101
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Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species. PLoS Genet 2016; 12:e1006404. [PMID: 27806045 PMCID: PMC5091853 DOI: 10.1371/journal.pgen.1006404] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/04/2016] [Indexed: 01/02/2023] Open
Abstract
Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi. The genus Candida is one of the leading causes of fungal morbidity in humans. Many pathogenic Candida species are diploid, and do not have have a full sexual cycle. The evolutionary origin of Candida orthopsilosis is unclear. Here, we use whole genome sequencing of 27 C. orthopsilosis isolates from around the world to show that C. orthopsilosis arose from hybridization (or mating) of two distinct parental species. Unusually, the hybridization event did not occur only once; we identify at least four events, and we suggest that hybridization is ongoing. The “species” C. orthopsilosis therefore does not have one single origin. We have identified one of the parental lineages involved, but the other remains elusive. Our results suggest that inter-species hybridization has an evolutionary advantage. However, unlike in plant pathogens, it does not appear to result in increased virulence of C. orthopsilosis.
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102
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Aguileta G, Badouin H, Hood ME, Møller AP, Le Prieur S, Snirc A, Siguenza S, Mousseau TA, Shykoff JA, Cuomo CA, Giraud T. Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl. Mol Ecol 2016; 25:3370-83. [PMID: 27136128 DOI: 10.1111/mec.13675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/04/2016] [Accepted: 04/15/2016] [Indexed: 12/24/2022]
Abstract
Nuclear disasters at Chernobyl and Fukushima provide examples of effects of acute ionizing radiation on mutations that can affect the fitness and distribution of species. Here, we investigated the prevalence of Microbotryum lychnidis-dioicae, a pollinator-transmitted fungal pathogen of plants causing anther-smut disease in Chernobyl, its viability, fertility and karyotype variation, and the accumulation of nonsynonymous mutations in its genome. We collected diseased flowers of Silene latifolia from locations ranging by more than two orders of magnitude in background radiation, from 0.05 to 21.03 μGy/h. Disease prevalence decreased significantly with increasing radiation level, possibly due to lower pollinator abundance and altered pollinator behaviour. Viability and fertility, measured as the budding rate of haploid sporidia following meiosis from the diploid teliospores, did not vary with increasing radiation levels and neither did karyotype overall structure and level of chromosomal size heterozygosity. We sequenced the genomes of twelve samples from Chernobyl and of four samples collected from uncontaminated areas and analysed alignments of 6068 predicted genes, corresponding to 1.04 × 10(7) base pairs. We found no dose-dependent differences in substitution rates (neither dN, dS, nor dN/dS). Thus, we found no significant evidence of increased deleterious mutation rates at higher levels of background radiation in this plant pathogen. We even found lower levels of nonsynonymous substitution rates in contaminated areas compared to control regions, suggesting that purifying selection was stronger in contaminated than uncontaminated areas. We briefly discuss the possibilities for a mechanistic basis of radio resistance in this nonmelanized fungus.
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Affiliation(s)
- Gabriela Aguileta
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Helene Badouin
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, MA 01002, USA
| | - Anders P Møller
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Stephanie Le Prieur
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Sophie Siguenza
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France.,CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Jacqui A Shykoff
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | | | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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103
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Boto L. Evolutionary change and phylogenetic relationships in light of horizontal gene transfer. J Biosci 2016; 40:465-72. [PMID: 25963270 DOI: 10.1007/s12038-015-9514-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Horizontal gene transfer has, over the past 25 years, become a part of evolutionary thinking. In the present paper I discuss horizontal gene transfer (HGT) in relation to contingency, natural selection, evolutionary change speed and the Tree-of-Life endeavour, with the aim of contributing to the understanding of the role of HGT in evolutionary processes. In addition, the challenges that HGT imposes on the current view of evolution are emphasized.
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Affiliation(s)
- Luis Boto
- Departamento de Biodiversidad y Biologia Evolutiva, Museo Nacional Ciencias Naturales, CSIC, C/ Jose Gutierrez Abascal 2, 28006, Madrid, Spain,
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104
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Nuclear dynamics and genetic rearrangement in heterokaryotic colonies of Fusarium oxysporum. Fungal Genet Biol 2016; 91:20-31. [PMID: 27013267 DOI: 10.1016/j.fgb.2016.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/31/2016] [Accepted: 03/15/2016] [Indexed: 10/22/2022]
Abstract
Recent studies have shown horizontal transfer of chromosomes to be a potential key contributor to genome plasticity in asexual fungal pathogens. However, the mechanisms behind horizontal chromosome transfer in eukaryotes are not well understood. Here we investigated the role of conidial anastomosis in heterokaryon formation between incompatible strains of Fusarium oxysporum and determined the importance of heterokaryons for horizontal chromosome transfer. Using live-cell imaging we demonstrate that conidial pairing of incompatible strains under carbon starvation can result in the formation of viable heterokaryotic hyphae in F. oxysporum. Nuclei of the parental lines presumably fuse at some stage as conidia with a single nucleus harboring both marker histones (GFP- and RFP-tagged) are produced. Upon colony formation, this hybrid offspring is subject to progressive and gradual genome rearrangement. The parental genomes appear to become spatially separated and RFP-tagged histones, deriving from one of the strains, Fol4287, are eventually lost. With a PCR-based method we showed that markers for most of the chromosomes of this strain are lost, indicating a lack of Fol4287 chromosomes. This leaves offspring with the genomic background of the other strain (Fo47), but in some cases together with one or two chromosomes from Fol4287, including the chromosome that confers pathogenicity towards tomato.
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105
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Wang JB, St Leger RJ, Wang C. Advances in Genomics of Entomopathogenic Fungi. ADVANCES IN GENETICS 2016; 94:67-105. [PMID: 27131323 DOI: 10.1016/bs.adgen.2016.01.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are the commonest pathogens of insects and crucial regulators of insect populations. The rapid advance of genome technologies has revolutionized our understanding of entomopathogenic fungi with multiple Metarhizium spp. sequenced, as well as Beauveria bassiana, Cordyceps militaris, and Ophiocordyceps sinensis among others. Phylogenomic analysis suggests that the ancestors of many of these fungi were plant endophytes or pathogens, with entomopathogenicity being an acquired characteristic. These fungi now occupy a wide range of habitats and hosts, and their genomes have provided a wealth of information on the evolution of virulence-related characteristics, as well as the protein families and genomic structure associated with ecological and econutritional heterogeneity, genome evolution, and host range diversification. In particular, their evolutionary transition from plant pathogens or endophytes to insect pathogens provides a novel perspective on how new functional mechanisms important for host switching and virulence are acquired. Importantly, genomic resources have helped make entomopathogenic fungi ideal model systems for answering basic questions in parasitology, entomology, and speciation. At the same time, identifying the selective forces that act upon entomopathogen fitness traits could underpin both the development of new mycoinsecticides and further our understanding of the natural roles of these fungi in nature. These roles frequently include mutualistic relationships with plants. Genomics has also facilitated the rapid identification of genes encoding biologically useful molecules, with implications for the development of pharmaceuticals and the use of these fungi as bioreactors.
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Affiliation(s)
- J B Wang
- University of Maryland, College Park, MD, United States
| | - R J St Leger
- University of Maryland, College Park, MD, United States
| | - C Wang
- Chinese Academy of Sciences, Shanghai, China
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106
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Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches. Sci Rep 2016; 6:22262. [PMID: 26915968 PMCID: PMC4768097 DOI: 10.1038/srep22262] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/10/2016] [Indexed: 11/10/2022] Open
Abstract
Evolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages.
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107
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Dutheil JY, Mannhaupt G, Schweizer G, M K Sieber C, Münsterkötter M, Güldener U, Schirawski J, Kahmann R. A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi. Genome Biol Evol 2016; 8:681-704. [PMID: 26872771 PMCID: PMC4824034 DOI: 10.1093/gbe/evw026] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Smut fungi are plant pathogens mostly parasitizing wild species of grasses as well as domesticated cereal crops. Genome analysis of several smut fungi including Ustilago maydis revealed a singular clustered organization of genes encoding secreted effectors. In U. maydis, many of these clusters have a role in virulence. Reconstructing the evolutionary history of clusters of effector genes is difficult because of their intrinsically fast evolution, which erodes the phylogenetic signal and homology relationships. Here, we describe the use of comparative evolutionary analyses of quality draft assemblies of genomes to study the mechanisms of this evolution. We report the genome sequence of a South African isolate of Sporisorium scitamineum, a smut fungus parasitizing sugar cane with a phylogenetic position intermediate to the two previously sequenced species U. maydis and Sporisorium reilianum. We show that the genome of S. scitamineum contains more and larger gene clusters encoding secreted effectors than any previously described species in this group. We trace back the origin of the clusters and find that their evolution is mainly driven by tandem gene duplication. In addition, transposable elements play a major role in the evolution of the clustered genes. Transposable elements are significantly associated with clusters of genes encoding fast evolving secreted effectors. This suggests that such clusters represent a case of genome compartmentalization that restrains the activity of transposable elements on genes under diversifying selection for which this activity is potentially beneficial, while protecting the rest of the genome from its deleterious effect.
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Affiliation(s)
- Julien Y Dutheil
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gertrud Mannhaupt
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gabriel Schweizer
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christian M K Sieber
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Münsterkötter
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ulrich Güldener
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jan Schirawski
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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108
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Gu Y, Xing S, He C. Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution. Genome Biol Evol 2016; 8:635-48. [PMID: 26868598 PMCID: PMC4824202 DOI: 10.1093/gbe/evw021] [Citation(s) in RCA: 9] [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: 02/01/2016] [Indexed: 02/07/2023] Open
Abstract
Gene loss is the driving force for changes in genome and morphology; however, this particular evolutionary event has been poorly investigated in leguminous plants. Legumes (Fabaceae) have some lineage-specific and diagnostic characteristics that are distinct from other angiosperms. To understand the potential role of gene loss in the evolution of legumes, we compared six genome-sequenced legume species of Papilionoideae, the largest representative clade of Fabaceae, such as Glycine max, with 34 nonlegume plant species, such as Arabidopsis thaliana. The results showed that the putative orthologs of the 34 Arabidopsis genes belonging to 29 gene families were absent in these legume species but these were conserved in the sequenced nonlegume angiosperm lineages. Further evolutionary analyses indicated that the orthologs of these genes were almost completely lost in the Papillionoideae ancestors, thus designated as the legume lost genes (LLGs), and these underwent purifying selection in nonlegume plants. Most LLGs were functionally unknown. In Arabidopsis, two LLGs were well-known genes that played a role in plant immunity such as HARMLESS TO OZONE LAYER 1 and HOPZ-ACTIVATED RESISTANCE 1, and 16 additional LLGs were predicted to participate in plant-pathogen interactions in in silico expression and protein-protein interaction network analyses. Most of these LLGs' orthologs in various plants were also found to be associated with biotic stress response, indicating the conserved role of these genes in plant defense. The evolutionary implication of LLGs during the development of the ability of symbiotic nitrogen fixation involving plant and bacterial interactions, which is a well-known characteristic of most legumes, is also discussed. Our work sheds light on the evolutionary implication of gene loss events in Papilionoideae evolution, as well as provides new insights into crop design to improve nitrogen fixation capacity.
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Affiliation(s)
- Yongzhe Gu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China Graduate University, Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Shilai Xing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China Graduate University, Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China
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109
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Lemaire C, De Gracia M, Leroy T, Michalecka M, Lindhard-Pedersen H, Guerin F, Gladieux P, Le Cam B. Emergence of new virulent populations of apple scab from nonagricultural disease reservoirs. THE NEW PHYTOLOGIST 2016; 209:1220-9. [PMID: 26428268 DOI: 10.1111/nph.13658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/15/2015] [Indexed: 05/11/2023]
Abstract
Plant pathogens adapt readily to new crop varieties in agrosystems, and it is crucial to understand the factors underlying the epidemic spread of new virulent strains if we are to develop more efficient strategies to control them. In this study we used multilocus microsatellite typing, molecular epidemiology tools and a large collection of isolates from cultivated, wild and ornamental apples to investigate the origin of new virulent populations of Venturia inaequalis, an ascomycete fungus causing apple scab on varieties carrying the Rvi6 resistance gene. We demonstrated a common origin at the European scale of populations infecting apples (Malus × domestica) carrying the Rvi6 resistance and Malus floribunda, the progenitor of the Rvi6 resistance. Demographic modeling indicated that the Rvi6-virulent lineage separated several thousands of years ago from populations infecting non-Rvi6 hosts, without detectable gene flow between the two lineages. These findings show that 'breakdowns' of plant resistance genes can be caused by the selection and migration of virulent genotypes from standing genetic variation maintained in environmental disease reservoirs, here ornamental crabapples. This work stresses the need to take better account of pathogen diversity in resistance screenings of breeding lines and in resistance deployment strategies, in order to enhance sustainable disease management.
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Affiliation(s)
- Christophe Lemaire
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES L'UNAM, Angers, 49075, France
| | - Marie De Gracia
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France
| | - Thibault Leroy
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES L'UNAM, Angers, 49075, France
- INRA, UMR 1202 BIOGECO, Cestas, 33612, France
| | - Monika Michalecka
- Department of Plant Pathology, Institute of Horticulture, Skierniewice, 96-100, Poland
| | | | - Fabien Guerin
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France
- Université de la Réunion, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, 97715, La Réunion, France
| | - Pierre Gladieux
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France
- INRA, UMR BGPI, Montpellier, 34398, France
- CIRAD, UMR BGPI, Montpellier, 34398, France
| | - Bruno Le Cam
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France
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110
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de Brito DM, Maracaja-Coutinho V, de Farias ST, Batista LV, do Rêgo TG. A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm. PLoS One 2016; 11:e0146352. [PMID: 26731657 PMCID: PMC4711805 DOI: 10.1371/journal.pone.0146352] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/16/2015] [Indexed: 01/04/2023] Open
Abstract
Genomic Islands (GIs) are regions of bacterial genomes that are acquired from other organisms by the phenomenon of horizontal transfer. These regions are often responsible for many important acquired adaptations of the bacteria, with great impact on their evolution and behavior. Nevertheless, these adaptations are usually associated with pathogenicity, antibiotic resistance, degradation and metabolism. Identification of such regions is of medical and industrial interest. For this reason, different approaches for genomic islands prediction have been proposed. However, none of them are capable of predicting precisely the complete repertory of GIs in a genome. The difficulties arise due to the changes in performance of different algorithms in the face of the variety of nucleotide distribution in different species. In this paper, we present a novel method to predict GIs that is built upon mean shift clustering algorithm. It does not require any information regarding the number of clusters, and the bandwidth parameter is automatically calculated based on a heuristic approach. The method was implemented in a new user-friendly tool named MSGIP—Mean Shift Genomic Island Predictor. Genomes of bacteria with GIs discussed in other papers were used to evaluate the proposed method. The application of this tool revealed the same GIs predicted by other methods and also different novel unpredicted islands. A detailed investigation of the different features related to typical GI elements inserted in these new regions confirmed its effectiveness. Stand-alone and user-friendly versions for this new methodology are available at http://msgip.integrativebioinformatics.me.
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Affiliation(s)
- Daniel M. de Brito
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Vinicius Maracaja-Coutinho
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Brazil
- Instituto Vandique, João Pessoa, Brazil
- Beagle Bioinformatics, Santiago, Chile
| | - Savio T. de Farias
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Leonardo V. Batista
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Thaís G. do Rêgo
- Departamento de Informática, Centro de Informática, Universidade Federal da Paraíba, João Pessoa, Brazil
- * E-mail:
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111
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Utilizing Genomics to Study Entomopathogenicity in the Fungal Phylum Entomophthoromycota. ADVANCES IN GENETICS 2016; 94:41-65. [DOI: 10.1016/bs.adgen.2016.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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112
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Gladieux P, Wilson BA, Perraudeau F, Montoya LA, Kowbel D, Hann-Soden C, Fischer M, Sylvain I, Jacobson DJ, Taylor JW. Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta. Mol Ecol 2015; 24:5657-75. [PMID: 26453896 DOI: 10.1111/mec.13417] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/30/2022]
Abstract
Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (~37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South-East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.
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Affiliation(s)
- Pierre Gladieux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Ecologie Systematique Evolution, Université Paris Sud, Batiment 360, 91405, Orsay, France
| | | | - Fanny Perraudeau
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Ecole Polytechnique, Route de Saclay, 91128, Palaiseau, France
| | - Liliam A Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - David Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Monika Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Iman Sylvain
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - David J Jacobson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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113
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Baer B, Millar AH. Proteomics in evolutionary ecology. J Proteomics 2015; 135:4-11. [PMID: 26453985 DOI: 10.1016/j.jprot.2015.09.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/09/2023]
Abstract
Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein modifications and protein interactions of interest with high accuracy and assess protein diversity and function. Therefore, proteomic technologies can be viewed as providing evolutionary biologist with exciting novel opportunities to understand very early events in functional variation of cellular molecular machinery that are acting as part of evolutionary processes.
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Affiliation(s)
- B Baer
- Centre for Integrative Bee Research (CIBER) and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, The University of Western Australia, 6009 Crawley, Australia.
| | - A H Millar
- Centre for Integrative Bee Research (CIBER) and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, The University of Western Australia, 6009 Crawley, Australia
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114
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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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115
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Chiapello H, Mallet L, Guérin C, Aguileta G, Amselem J, Kroj T, Ortega-Abboud E, Lebrun MH, Henrissat B, Gendrault A, Rodolphe F, Tharreau D, Fournier E. Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants. Genome Biol Evol 2015; 7:2896-912. [PMID: 26454013 PMCID: PMC4684704 DOI: 10.1093/gbe/evv187] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).
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Affiliation(s)
- Hélène Chiapello
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Ludovic Mallet
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Cyprien Guérin
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Gabriela Aguileta
- CNRS, UMR 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France Center for Genomic Regulation, Barcelona, Spain
| | - Joëlle Amselem
- INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Thomas Kroj
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Enrique Ortega-Abboud
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Marc-Henri Lebrun
- INRA-AgroParisTech, UMR 1190, Biologie et Gestion des Risques en Agriculture BIOGER-CPP, Campus AgroParisTech, Thiverval-Grignon, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université d'Aix Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Annie Gendrault
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - François Rodolphe
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Didier Tharreau
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Elisabeth Fournier
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
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Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E, Dumas É, Lacoste S, Debuchy R, Dupont J, Branca A, Giraud T. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi. Curr Biol 2015; 25:2562-9. [PMID: 26412136 PMCID: PMC4598740 DOI: 10.1016/j.cub.2015.08.025] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 07/09/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022]
Abstract
Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1–5]. Few studies have focused on the domestication of fungi, with notable exceptions [6–11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making—P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13–15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes. New HTRs are found in cheese fungi HTRs are flanked by specific transposable elements HTRs have spread in cheese-associated fungi through recent selective sweeps Experiments link two HTRs to growth and competitive advantages on cheese
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Affiliation(s)
- Jeanne Ropars
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Manuela López-Villavicencio
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, INRA, Castanet-Tolosan 31326, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, CNRS, Castanet-Tolosan 31326, France
| | - Erika Sallet
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, INRA, Castanet-Tolosan 31326, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, CNRS, Castanet-Tolosan 31326, France
| | - Émilie Dumas
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Sandrine Lacoste
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Robert Debuchy
- Institut de Génétique et Microbiologie, UMR8621, Univ. Paris-Sud, 91405 Orsay, France; Institut de Génétique et Microbiologie, UMR8621, CNRS, 91405 Orsay, France
| | - Joëlle Dupont
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France.
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France.
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117
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Skrede I, Brandström Durling M. Population genomic analyses reveal possible drivers of population divergence. Mol Ecol 2015; 24:2598-600. [PMID: 26013991 DOI: 10.1111/mec.13209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/16/2015] [Indexed: 11/26/2022]
Abstract
Recent advances in sequencing technology and efficiency enable new and improved methods to investigate how populations diverge and species evolve. Fungi have relatively small and simple genomes and can often be cultured in the laboratory. Fungal populations can thus be sequenced for a relatively low cost, which makes them ideal for population genomic analyses. In several recent population genomic studies, wild populations of fungal model organisms and human pathogens have been analysed, for example Neurospora crassa (Ellison et al. ), Saccharomyces uvarum (Almeida et al. ), Coccidioides spp. (Neafsey et al. ) and Cryptococcus gatti (Engelthaler et al. ). In this issue of Molecular Ecology, Branco et al. () apply population genomic tools to understand population divergence and adaptation in a symbiotic (mycorrhizal) fungus. This study exemplifies the possibilities of diving deeper into the genomic features involved in population divergence and speciation, also for nonmodel organisms, and how molecular and analytical tools will improve our understanding of the patterns and mechanisms that underlie adaptation to habitats, population divergence and dispersal limitation of fungi.
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Affiliation(s)
- Inger Skrede
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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118
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Marsit S, Mena A, Bigey F, Sauvage FX, Couloux A, Guy J, Legras JL, Barrio E, Dequin S, Galeote V. Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts. Mol Biol Evol 2015; 32:1695-707. [PMID: 25750179 PMCID: PMC4476156 DOI: 10.1093/molbev/msv057] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although an increasing number of horizontal gene transfers have been reported in eukaryotes, experimental evidence for their adaptive value is lacking. Here, we report the recent transfer of a 158-kb genomic region between Torulaspora microellipsoides and Saccharomyces cerevisiae wine yeasts or closely related strains. This genomic region has undergone several rearrangements in S. cerevisiae strains, including gene loss and gene conversion between two tandemly duplicated FOT genes encoding oligopeptide transporters. We show that FOT genes confer a strong competitive advantage during grape must fermentation by increasing the number and diversity of oligopeptides that yeast can utilize as a source of nitrogen, thereby improving biomass formation, fermentation efficiency, and cell viability. Thus, the acquisition of FOT genes has favored yeast adaptation to the nitrogen-limited wine fermentation environment. This finding indicates that anthropic environments offer substantial ecological opportunity for evolutionary diversification through gene exchange between distant yeast species.
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Affiliation(s)
- Souhir Marsit
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Adriana Mena
- Department of Genetics, University of Valencia, and Department of Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - Frédéric Bigey
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - François-Xavier Sauvage
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Arnaud Couloux
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, Evry, France
| | - Julie Guy
- CEA, Institut de Génomique, Genoscope, Centre National de Séquençage, Evry, France
| | - Jean-Luc Legras
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Eladio Barrio
- Department of Genetics, University of Valencia, and Department of Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - Sylvie Dequin
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
| | - Virginie Galeote
- INRA, UMR1083, SPO, F-34060 Montpellier, France Montpellier SupAgro, UMR1083, SPO, F-34060 Montpellier, France Montpellier University, UMR1083, SPO, F-34060 Montpellier, France
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Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldón T, Tinsley CR, Casaregola S. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep 2015; 5:11571. [PMID: 26108467 PMCID: PMC4479816 DOI: 10.1038/srep11571] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
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Affiliation(s)
- Guillaume Morel
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Lieven Sterck
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Dominique Swennen
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Djamila Onesime
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Anthony Levasseur
- INRA UMR1163, Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Noémie Jacques
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Sandrine Mallet
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Arnaux Couloux
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Karine Labadie
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Joëlle Amselem
- INRA UR1164, Unité de Recherche Génomique – Info, 78000 Versailles, France
| | - Jean-Marie Beckerich
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | | | - Yves Van de Peer
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
- Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - Patrick Wincker
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry, 91000, France
- Université d’Evry, Bd François Mitterand, Evry,91025, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, Strasbourg, 67000, France
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Colin R. Tinsley
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Serge Casaregola
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
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120
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Gillot G, Jany JL, Coton M, Le Floch G, Debaets S, Ropars J, López-Villavicencio M, Dupont J, Branca A, Giraud T, Coton E. Insights into Penicillium roqueforti Morphological and Genetic Diversity. PLoS One 2015; 10:e0129849. [PMID: 26091176 PMCID: PMC4475020 DOI: 10.1371/journal.pone.0129849] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022] Open
Abstract
Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection.
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Affiliation(s)
- Guillaume Gillot
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Jean-Luc Jany
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Monika Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Gaétan Le Floch
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Stella Debaets
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Jeanne Ropars
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d’Histoire Naturelle, CP39, Paris Cedex 05, France
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay cedex, France
- CNRS, Orsay cedex, France
| | - Manuela López-Villavicencio
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d’Histoire Naturelle, CP39, Paris Cedex 05, France
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d’Histoire Naturelle, CP39, Paris Cedex 05, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay cedex, France
- CNRS, Orsay cedex, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay cedex, France
- CNRS, Orsay cedex, France
| | - Emmanuel Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d’Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
- * E-mail:
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Morales-Cruz A, Amrine KCH, Blanco-Ulate B, Lawrence DP, Travadon R, Rolshausen PE, Baumgartner K, Cantu D. Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens. BMC Genomics 2015; 16:469. [PMID: 26084502 PMCID: PMC4472170 DOI: 10.1186/s12864-015-1624-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development. RESULTS The integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution. CONCLUSIONS This study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
| | - Katherine C H Amrine
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
| | - Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
| | - Daniel P Lawrence
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA.
| | - Renaud Travadon
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616, USA.
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA.
| | - Kendra Baumgartner
- United States Department of Agriculture - Agricultural Research Service, Crops Pathology and Genetics Research Unit, Davis, CA, 95616, USA.
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
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122
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Perlin MH, Amselem J, Fontanillas E, Toh SS, Chen Z, Goldberg J, Duplessis S, Henrissat B, Young S, Zeng Q, Aguileta G, Petit E, Badouin H, Andrews J, Razeeq D, Gabaldón T, Quesneville H, Giraud T, Hood ME, Schultz DJ, Cuomo CA. Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics 2015; 16:461. [PMID: 26076695 PMCID: PMC4469406 DOI: 10.1186/s12864-015-1660-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 05/28/2015] [Indexed: 12/11/2022] Open
Abstract
Background The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. Results We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14 % of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions. Conclusions The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1660-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | - Joelle Amselem
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Versailles, France. .,Institut National de la Recherche Agronomique (INRA), Biologie et gestion des risques en agriculture (BIOGER), Thiverval-Grignon, France.
| | - Eric Fontanillas
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. .,CNRS, F-91405, Orsay, France.
| | - Su San Toh
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | | | - Sebastien Duplessis
- INRA, UMR 1136, Interactions Arbres-Microorganismes, Champenoux, France. .,UMR 1136, Université de Lorraine, Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, France.
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 13288, Marseille, France. .,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | | | - Elsa Petit
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. .,CNRS, F-91405, Orsay, France. .,Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 13288, Marseille, France.
| | - Helene Badouin
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. .,CNRS, F-91405, Orsay, France.
| | - Jared Andrews
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | - Dominique Razeeq
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institució Catalana d'Estudis Avançats (ICREA), Barcelona, Spain.
| | - Hadi Quesneville
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Versailles, France.
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. .,CNRS, F-91405, Orsay, France.
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, 01002, USA.
| | - David J Schultz
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
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123
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Zhao J, Gladieux P, Hutchison E, Bueche J, Hall C, Perraudeau F, Glass NL. Identification of Allorecognition Loci in Neurospora crassa by Genomics and Evolutionary Approaches. Mol Biol Evol 2015; 32:2417-32. [PMID: 26025978 PMCID: PMC4540973 DOI: 10.1093/molbev/msv125] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Understanding the genetic and molecular bases of the ability to distinguish self from nonself (allorecognition) and mechanisms underlying evolution of allorecognition systems is an important endeavor for understanding cases where it becomes dysfunctional, such as in autoimmune disorders. In filamentous fungi, allorecognition can result in vegetative or heterokaryon incompatibility, which is a type of programmed cell death that occurs following fusion of genetically different cells. Allorecognition is genetically controlled by het loci, with coexpression of any combination of incompatible alleles triggering vegetative incompatibility. Herein, we identified, characterized, and inferred the evolutionary history of candidate het loci in the filamentous fungus Neurospora crassa. As characterized het loci encode proteins carrying an HET domain, we annotated HET domain genes in 25 isolates from a natural population along with the N. crassa reference genome using resequencing data. Because allorecognition systems can be affected by frequency-dependent selection favoring rare alleles (i.e., balancing selection), we mined resequencing data for HET domain loci whose alleles displayed elevated levels of variability, excess of intermediate frequency alleles, and deep gene genealogies. From these analyses, 34 HET domain loci were identified as likely to be under balancing selection. Using transformation, incompatibility assays and genetic analyses, we determined that one of these candidates functioned as a het locus (het-e). The het-e locus has three divergent allelic groups that showed signatures of positive selection, intra- and intergroup recombination, and trans-species polymorphism. Our findings represent a compelling case of balancing selection functioning on multiple alleles across multiple loci potentially involved in allorecognition.
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Affiliation(s)
- Jiuhai Zhao
- Plant and Microbial Biology Department, University of California, Berkeley
| | - Pierre Gladieux
- Plant and Microbial Biology Department, University of California, Berkeley INRA, UMR BGPI, TA A54/K, Montpellier, France; CIRAD, Montpellier, France
| | - Elizabeth Hutchison
- Plant and Microbial Biology Department, University of California, Berkeley Biology Department, 1 College Circle SUNY Geneseo, Geneseo, NY
| | - Joanna Bueche
- Plant and Microbial Biology Department, University of California, Berkeley
| | - Charles Hall
- Plant and Microbial Biology Department, University of California, Berkeley
| | - Fanny Perraudeau
- Plant and Microbial Biology Department, University of California, Berkeley Ecole Polytechnique, Palaiseau, France
| | - N Louise Glass
- Plant and Microbial Biology Department, University of California, Berkeley
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124
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Sperschneider J, Gardiner DM, Thatcher LF, Lyons R, Singh KB, Manners JM, Taylor JM. Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity. Genome Biol Evol 2015; 7:1613-27. [PMID: 25994930 PMCID: PMC4494044 DOI: 10.1093/gbe/evv092] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pathogens and hosts are in an ongoing arms race and genes involved in host–pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, we analyzed the genomes of three Fusarium plant pathogens for genes that are under diversifying selection. We found a two-speed genome structure both on the chromosome and gene group level. Diversifying selection acts strongly on the dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici and on distinct core chromosome regions in Fusarium graminearum, all of which have associations with virulence. Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens. Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function. In summary, diversifying selection in Fusarium is strongly reflected as genomic footprints and can be used to predict a small gene set likely to be involved in host–pathogen interactions for experimental verification.
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Affiliation(s)
- Jana Sperschneider
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia
| | - Donald M Gardiner
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Louise F Thatcher
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia
| | - Rebecca Lyons
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Karam B Singh
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - John M Manners
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
| | - Jennifer M Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
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125
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Branco S, Gladieux P, Ellison CE, Kuo A, LaButti K, Lipzen A, Grigoriev IV, Liao HL, Vilgalys R, Peay KG, Taylor JW, Bruns TD. Genetic isolation between two recently diverged populations of a symbiotic fungus. Mol Ecol 2015; 24:2747-58. [DOI: 10.1111/mec.13132] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Sara Branco
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720 USA
| | - Pierre Gladieux
- Laboratoire d'Ecologie; Systematique et Evolution; Bâtiment 360; 91405 Orsay France
- CNRS; Bâtiment 360; 91405 Orsay France
| | | | - Alan Kuo
- Department of Energy; Joint Genome Institute; 2800 Mitchell Dr.; Walnut Creek CA 94598 USA
| | - Kurt LaButti
- Department of Energy; Joint Genome Institute; 2800 Mitchell Dr.; Walnut Creek CA 94598 USA
| | - Anna Lipzen
- Department of Energy; Joint Genome Institute; 2800 Mitchell Dr.; Walnut Creek CA 94598 USA
| | - Igor V. Grigoriev
- Department of Energy; Joint Genome Institute; 2800 Mitchell Dr.; Walnut Creek CA 94598 USA
| | - Hui-Ling Liao
- Department of Biology; Duke University; Durham NC 27708 USA
| | - Rytas Vilgalys
- Department of Biology; Duke University; Durham NC 27708 USA
| | - Kabir G. Peay
- Department of Biology; Stanford University; Stanford CA 94305 USA
| | - John W. Taylor
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720 USA
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720 USA
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126
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Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. The population biology of fungal invasions. Mol Ecol 2015; 24:1969-86. [DOI: 10.1111/mec.13028] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/16/2022]
Affiliation(s)
- P. Gladieux
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - A. Feurtey
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - M. E. Hood
- Department of Biology; Amherst College; Amherst Massachusetts 01002 USA
| | - A. Snirc
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - J. Clavel
- Conservation des Espèces; Restauration et Suivi des Populations - CRBPO; Muséum National d'Histoire Naturelle-CNRS-Université Pierre et Marie Curie; 55 rue Buffon 75005 Paris France
| | - C. Dutech
- Biodiversité Gènes et Communautés; INRA-Université Bordeaux 1; Site de Pierroton 33610 Cestas France
| | - M. Roy
- Evolution et Diversité Biologique; Université Toulouse Paul Sabatier-Ecole Nationale de Formation Agronomique-CNRS; 118 route de Narbonne 31062 Toulouse France
| | - T. Giraud
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
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127
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Wang C. A vision for the innovative study of fungal biology in China: Presidential address. Mycology 2015; 6:1-3. [PMID: 26000193 PMCID: PMC4409049 DOI: 10.1080/21501203.2015.1026112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
I am proud to be elected as the sixth president of the Mycological Society of China, and highly pleased to have a chance to share my personal opinion here with my fellow mycologists and students regarding the innovative performance of fungal biology studies in China. A stepwise buildup of knowledge and sharp scientific vision is the prerequisite for innovative studies. Taken together with the most advanced techniques and elegant experimental designs, the scholars would have a better chance to acquire novel and conceptual results rather than the “me too” stories by focusing on the mechanisms related with fungal unique biology.
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Affiliation(s)
- Chengshu Wang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China
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128
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Rieseberg L, Vines T, Gow J, Geraldes A. Editorial 2015. Mol Ecol 2015; 24:1-17. [DOI: 10.1111/mec.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
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129
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Kong S, Park SY, Lee YH. Systematic characterization of the bZIP transcription factor gene family in the rice blast fungus, Magnaporthe oryzae. Environ Microbiol 2014; 17:1425-43. [PMID: 25314920 DOI: 10.1111/1462-2920.12633] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 09/10/2014] [Accepted: 09/10/2014] [Indexed: 01/26/2023]
Abstract
Regulatory roles of the basic leucine zipper (bZIP) transcription factors (TFs) in fungi have been identified in diverse cellular processes such as development, nutrient utilization and various stress responses. In this study, the 22 Magnaporthe oryzae genes encoding bZIP TFs were systematically characterized. Phylogenetic analysis of fungal bZIP TFs revealed that seven MobZIPs are Magnaporthe-specific, while others belongs to 15 clades of orthologous Ascomycota genes. Expression patterns of MobZIPs under various conditions showed that they are highly stress responsive. We generated deletion mutants for 13 MobZIPs: nine with orthologues in other fungal species and four Magnaporthe-specific ones. Seven of them exhibited defects in mycelial growth, development and/or pathogenicity. Consistent with the conserved functions of the orthologues, MobZIP22 and MobZIP13 played a role in sulfur metabolism and iron homeostasis respectively. Along with MobZIP22 and MobZIP13, one Magnaporthe-specific gene, MobZIP11 is essential for pathogenicity in a reactive oxygen species-dependent manner. Taken together, our results will contribute to understanding the regulatory mechanisms of the bZIP TF gene family in fungal development, adaptation to environmental stresses and pathogenicity in the rice blast fungus.
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Affiliation(s)
- Sunghyung Kong
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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130
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Abstract
Owing to their small size and paucity of phenotypic characters, progress in the evolutionary biology of microbes in general, and human pathogenic fungi in particular, has been linked to a series of advances in DNA sequencing over the past quarter century. Phylogenetics was the first area to benefit, with the achievement of a basic understanding of fungal phylogeny. Population genetics was the next advance, finding cryptic species everywhere, and recombination in species previously thought to be asexual. Comparative genomics saw the next advance, in which variation in gene content and changes in gene family size were found to be important sources of variation. Fungal population genomics is showing that gene flow among closely related populations and species provides yet another source of adaptive, genetic variation. Now, two means to associate genetic variation with phenotypic variation, "reverse ecology" for adaptive phenotypes, and genome-wide association of any phenotype, are letting evolutionary biology make a profound contribution to molecular developmental biology of pathogenic fungi.
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Affiliation(s)
- John W Taylor
- University of California, Berkeley, California 94720-3102
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131
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Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation. Proc Natl Acad Sci U S A 2014; 111:16796-801. [PMID: 25368161 DOI: 10.1073/pnas.1412662111] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Much remains unknown regarding speciation. Host-pathogen interactions are a major driving force for diversification, but the genomic basis for speciation and host shifting remains unclear. The fungal genus Metarhizium contains species ranging from specialists with very narrow host ranges to generalists that attack a wide range of insects. By genomic analyses of seven species, we demonstrated that generalists evolved from specialists via transitional species with intermediate host ranges and that this shift paralleled insect evolution. We found that specialization was associated with retention of sexuality and rapid evolution of existing protein sequences whereas generalization was associated with protein-family expansion, loss of genome-defense mechanisms, genome restructuring, horizontal gene transfer, and positive selection that accelerated after reinforcement of reproductive isolation. These results advance understanding of speciation and genomic signatures that underlie pathogen adaptation to hosts.
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132
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Gross A, Hosoya T, Queloz V. Population structure of the invasive forest pathogen Hymenoscyphus pseudoalbidus. Mol Ecol 2014; 23:2943-60. [PMID: 24819666 DOI: 10.1111/mec.12792] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 12/21/2022]
Abstract
Understanding the genetic diversity and structure of invasive pathogens in source and in introduced areas is crucial to the revelation of hidden biological features of an organism, to the reconstruction of the course of invasions and to the establishment of effective control measures. Hymenoscyphus pseudoalbidus (anamorph: Chalara fraxinea) is an invasive and highly destructive fungal pathogen found on common ash Fraxinus excelsior in Europe and is native to East Asia. To gain insights into its dispersal mechanisms and history of invasion, we used microsatellite markers and characterized the genetic structure and diversity of H. pseudoalbidus populations at three spatial levels: (i) between Europe and Japan, (ii) in Europe and (iii) at the epidemic's front in Switzerland. Phylogenetic and network analysis demonstrated that individuals from both regions are conspecific. However, populations from Japan harboured a higher genetic diversity and were genetically differentiated from European ones. No evident population structure was found among the 1208 European strains using Bayesian and multivariate clustering analysis. Only the distribution of genetic diversity in space, pairwise population differentiation (GST) and the spatial analysis of principal components revealed a faint geographical pattern around Europe. A significant allele deficiency in most European populations pointed to a recent genetic bottleneck, whereas no pattern of isolation by distance was found. Our data suggest that H. pseudoalbidus was introduced just once by at least two individuals. The potential source region of H. pseudoalbidus is vast, and further investigations are required for a more accurate localization of the source population.
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Affiliation(s)
- Andrin Gross
- Forest Pathology and Dendrology, Institute of Integrative Biology (IBZ), ETH Zurich, Universitätsstrasse 16, Zurich, 8092, Switzerland
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133
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Peris D, Sylvester K, Libkind D, Gonçalves P, Sampaio JP, Alexander WG, Hittinger CT. Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids. Mol Ecol 2014; 23:2031-45. [PMID: 24612382 DOI: 10.1111/mec.12702] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 12/17/2022]
Abstract
Reticulate evolution can be a major driver of diversification into new niches, especially in disturbed habitats and at the edges of ranges. Industrial fermentation strains of yeast provide a window into these processes, but progress has been hampered by a limited understanding of the natural diversity and distribution of Saccharomyces species and populations. For example, lager beer is brewed with Saccharomyces pastorianus, an alloploid hybrid of S. cerevisiae and S. eubayanus, a species only recently discovered in Patagonia, Argentina. Here, we report that genetically diverse strains of S. eubayanus are readily isolated from Patagonia, demonstrating that the species is well established there. Analyses of multilocus sequence data strongly suggest that there are two diverse and highly differentiated Patagonian populations. The low nucleotide diversity found in the S. eubayanus moiety of hybrid European brewing strains suggests that their alleles were drawn from a small subpopulation that is closely related to one of the Patagonian populations. For the first time, we also report the rare isolation of S. eubayanus outside Patagonia, in Wisconsin, USA. In contrast to the clear population differentiation in Patagonia, the North American strains represent a recent and possibly transient admixture of the two Patagonian populations. These complex and varied reticulation events are not adequately captured by conventional phylogenetic methods and required analyses of Bayesian concordance factors and phylogenetic networks to accurately summarize and interpret. These findings show how genetically diverse eukaryotic microbes can produce rare but economically important hybrids with low genetic diversity when they migrate from their natural ecological context.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
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Stam R, Mantelin S, McLellan H, Thilliez G. The role of effectors in nonhost resistance to filamentous plant pathogens. FRONTIERS IN PLANT SCIENCE 2014; 5:582. [PMID: 25426123 PMCID: PMC4224059 DOI: 10.3389/fpls.2014.00582] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/08/2014] [Indexed: 05/18/2023]
Abstract
In nature, most plants are resistant to a wide range of phytopathogens. However, mechanisms contributing to this so-called nonhost resistance (NHR) are poorly understood. Besides constitutive defenses, plants have developed two layers of inducible defense systems. Plant innate immunity relies on recognition of conserved pathogen-associated molecular patterns (PAMPs). In compatible interactions, pathogenicity effector molecules secreted by the invader can suppress host defense responses and facilitate the infection process. Additionally, plants have evolved pathogen-specific resistance mechanisms based on recognition of these effectors, which causes secondary defense responses. The current effector-driven hypothesis is that NHR in plants that are distantly related to the host plant is triggered by PAMP recognition that cannot be efficiently suppressed by the pathogen, whereas in more closely related species, nonhost recognition of effectors would play a crucial role. In this review we give an overview of current knowledge of the role of effector molecules in host and NHR and place these findings in the context of the model. We focus on examples from filamentous pathogens (fungi and oomycetes), discuss their implications for the field of plant-pathogen interactions and relevance in plant breeding strategies for development of durable resistance in crops.
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Affiliation(s)
- Remco Stam
- Division of Plant Sciences, University of Dundee – The James Hutton InstituteDundee, UK
- *Correspondence: Remco Stam, Division of Plant Sciences, University of Dundee – The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, UK e-mail:
| | - Sophie Mantelin
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
| | - Hazel McLellan
- Division of Plant Sciences, University of Dundee – The James Hutton InstituteDundee, UK
| | - Gaëtan Thilliez
- Division of Plant Sciences, University of Dundee – The James Hutton InstituteDundee, UK
- Cell and Molecular Sciences, The James Hutton InstituteDundee, UK
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