283.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 06/01/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are involved in one of the most widespread plant-fungus interactions. A number of studies on the population dynamics of AM fungi have used mitochondrial (mt) DNA sequences, and yet mt AM fungus genomes are poorly known. To date, four mt genomes of three species of AM fungi are available, among which are two from Rhizophagus irregularis. In order to study intra- and interstrain mt genome variability of R. irregularis, we sequenced and de novo assembled four additional mt genomes of this species. We used 454 pyrosequencing and Illumina technologies to directly sequence mt genomes from total genomic DNA. The mt genomes are unique within each strain. Interstrain divergences in genome size, as a result of highly polymorphic intergenic and intronic sequences, were observed. The polymorphism is brought about by three types of variability generating element (VGE): homing endonucleases, DNA polymerase domain-containing open reading frames and small inverted repeats. Based on VGE positioning, mt sequences and nuclear markers, two subclades of R. irregularis were characterized. The discovery of VGEs highlights the great intraspecific plasticity of the R. irregularis mt genome. VGEs allow the design of powerful mt markers for the typing and monitoring of R. irregularis strains in genetic and population studies.
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Affiliation(s)
- Damien Formey
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, BP42617, F-31326, Castanet-Tolosan Cedex, France
- CNRS, UMR5546, BP 42617, F-31326, Castanet-Tolosan Cedex, France
- Agro-Nutrition, Parc Activestre, 3 avenue de l'orchidée, F-31390, Carbonne, France
| | - Marion Molès
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, BP42617, F-31326, Castanet-Tolosan Cedex, France
- CNRS, UMR5546, BP 42617, F-31326, Castanet-Tolosan Cedex, France
| | - Alexandra Haouy
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, BP42617, F-31326, Castanet-Tolosan Cedex, France
- CNRS, UMR5546, BP 42617, F-31326, Castanet-Tolosan Cedex, France
| | - Bruno Savelli
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, BP42617, F-31326, Castanet-Tolosan Cedex, France
- CNRS, UMR5546, BP 42617, F-31326, Castanet-Tolosan Cedex, France
| | - Olivier Bouchez
- Plateforme Génomique, Campus INRA Chemin de Borde-Rouge, F-31326, Castanet-Tolosan Cedex, France
| | - Guillaume Bécard
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, BP42617, F-31326, Castanet-Tolosan Cedex, France
- CNRS, UMR5546, BP 42617, F-31326, Castanet-Tolosan Cedex, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UPS, UMR5546, BP42617, F-31326, Castanet-Tolosan Cedex, France
- CNRS, UMR5546, BP 42617, F-31326, Castanet-Tolosan Cedex, France
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Ropars J, Dupont J, Fontanillas E, Rodríguez de la Vega RC, Malagnac F, Coton M, Giraud T, López-Villavicencio M. Sex in cheese: evidence for sexuality in the fungus Penicillium roqueforti. PLoS One 2012. [PMID: 23185400 PMCID: PMC3504111 DOI: 10.1371/journal.pone.0049665] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although most eukaryotes reproduce sexually at some moment of their life cycle, as much as a fifth of fungal species were thought to reproduce exclusively asexually. Nevertheless, recent studies have revealed the occurrence of sex in some of these supposedly asexual species. For industrially relevant fungi, for which inoculums are produced by clonal-subcultures since decades, the potentiality for sex is of great interest for strain improvement strategies. Here, we investigated the sexual capability of the fungus Penicillium roqueforti, used as starter for blue cheese production. We present indirect evidence suggesting that recombination could be occurring in this species. The screening of a large sample of strains isolated from diverse substrates throughout the world revealed the existence of individuals of both mating types, even in the very same cheese. The MAT genes, involved in fungal sexual compatibility, appeared to evolve under purifying selection, suggesting that they are still functional. The examination of the recently sequenced genome of the FM 164 cheese strain enabled the identification of the most important genes known to be involved in meiosis, which were found to be highly conserved. Linkage disequilibria were not significant among three of the six marker pairs and 11 out of the 16 possible allelic combinations were found in the dataset. Finally, the detection of signatures of repeat induced point mutations (RIP) in repeated sequences and transposable elements reinforces the conclusion that P. roqueforti underwent more or less recent sex events. In this species of high industrial importance, the induction of a sexual cycle would open the possibility of generating new genotypes that would be extremely useful to diversify cheese products.
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Affiliation(s)
- Jeanne Ropars
- Department Systématique et Evolution, Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, Paris, France.
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63
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Abstract
The arbuscular mycorrhizal fungi (AMF) are important symbionts of land plants, which are known for their tremendous positive effects on terrestrial ecosystems, their peculiar cellular features, and their very old evolutionary history. To date, no sexual stage or apparatus have ever been observed in these organisms; a remarkable absence for a eukaryotic lineage. For this reason, AMF have long been considered an evolutionary oddity, having evolved for over 500 millions of years in the absence of sexual reproduction and meiosis. Here, we discuss the recent identification across a number of AMF genomes, of many genes that are known to be involved in the process of meiosis in several eukaryotic model species. The presence of these genes in AMF is a previously unsuspected and highly intriguing finding, which suggests the presence of a “hidden” sexual (or parasexual) reproduction that awaits formal observation in these poorly studied fungi.
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Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research; Department of Biology; University of Ottawa; Ottawa, ON Canada
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Vankuren NW, den Bakker HC, Morton JB, Pawlowska TE. Ribosomal RNA gene diversity, effective population size, and evolutionary longevity in asexual glomeromycota. Evolution 2012; 67:207-24. [PMID: 23289573 DOI: 10.1111/j.1558-5646.2012.01747.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Arbuscular mycorrhizal fungi (phylum Glomeromycota) are among the oldest and most successful symbionts of land plants. With no evidence of sexual reproduction, their evolutionary success is inconsistent with the prediction that asexual taxa are vulnerable to extinction due to accumulation of deleterious mutations. To explore why Glomeromycota defy this prediction, we studied ribosomal RNA (rRNA) gene evolution in the Claroideoglomus lineage and estimated effective population size, N(e) , in C. etunicatum. We found that rRNA genes of these fungi exhibit unusual and complex patterns of molecular evolution. In C. etunicatum, these patterns can be collectively explained by an unexpectedly large N(e) combined with imperfect genome-wide and population-level rRNA gene repeat homogenization. The mutations accumulated in rRNA gene sequences indicate that natural selection is effective at purging deleterious mutations in the Claroideoglomus lineage, which is also consistent with the large N(e) of C. etunicatum. We propose that in the near absence of recombination, asexual reproduction involving massively multinucleate spores typical for Glomeromycota is responsible for the improved efficacy of selection relative to drift. We postulate that large effective population sizes contribute to the evolutionary longevity of Glomeromycota.
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Affiliation(s)
- Nicholas W Vankuren
- Department of Plant Pathology and Plant Microbe-Biology, Cornell University, Ithaca, NY 14853, USA
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Lanfranco L, Young JPW. Genetic and genomic glimpses of the elusive arbuscular mycorrhizal fungi. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:454-61. [PMID: 22673109 DOI: 10.1016/j.pbi.2012.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/25/2012] [Indexed: 05/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF), which form an ancient and widespread mutualistic symbiosis with plants, are a crucial but still enigmatic component of the plant microbiome. Nowadays, their obligate biotrophy is no longer an obstacle to deciphering the role played by AMF in this fascinating symbiosis. The first genome-wide transcriptomic analysis of an AMF showed a metabolic complexity with no sign of massive gene loss, and the presence of genes for meiotic recombination suggests that AMF are not simple clonal organisms, as originally thought. New findings on suppression of host defenses and nutrient exchange processes have shed light on the mechanisms that contribute to such an intimate and long-lasting integration between living plant and fungal cells.
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Affiliation(s)
- Luisa Lanfranco
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, and IPP-CNR, Viale Mattioli 25, 10125 Torino, Italy.
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Pelin A, Pombert JF, Salvioli A, Bonen L, Bonfante P, Corradi N. The mitochondrial genome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals two unsuspected trans-splicing events of group I introns. THE NEW PHYTOLOGIST 2012; 194:836-845. [PMID: 22320438 DOI: 10.1111/j.1469-8137.2012.04072.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
• Arbuscular mycorrhizal fungi (AMF) are ubiquitous organisms that benefit ecosystems through the establishment of an association with the roots of most plants: the mycorrhizal symbiosis. Despite their ecological importance, however, these fungi have been poorly studied at the genome level. • In this study, total DNA from the AMF Gigaspora margarita was subjected to a combination of 454 and Illumina sequencing, and the resulting reads were used to assemble its mitochondrial genome de novo. This genome was annotated and compared with those of other relatives to better comprehend the evolution of the AMF lineage. • The mitochondrial genome of G. margarita is unique in many ways, exhibiting a large size (97 kbp) and elevated GC content (45%). This genome also harbors molecular events that were previously unknown to occur in fungal mitochondrial genomes, including trans-splicing of group I introns from two different genes coding for the first subunit of the cytochrome oxidase and for the small subunit of the rRNA. • This study reports the second published genome from an AMF organelle, resulting in relevant DNA sequence information from this poorly studied fungal group, and providing new insights into the frequency, origin and evolution of trans-spliced group I introns found across the mitochondrial genomes of distantly related organisms.
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Affiliation(s)
- Adrian Pelin
- Department of Biology, University of Ottawa, Ottawa, K1N 6N5, ON, Canada
| | - Jean-François Pombert
- Department of Botany, University of British Columbia; Vancouver, V6T 1Z4, BC, Canada
| | - Alessandra Salvioli
- Dipartimento di Biologia Vegetale, Università di Torino, Torino, I-10125, Italy
| | - Linda Bonen
- Department of Biology, University of Ottawa, Ottawa, K1N 6N5, ON, Canada
| | - Paola Bonfante
- Dipartimento di Biologia Vegetale, Università di Torino, Torino, I-10125, Italy
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, K1N 6N5, ON, Canada
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Billiard S, López-Villavicencio M, Hood ME, Giraud T. Sex, outcrossing and mating types: unsolved questions in fungi and beyond. J Evol Biol 2012; 25:1020-38. [PMID: 22515640 DOI: 10.1111/j.1420-9101.2012.02495.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Variability in the way organisms reproduce raises numerous, and still unsolved, questions in evolutionary biology. In this study, we emphasize that fungi deserve a much greater emphasis in efforts to address these questions because of their multiple advantages as model eukaryotes. A tremendous diversity of reproductive modes and mating systems can be found in fungi, with many evolutionary transitions among closely related species. In addition, fungi show some peculiarities in their mating systems that have received little attention so far, despite the potential for providing insights into important evolutionary questions. In particular, selfing can occur at the haploid stage in addition to the diploid stage in many fungi, which is generally not possible in animals and plants but has a dramatic influence upon the structure of genetic systems. Fungi also present several advantages that make them tractable models for studies in experimental evolution. Here, we briefly review the unsolved questions and extant hypotheses about the evolution and maintenance of asexual vs. sexual reproduction and of selfing vs. outcrossing, focusing on fungal life cycles. We then propose how fungi can be used to address these long-standing questions and advance our understanding of sexual reproduction and mating systems across all eukaryotes.
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Affiliation(s)
- S Billiard
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016, Université des Sciences et Technologies de Lille - Lille1, Villeneuve d'Ascq Cedex, France.
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Corradi N, Bonfante P. The arbuscular mycorrhizal symbiosis: origin and evolution of a beneficial plant infection. PLoS Pathog 2012; 8:e1002600. [PMID: 22532798 PMCID: PMC3330121 DOI: 10.1371/journal.ppat.1002600] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
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Rosendahl S. The first glance into the Glomus genome: an ancient asexual scandal with meiosis? THE NEW PHYTOLOGIST 2012; 193:546-548. [PMID: 22235984 DOI: 10.1111/j.1469-8137.2011.04028.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Søren Rosendahl
- Department of Biology, University of Copenhagen, Oster Farimagsgade 2D, DK-1353K, Copenhagen, Denmark (tel +45 2267 0711; email )
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Tisserant E, Kohler A, Dozolme-Seddas P, Balestrini R, Benabdellah K, Colard A, Croll D, Da Silva C, Gomez SK, Koul R, Ferrol N, Fiorilli V, Formey D, Franken P, Helber N, Hijri M, Lanfranco L, Lindquist E, Liu Y, Malbreil M, Morin E, Poulain J, Shapiro H, van Tuinen D, Waschke A, Azcón-Aguilar C, Bécard G, Bonfante P, Harrison MJ, Küster H, Lammers P, Paszkowski U, Requena N, Rensing SA, Roux C, Sanders IR, Shachar-Hill Y, Tuskan G, Young JPW, Gianinazzi-Pearson V, Martin F. The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont. THE NEW PHYTOLOGIST 2012; 193:755-769. [PMID: 22092242 DOI: 10.1111/j.1469-8137.2011.03948.x] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
• The arbuscular mycorrhizal symbiosis is arguably the most ecologically important eukaryotic symbiosis, yet it is poorly understood at the molecular level. To provide novel insights into the molecular basis of symbiosis-associated traits, we report the first genome-wide analysis of the transcriptome from Glomus intraradices DAOM 197198. • We generated a set of 25,906 nonredundant virtual transcripts (NRVTs) transcribed in germinated spores, extraradical mycelium and symbiotic roots using Sanger and 454 sequencing. NRVTs were used to construct an oligoarray for investigating gene expression. • We identified transcripts coding for the meiotic recombination machinery, as well as meiosis-specific proteins, suggesting that the lack of a known sexual cycle in G. intraradices is not a result of major deletions of genes essential for sexual reproduction and meiosis. Induced expression of genes encoding membrane transporters and small secreted proteins in intraradical mycelium, together with the lack of expression of hydrolytic enzymes acting on plant cell wall polysaccharides, are all features of G. intraradices that are shared with ectomycorrhizal symbionts and obligate biotrophic pathogens. • Our results illuminate the genetic basis of symbiosis-related traits of the most ancient lineage of plant biotrophs, advancing future research on these agriculturally and ecologically important symbionts.
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Affiliation(s)
- E Tisserant
- Institut National de la Recherche Agronomique (INRA), UMR 1136 INRA/University Henri Poincaré, Interactions Arbres/Micro-organismes, Centre de Nancy, 54280 Champenoux, France
| | - A Kohler
- Institut National de la Recherche Agronomique (INRA), UMR 1136 INRA/University Henri Poincaré, Interactions Arbres/Micro-organismes, Centre de Nancy, 54280 Champenoux, France
| | - P Dozolme-Seddas
- UMR 1088 INRA/5184 CNRS/Burgundy University Plante-Microbe-Environnement, INRA-CMSE, BP 86510, 21065 Dijon, France
| | - R Balestrini
- Istituto per la Protezione delle Piante del CNR, sez. di Torino and Dipartimento di Biologia Vegetale, Universita` degli Studi di Torino, Viale Mattioli, 25, 10125 Torino, Italy
| | - K Benabdellah
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, C. Profesor Albareda, 1, 18008 Granada, Spain
| | - A Colard
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
- ETH Zürich, Plant Pathology, Universitätsstrasse 3, CH-8092 Zürich, Switzerland
| | - D Croll
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
- ETH Zürich, Plant Pathology, Universitätsstrasse 3, CH-8092 Zürich, Switzerland
| | - C Da Silva
- CEA, IG, Genoscope, 2 rue Gaston Crémieux CP5702, F-91057 Evry, France
| | - S K Gomez
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853-1801, USA
| | - R Koul
- Department of Chemistry and Biochemistry, New Mexico State University, Department 3MLS, PO Box 3001, Las Cruces, NM 88003-8001, USA
| | - N Ferrol
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, C. Profesor Albareda, 1, 18008 Granada, Spain
| | - V Fiorilli
- Istituto per la Protezione delle Piante del CNR, sez. di Torino and Dipartimento di Biologia Vegetale, Universita` degli Studi di Torino, Viale Mattioli, 25, 10125 Torino, Italy
| | - D Formey
- Université de Toulouse & CNRS, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France
| | - Ph Franken
- Leibniz-Institute of Vegetable and Ornamental Crops, Department of Plant Nutrition, Theodor-Echtermeyer-Weg 1, D-14979 Grossbeeren, Germany
| | - N Helber
- Karlsruhe Institute of Technology, Botanical Institute, Plant-Microbial Interaction, Hertzstrasse 16, D-76187 Karlsruhe, Germany
| | - M Hijri
- Institut de la Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, Que., Canada H1X 2B2
| | - L Lanfranco
- Istituto per la Protezione delle Piante del CNR, sez. di Torino and Dipartimento di Biologia Vegetale, Universita` degli Studi di Torino, Viale Mattioli, 25, 10125 Torino, Italy
| | - E Lindquist
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Y Liu
- UMR 1088 INRA/5184 CNRS/Burgundy University Plante-Microbe-Environnement, INRA-CMSE, BP 86510, 21065 Dijon, France
| | - M Malbreil
- Université de Toulouse & CNRS, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France
| | - E Morin
- Institut National de la Recherche Agronomique (INRA), UMR 1136 INRA/University Henri Poincaré, Interactions Arbres/Micro-organismes, Centre de Nancy, 54280 Champenoux, France
| | - J Poulain
- CEA, IG, Genoscope, 2 rue Gaston Crémieux CP5702, F-91057 Evry, France
| | - H Shapiro
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - D van Tuinen
- UMR 1088 INRA/5184 CNRS/Burgundy University Plante-Microbe-Environnement, INRA-CMSE, BP 86510, 21065 Dijon, France
| | - A Waschke
- Leibniz-Institute of Vegetable and Ornamental Crops, Department of Plant Nutrition, Theodor-Echtermeyer-Weg 1, D-14979 Grossbeeren, Germany
| | - C Azcón-Aguilar
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, C. Profesor Albareda, 1, 18008 Granada, Spain
| | - G Bécard
- Université de Toulouse & CNRS, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France
| | - P Bonfante
- Istituto per la Protezione delle Piante del CNR, sez. di Torino and Dipartimento di Biologia Vegetale, Universita` degli Studi di Torino, Viale Mattioli, 25, 10125 Torino, Italy
| | - M J Harrison
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853-1801, USA
| | - H Küster
- Institut für Pflanzengenetik, Naturwissenschaftliche Fakultät, Leibniz Universität Hannover, D-30419 Hannover, Germany
| | - P Lammers
- Department of Chemistry and Biochemistry, New Mexico State University, Department 3MLS, PO Box 3001, Las Cruces, NM 88003-8001, USA
| | - U Paszkowski
- Department de Biologie Moléculaire Végétale, Université de Lausanne, Biophore, 4419, CH-1015 Lausanne, Switzerland
| | - N Requena
- Karlsruhe Institute of Technology, Botanical Institute, Plant-Microbial Interaction, Hertzstrasse 16, D-76187 Karlsruhe, Germany
| | - S A Rensing
- BIOSS Centre for Biological Signalling Studies, Freiburg Initiative for Systems Biology and Faculty of Biology, University of Freiburg, Hauptstr. 1, D-79104 Freiburg, Germany
| | - C Roux
- Université de Toulouse & CNRS, UPS, UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France
| | - I R Sanders
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Y Shachar-Hill
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824-1312, USA
| | - G Tuskan
- Oak Ridge National Laboratory, BioSciences, PO Box 2008, Oak Ridge, TN 37831, USA
| | - J P W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - V Gianinazzi-Pearson
- UMR 1088 INRA/5184 CNRS/Burgundy University Plante-Microbe-Environnement, INRA-CMSE, BP 86510, 21065 Dijon, France
| | - F Martin
- Institut National de la Recherche Agronomique (INRA), UMR 1136 INRA/University Henri Poincaré, Interactions Arbres/Micro-organismes, Centre de Nancy, 54280 Champenoux, France
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