1
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Treindl AD, Stapley J, Croll D, Leuchtmann A. Two-speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations. Mol Ecol 2024; 33:e17242. [PMID: 38084851 DOI: 10.1111/mec.17242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host-specific species that can sterilize their grass hosts. We performed selection scans using genome-wide SNP data from seven natural populations of two co-occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT-rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall-degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems.
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Affiliation(s)
- Artemis D Treindl
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jessica Stapley
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Adrian Leuchtmann
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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2
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Duhamel M, Hood ME, Rodríguez de la Vega RC, Giraud T. Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi. Nat Commun 2023; 14:5692. [PMID: 37709766 PMCID: PMC10502011 DOI: 10.1038/s41467-023-41413-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
In the absence of recombination, the number of transposable elements (TEs) increases due to less efficient selection, but the dynamics of such TE accumulations are not well characterized. Leveraging a dataset of 21 independent events of recombination cessation of different ages in mating-type chromosomes of Microbotryum fungi, we show that TEs rapidly accumulated in regions lacking recombination, but that TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 million years following recombination suppression. The same TE superfamilies have expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements (Helitrons). Long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies also expanded, through transposition bursts (distinguished from gene conversion based on LTR divergence), with both non-recombining regions and autosomes affected, suggesting that non-recombining regions constitute TE reservoirs. This study improves our knowledge of genome evolution by showing that TEs can accumulate through bursts, following non-linear decelerating dynamics.
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Affiliation(s)
- Marine Duhamel
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France.
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
| | - Michael E Hood
- Department of Biology, Amherst College, 01002-5000, Amherst, MA, USA
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
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3
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Lovelace AH, Dorhmi S, Hulin MT, Li Y, Mansfield JW, Ma W. Effector Identification in Plant Pathogens. PHYTOPATHOLOGY 2023; 113:637-650. [PMID: 37126080 DOI: 10.1094/phyto-09-22-0337-kd] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Effectors play a central role in determining the outcome of plant-pathogen interactions. As key virulence proteins, effectors are collectively indispensable for disease development. By understanding the virulence mechanisms of effectors, fundamental knowledge of microbial pathogenesis and disease resistance have been revealed. Effectors are also considered double-edged swords because some of them activate immunity in disease resistant plants after being recognized by specific immune receptors, which evolved to monitor pathogen presence or activity. Characterization of effector recognition by their cognate immune receptors and the downstream immune signaling pathways is instrumental in implementing resistance. Over the past decades, substantial research effort has focused on effector biology, especially concerning their interactions with virulence targets or immune receptors in plant cells. A foundation of this research is robust identification of the effector repertoire from a given pathogen, which depends heavily on bioinformatic prediction. In this review, we summarize methodologies that have been used for effector mining in various microbial pathogens which use different effector delivery mechanisms. We also discuss current limitations and provide perspectives on how recently developed analytic tools and technologies may facilitate effector identification and hence generation of a more complete vision of host-pathogen interactions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
| | - Sara Dorhmi
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
- Department of Microbiology and Plant Pathology, University of California Riverside, CA 92521, U.S.A
| | | | - Yufei Li
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
| | - John W Mansfield
- Faculty of Natural Sciences, Imperial College London, London, SW7 2BX, U.K
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
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4
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The use of evolutionary analyses to predict functionally relevant traits in filamentous plant pathogens. Curr Opin Microbiol 2023; 73:102244. [PMID: 36889024 DOI: 10.1016/j.mib.2022.102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 03/08/2023]
Abstract
Identifying traits involved in plant-pathogen interactions is one of the major objectives in molecular plant pathology. Evolutionary analyses may assist in the identification of genes encoding traits that are involved in virulence and local adaptation, including adaptation to agricultural intervention strategies. In the past decades, the number of available genome sequences of fungal plant pathogens has rapidly increased, providing a rich source for the discovery of functionally important genes as well as inference of species histories. Positive selection in the form of diversifying or directional selection leaves particular signatures in genome alignments and can be identified with statistical genetics methods. This review summarises the concepts and approaches used in evolutionary genomics and lists major discoveries related to plant-pathogen adaptative evolution. We underline the significant contribution of evolutionary genomics in discovering virulence-related traits and the study of plant-pathogen ecology and adaptive evolution.
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5
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Guerillot P, Salamov A, Louet C, Morin E, Frey P, Grigoriev IV, Duplessis S. A Remarkable Expansion of Oligopeptide Transporter Genes in Rust Fungi (Pucciniales) Suggests a Specialization in Nutrient Acquisition for Obligate Biotrophy. PHYTOPATHOLOGY 2023; 113:252-264. [PMID: 36044359 DOI: 10.1094/phyto-04-22-0128-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nutrient acquisition by rust fungi during their biotrophic growth has been assigned to a few transporters expressed in haustorial infection structures. We performed a comparative genomic analysis of all transporter genes (hereafter termed transportome) classified according to the Transporter Classification Database, focusing specifically on rust fungi (order Pucciniales) versus other species in the Dikarya. We also surveyed expression of transporter genes in the poplar rust fungus for which transcriptomics data are available across the whole life cycle. Despite a significant increase in gene number, rust fungi presented a reduced transportome compared with most fungi in the Dikarya. However, a few transporter families in the subclass Porters showed significant expansions. Notably, three metal transport-related families involved in the import, export, and sequestration of metals were expanded in Pucciniales and expressed at various stages of the rust life cycle, suggesting a tight regulation of metal homeostasis. The most remarkable gene expansion in the Pucciniales was observed for the oligopeptide transporter (OPT) family, with 25 genes on average compared with seven to 14 genes in the other surveyed taxonomical ranks. A phylogenetic analysis showed several specific expansion events at the root of the order Pucciniales with subsequent expansions in rust taxonomical families. The OPT genes showed dynamic expression patterns along the rust life cycle and more particularly during infection of the poplar host tree, suggesting a possible specialization for the acquisition of nitrogen and sulfur through the transport of oligopeptides from the host during biotrophic growth.
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Affiliation(s)
- Pamela Guerillot
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Clémentine Louet
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Pascal Frey
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, U.S.A
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6
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Souilmi Y, Tobler R, Johar A, Williams M, Grey ST, Schmidt J, Teixeira JC, Rohrlach A, Tuke J, Johnson O, Gower G, Turney C, Cox M, Cooper A, Huber CD. Admixture has obscured signals of historical hard sweeps in humans. Nat Ecol Evol 2022; 6:2003-2015. [PMID: 36316412 PMCID: PMC9715430 DOI: 10.1038/s41559-022-01914-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.
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Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Angad Johar
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
| | - Matthew Williams
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Shane T Grey
- Transplantation Immunology Group, Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, New South Wales, Australia
| | - Joshua Schmidt
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - João C Teixeira
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adam Rohrlach
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jonathan Tuke
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Olivia Johnson
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Graham Gower
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Chris Turney
- Chronos 14Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Murray Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia.
- BlueSky Genetics, Ashton, South Australia, Australia.
| | - Christian D Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Biology, Penn State University, University Park, PA, USA.
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7
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Bazzicalupo A. Local adaptation in fungi. FEMS Microbiol Rev 2022; 46:6604384. [PMID: 35675293 DOI: 10.1093/femsre/fuac026] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 01/09/2023] Open
Abstract
In this review, I explore the pervasive but underappreciated role of local adaptation in fungi. It has been difficult historically to study local adaptation in fungi because of the limited understanding of fungal species and their traits, but new hope has been offered with technological advances in sequencing. The filamentous nature of fungi invalidates some assumptions made in evolution because of their ability to exist as multinucleate entities with genetically different nuclei sharing the same cytoplasm. Many insights on local adaptation have come from studying fungi, and much of the empirical evidence gathered about local adaptation in the context of host-pathogen interactions comes from studying fungal virulence genes, drug resistance, and environmental adaptation. Together, these insights paint a picture of the variety of processes involved in fungal local adaptation and their connections to the unusual cell biology of Fungi (multinucleate, filamentous habit), but there is much that remains unknown, with major gaps in our knowledge of fungal species, their phenotypes, and the ways by which they adapt to local conditions.
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Affiliation(s)
- Anna Bazzicalupo
- Department of Zoology, University of British Columbia, 4200 - 6270 University Blvd., Vancouver V6T 1Z4, Canada
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8
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Wang L, Liu Q, Ge S, Liang W, Liao W, Li W, Jiao G, Wei X, Shao G, Xie L, Sheng Z, Hu S, Tang S, Hu P. Genomic footprints related with adaptation and fumonisins production in Fusarium proliferatum. Front Microbiol 2022; 13:1004454. [PMID: 36212817 PMCID: PMC9532532 DOI: 10.3389/fmicb.2022.1004454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Fusarium proliferatum is the principal etiological agent of rice spikelet rot disease (RSRD) in China, causing yield losses and fumonisins contamination in rice. The intraspecific variability and evolution pattern of the pathogen is poorly understood. Here, we performed whole-genome resequencing of 67 F. proliferatum strains collected from major rice-growing regions in China. Population structure indicated that eastern population of F. proliferatum located in Yangtze River with the high genetic diversity and recombinant mode that was predicted as the putative center of origin. Southern population and northeast population were likely been introduced into local populations through gene flow, and genetic differentiation between them might be shaped by rice-driven domestication. A total of 121 distinct genomic loci implicated 85 candidate genes were suggestively associated with variation of fumonisin B1 (FB1) production by genome-wide association study (GWAS). We subsequently tested the function of five candidate genes (gabap, chsD, palA, hxk1, and isw2) mapped in our association study by FB1 quantification of deletion strains, and mutants showed the impact on FB1 production as compared to the wide-type strain. Together, this is the first study to provide insights into the evolution and adaptation in natural populations of F. proliferatum on rice, as well as the complex genetic architecture for fumonisins biosynthesis.
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9
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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10
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Pereira D, Oggenfuss U, McDonald BA, Croll D. Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen. Microb Genom 2021; 7:000540. [PMID: 34424154 PMCID: PMC8549362 DOI: 10.1099/mgen.0.000540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.
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Affiliation(s)
- Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Present address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, D-24306 Plön, Germany
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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11
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Quo vadis: signaling molecules and small secreted proteins from mycorrhizal fungi at the early stage of mycorrhiza formation. Symbiosis 2021. [DOI: 10.1007/s13199-021-00793-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Märkle H, John S, Cornille A, Fields PD, Tellier A. Novel genomic approaches to study antagonistic coevolution between hosts and parasites. Mol Ecol 2021; 30:3660-3676. [PMID: 34038012 DOI: 10.1111/mec.16001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/09/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Host-parasite coevolution is ubiquitous, shaping genetic and phenotypic diversity and the evolutionary trajectory of interacting species. With the advances of high throughput sequencing technologies applicable to model and non-model organisms alike, it is now feasible to study in greater detail (a) the genetic underpinnings of coevolution, (b) the speed and type of dynamics at coevolving loci, and (c) the genomic consequences of coevolution. This review focuses on three recently developed approaches that leverage information from host and parasite full genome data simultaneously to pinpoint coevolving loci and draw inference on the coevolutionary history. First, co-genome-wide association study (co-GWAS) methods allow pinpointing the loci underlying host-parasite interactions. These methods focus on detecting associations between genetic variants and the outcome of experimental infection tests or on correlations between genomes of naturally infected hosts and their infecting parasites. Second, extensions to population genomics methods can detect genes under coevolution and infer the coevolutionary history, such as fitness costs. Third, correlations between host and parasite population size in time are indicative of coevolution, and polymorphism levels across independent spatially distributed populations of hosts and parasites can reveal coevolutionary loci and infer coevolutionary history. We describe the principles of these three approaches and discuss their advantages and limitations based on coevolutionary theory. We present recommendations for their application to various host (prokaryotes, fungi, plants, and animals) and parasite (viruses, bacteria, fungi, and macroparasites) species. We conclude by pointing out methodological and theoretical gaps to be filled to extract maximum information from full genome data and thereby to shed light on the molecular underpinnings of coevolution.
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Affiliation(s)
- Hanna Märkle
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Sona John
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Amandine Cornille
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Peter D Fields
- Department of Environmental Sciences, University of Basel, Zoology, Basel, Switzerland
| | - Aurélien Tellier
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
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Abstract
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance.IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
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14
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Eschenbrenner CJ, Feurtey A, Stukenbrock EH. Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments. Methods Mol Biol 2021; 2090:337-355. [PMID: 31975174 DOI: 10.1007/978-1-0716-0199-0_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genome sequencing of fungal pathogens have documented extensive variation in genome structure and composition between species and in many cases between individuals of the same species. This type of genomic variation can be adaptive for pathogens to rapidly evolve new virulence phenotypes. Analyses of genome-wide variation in fungal pathogen genomes rely on high quality assemblies and methods to detect and quantify structural variation. Population genomic studies in fungi have addressed the underlying mechanisms whereby structural variation can be rapidly generated. Transposable elements, high mutation and recombination rates as well as incorrect chromosome segregation during mitosis and meiosis contribute to extensive variation observed in many species. We here summarize key findings in the field of fungal pathogen genomics and we discuss methods to detect and characterize structural variants including an alignment-based pipeline to study variation in population genomic data.
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Affiliation(s)
- Christoph J Eschenbrenner
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Alice Feurtey
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
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15
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Everhart S, Gambhir N, Stam R. Population Genomics of Filamentous Plant Pathogens-A Brief Overview of Research Questions, Approaches, and Pitfalls. PHYTOPATHOLOGY 2021; 111:12-22. [PMID: 33337245 DOI: 10.1094/phyto-11-20-0527-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With ever-decreasing sequencing costs, research on the population biology of plant pathogens is transitioning from population genetics-using dozens of genetic markers or polymorphism data of several genes-to population genomics-using several hundred to tens of thousands of markers or whole-genome sequence data. The field of population genomics is characterized by rapid theoretical and methodological advances and by numerous steps and pitfalls in its technical and analytical workflow. In this article, we aim to provide a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens and direct readers to more extensive reviews for in-depth understanding. We briefly discuss different types of population genomics-inspired research questions and give insights into the sampling strategies that can be used to answer such questions. We then consider different sequencing strategies, the various options available for data processing, and some of the currently available tools for population genomic data analysis. We conclude by highlighting some of the hurdles along the population genomic workflow, providing cautionary warnings relative to assumptions and technical challenges, and presenting our own future perspectives of the field of population genomics for filamentous plant pathogens.
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Affiliation(s)
- Sydney Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Nikita Gambhir
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583, U.S.A
| | - Remco Stam
- Phytopathology, School of Life Sciences Weihenstephan, Technical University Munich, Germany
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16
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Hartmann FE, Rodríguez de la Vega RC, Gladieux P, Ma WJ, Hood ME, Giraud T. Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence. Mol Biol Evol 2020; 37:668-682. [PMID: 31651949 PMCID: PMC7038665 DOI: 10.1093/molbev/msz252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Wen-Juan Ma
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Michael E Hood
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
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17
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Bueker B, Guerreiro MA, Hood ME, Brachmann A, Rahmann S, Begerow D. Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicity. BMC Evol Biol 2020; 20:123. [PMID: 32942986 PMCID: PMC7499883 DOI: 10.1186/s12862-020-01689-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 09/10/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Hybridization is a central mechanism in evolution, producing new species or introducing important genetic variation into existing species. In plant-pathogenic fungi, adaptation and specialization to exploit a host species are key determinants of evolutionary success. Here, we performed experimental crosses between the two pathogenic Microbotryum species, M. lychnidis-dioicae and M. silenes-acaulis that are specialized to different hosts. The resulting offspring were analyzed on phenotypic and genomic levels to describe genomic characteristics of hybrid offspring and genetic factors likely involved in host-specialization. RESULTS Genomic analyses of interspecific fungal hybrids revealed that individuals were most viable if the majority of loci were inherited from one species. Interestingly, species-specific loci were strictly controlled by the species' origin of the mating type locus. Moreover we detected signs of crossing over and chromosome duplications in the genomes of the analyzed hybrids. In Microbotryum, mitochondrial DNA was found to be uniparentally inherited from the a2 mating type. Genome comparison revealed that most gene families are shared and the majority of genes are conserved between the two species, indicating very similar biological features, including infection and pathogenicity processes. Moreover, we detected 211 candidate genes that were retained under host-driven selection of backcrossed lines. These genes and might therefore either play a crucial role in host specialization or be linked to genes that are essential for specialization. CONCLUSION The combination of genome analyses with experimental selection and hybridization is a promising way to investigate host-pathogen interactions. This study manifests genetic factors of host specialization that are required for successful biotrophic infection of the post-zygotic stage, but also demonstrates the strong influence of intra-genomic conflicts or instabilities on the viability of hybrids in the haploid host-independent stage.
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Affiliation(s)
- Britta Bueker
- AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
- Department of Biology, Amherst College, 220 South Pleasant Street, Amherst, MA, 01002, USA.
| | | | - Michael E Hood
- Department of Biology, Amherst College, 220 South Pleasant Street, Amherst, MA, 01002, USA
| | - Andreas Brachmann
- Biocenter of the LMU Munich, Genetics Section, Grosshaderner Str. 2-4, 82152, Planegg- Martinsried, Germany
| | - Sven Rahmann
- Genominformatik, Institut für Humangenetik, Medizinische Fakultät, Universität Duisburg-Essen, Hufelandstraße 55, 45122, Essen, Germany
| | - Dominik Begerow
- AG Geobotanik, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany
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18
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Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet 2020; 21:754-768. [PMID: 32860017 DOI: 10.1038/s41576-020-0269-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
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Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
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19
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de Vries S, Stukenbrock EH, Rose LE. Rapid evolution in plant-microbe interactions - an evolutionary genomics perspective. THE NEW PHYTOLOGIST 2020; 226:1256-1262. [PMID: 31997351 DOI: 10.1111/nph.16458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 01/13/2020] [Indexed: 05/22/2023]
Abstract
Access to greater genomic resolution through new sequencing technologies is transforming the field of plant pathology. As scientists embrace these new methods, some overarching patterns and observations come into focus. Evolutionary genomic studies are used to determine not only the origins of pathogen lineages and geographic patterns of genetic diversity, but also to discern how natural selection structures genetic variation across the genome. With greater and greater resolution, we can now pinpoint the targets of selection on a large scale. At multiple levels, crypsis and convergent evolution are evident. Host jumps and shifts may be more pervasive than once believed, and hybridization and horizontal gene transfer (HGT) likely play important roles in the emergence of genetic novelty.
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Affiliation(s)
- Sophie de Vries
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- The Botanical Institute, Christian-Albrechts University of Kiel, Am Botanischen Garden 9-11, 24118, Kiel, Germany
| | - Laura E Rose
- Institute of Population Genetics, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
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20
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Derbyshire MC. Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action. Front Microbiol 2020; 11:644. [PMID: 32328056 PMCID: PMC7160247 DOI: 10.3389/fmicb.2020.00644] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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21
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Ma WJ, Carpentier F, Giraud T, Hood ME. Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration. Genome Biol Evol 2020; 12:243-258. [PMID: 32058544 PMCID: PMC7150583 DOI: 10.1093/gbe/evaa028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2020] [Indexed: 12/13/2022] Open
Abstract
Degenerative mutations in non-recombining regions, such as in sex chromosomes, may lead to differential expression between alleles if mutations occur stochastically in one or the other allele. Reduced allelic expression due to degeneration has indeed been suggested to occur in various sex-chromosome systems. However, whether an association occurs between specific signatures of degeneration and differential expression between alleles has not been extensively tested, and sexual antagonism can also cause differential expression on sex chromosomes. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal for testing associations between specific degenerative signatures and differential expression because 1) there are multiple evolutionary strata on the mating-type chromosomes, reflecting successive recombination suppression linked to mating-type loci; 2) separate haploid cultures of opposite mating types help identify differential expression between alleles; and 3) there is no sexual antagonism as a confounding factor accounting for differential expression. We found that differentially expressed genes were enriched in the four oldest evolutionary strata compared with other genomic compartments, and that, within compartments, several signatures of sequence degeneration were greater for differentially expressed than non-differentially expressed genes. Two particular degenerative signatures were significantly associated with lower expression levels within differentially expressed allele pairs: upstream insertion of transposable elements and mutations truncating the protein length. Other degenerative mutations associated with differential expression included nonsynonymous substitutions and altered intron or GC content. The association between differential expression and allele degeneration is relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions where recombination is suppressed.
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Affiliation(s)
- Wen-Juan Ma
- Department of Biology, Amherst College, Amherst, MA
| | - Fantin Carpentier
- Ecologie Systematique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, Orsay, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, Université Paris-Saclay, CNRS, AgroParisTech, Orsay, France
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22
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Hartmann FE, Snirc A, Cornille A, Godé C, Touzet P, Van Rossum F, Fournier E, Le Prieur S, Shykoff J, Giraud T. Congruent population genetic structures and divergence histories in anther‐smut fungi and their host plants
Silene italica
and the
Silene nutans
species complex. Mol Ecol 2020; 29:1154-1172. [DOI: 10.1111/mec.15387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Fanny E. Hartmann
- Ecologie Systematique Evolution Batiment 360 AgroParisTech CNRS Universite Paris‐Saclay Orsay France
| | - Alodie Snirc
- Ecologie Systematique Evolution Batiment 360 AgroParisTech CNRS Universite Paris‐Saclay Orsay France
| | - Amandine Cornille
- Genetique Quantitative et Evolution–Le Moulon AgroParisTech CNRS INRAE Universite Paris‐Saclay Gif‐sur‐Yvette France
| | - Cécile Godé
- UMR 8198 ‐ Evo‐Eco‐Paleo CNRS Univ. Lille Lille France
| | - Pascal Touzet
- UMR 8198 ‐ Evo‐Eco‐Paleo CNRS Univ. Lille Lille France
| | - Fabienne Van Rossum
- Meise Botanic Garden Meise Belgium
- Fédération Wallonie–Bruxelles Brussels Belgium
| | | | - Stéphanie Le Prieur
- Ecologie Systematique Evolution Batiment 360 AgroParisTech CNRS Universite Paris‐Saclay Orsay France
| | - Jacqui Shykoff
- Ecologie Systematique Evolution Batiment 360 AgroParisTech CNRS Universite Paris‐Saclay Orsay France
| | - Tatiana Giraud
- Ecologie Systematique Evolution Batiment 360 AgroParisTech CNRS Universite Paris‐Saclay Orsay France
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23
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Hartfield M, Bataillon T. Selective Sweeps Under Dominance and Inbreeding. G3 (BETHESDA, MD.) 2020; 10:1063-1075. [PMID: 31974096 PMCID: PMC7056974 DOI: 10.1534/g3.119.400919] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/18/2020] [Indexed: 12/26/2022]
Abstract
A major research goal in evolutionary genetics is to uncover loci experiencing positive selection. One approach involves finding 'selective sweeps' patterns, which can either be 'hard sweeps' formed by de novo mutation, or 'soft sweeps' arising from recurrent mutation or existing standing variation. Existing theory generally assumes outcrossing populations, and it is unclear how dominance affects soft sweeps. We consider how arbitrary dominance and inbreeding via self-fertilization affect hard and soft sweep signatures. With increased self-fertilization, they are maintained over longer map distances due to reduced effective recombination and faster beneficial allele fixation times. Dominance can affect sweep patterns in outcrossers if the derived variant originates from either a single novel allele, or from recurrent mutation. These models highlight the challenges in distinguishing hard and soft sweeps, and propose methods to differentiate between scenarios.
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Affiliation(s)
- Matthew Hartfield
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario M5S 3B2, Canada,
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, and
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, and
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24
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Mei L, Chen M, Shang Y, Tang G, Tao Y, Zeng L, Huang B, Li Z, Zhan S, Wang C. Population genomics and evolution of a fungal pathogen after releasing exotic strains to control insect pests for 20 years. ISME JOURNAL 2020; 14:1422-1434. [PMID: 32111946 PMCID: PMC7242398 DOI: 10.1038/s41396-020-0620-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/04/2020] [Accepted: 02/17/2020] [Indexed: 12/31/2022]
Abstract
Entomopathogenic fungi are one of the key regulators of insect populations in nature. Some species such as Beauveria bassiana with a wide host range have been developed as promising alternatives to chemical insecticides for the biocontrol of insect pests. However, the long-term persistence of the released strains, the effect on non-target hosts and local fungal populations remains elusive, but they are considerable concerns with respect to environmental safety. Here we report the temporal features of the Beauveria population genomics and evolution over 20 years after releasing exotic strains to control pine caterpillar pests. We found that the isolates within the biocontrol site were mostly of clonal origins. The released strains could persist in the environment for a long time but with low recovery rates. Similar to the reoccurrence of host jumping by local isolates, the infection of non-target insects by the released strains was evident to endemically occur in association with host seasonality. No obvious dilution effect on local population structure was evident by the releases. However, the population was largely replaced by genetically divergent isolates once per decade but evolved with a pattern of balancing selection and towards expansion through adaptation, non-random outcrossing and isolate migration. This study not only unveils the real-time features of entomopathogenic fungal population genomics and evolution but also provides added values to alleviate the concerns of environmental safety regarding the biocontrol application of mycoinsecticides.
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Affiliation(s)
- Lijuan Mei
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,CAS Center for Excellence in Biotic interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingjun Chen
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230031, China
| | - Yanfang Shang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Guirong Tang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ye Tao
- Biozeron Biotech Ltd., Shanghai, 201800, China
| | - Liang Zeng
- Biozeron Biotech Ltd., Shanghai, 201800, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230031, China
| | - Zengzhi Li
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230031, China
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Chengshu Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. .,CAS Center for Excellence in Biotic interactions, University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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25
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Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi. mBio 2019; 10:mBio.02391-19. [PMID: 31690676 PMCID: PMC6831777 DOI: 10.1128/mbio.02391-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant pathogens use molecular weapons to successfully infect their hosts, secreting a large portfolio of various proteins and enzymes. Different plant species are often parasitized by host-specific pathogens; however, it is still unclear whether the molecular basis of such host specialization involves species-specific weapons or different variants of the same weapons. We therefore compared the genes encoding secreted proteins in three plant-castrating pathogens parasitizing different host plants, producing their spores in plant anthers by replacing pollen. We validated our predictions for secretion signals for some genes and checked that our predicted secreted proteins were often highly expressed during plant infection. While we found few species-specific secreted proteins, numerous genes encoding secreted proteins showed signs of rapid evolution and of natural selection. Our study thus found that most changes among closely related host-specific pathogens involved rapid adaptive changes in shared molecular weapons rather than innovations for new weapons. Plant pathogens utilize a portfolio of secreted effectors to successfully infect and manipulate their hosts. It is, however, still unclear whether changes in secretomes leading to host specialization involve mostly effector gene gains/losses or changes in their sequences. To test these hypotheses, we compared the secretomes of three host-specific castrating anther smut fungi (Microbotryum), two being sister species. To address within-species evolution, which might involve coevolution and local adaptation, we compared the secretomes of strains from differentiated populations. We experimentally validated a subset of signal peptides. Secretomes ranged from 321 to 445 predicted secreted proteins (SPs), including a few species-specific proteins (42 to 75), and limited copy number variation, i.e., little gene family expansion or reduction. Between 52% and 68% of the SPs did not match any Pfam domain, a percentage that reached 80% for the small secreted proteins, indicating rapid evolution. In comparison to background genes, we indeed found SPs to be more differentiated among species and strains, more often under positive selection, and highly expressed in planta; repeat-induced point mutations (RIPs) had no role in effector diversification, as SPs were not closer to transposable elements than background genes and were not more RIP affected. Our study thus identified both conserved core proteins, likely required for the pathogenic life cycle of all Microbotryum species, and proteins that were species specific or evolving under positive selection; these proteins may be involved in host specialization and/or coevolution. Most changes among closely related host-specific pathogens, however, involved rapid changes in sequences rather than gene gains/losses.
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26
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Richards JK, Stukenbrock EH, Carpenter J, Liu Z, Cowger C, Faris JD, Friesen TL. Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States. PLoS Genet 2019; 15:e1008223. [PMID: 31626626 PMCID: PMC6821140 DOI: 10.1371/journal.pgen.1008223] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/30/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022] Open
Abstract
Filamentous fungi rapidly evolve in response to environmental selection pressures in part due to their genomic plasticity. Parastagonospora nodorum, a fungal pathogen of wheat and causal agent of septoria nodorum blotch, responds to selection pressure exerted by its host, influencing the gain, loss, or functional diversification of virulence determinants, known as effector genes. Whole genome resequencing of 197 P. nodorum isolates collected from spring, durum, and winter wheat production regions of the United States enabled the examination of effector diversity and genomic regions under selection specific to geographically discrete populations. 1,026,859 SNPs/InDels were used to identify novel loci, as well as SnToxA and SnTox3 as factors in disease. Genes displaying presence/absence variation, predicted effector genes, and genes localized on an accessory chromosome had significantly higher pN/pS ratios, indicating a higher rate of sequence evolution. Population structure analyses indicated two P. nodorum populations corresponding to the Upper Midwest (Population 1) and Southern/Eastern United States (Population 2). Prevalence of SnToxA varied greatly between the two populations which correlated with presence of the host sensitivity gene Tsn1 in the most prevalent cultivars in the corresponding regions. Additionally, 12 and 5 candidate effector genes were observed to be under diversifying selection among isolates from Population 1 and 2, respectively, but under purifying selection or neutrally evolving in the opposite population. Selective sweep analysis revealed 10 and 19 regions that had recently undergone positive selection in Population 1 and 2, respectively, involving 92 genes in total. When comparing genes with and without presence/absence variation, those genes exhibiting this variation were significantly closer to transposable elements. Taken together, these results indicate that P. nodorum is rapidly adapting to distinct selection pressures unique to spring and winter wheat production regions by rapid adaptive evolution and various routes of genomic diversification, potentially facilitated through transposable element activity.
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Affiliation(s)
- Jonathan K. Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - Eva H. Stukenbrock
- Department of Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jessica Carpenter
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Christina Cowger
- Plant Science Research Unit, USDA-ARS, Raleigh, North Carolina, United States of America
| | - Justin D. Faris
- Cereal Crops Research Unit, Edward T. Schaefer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
| | - Timothy L. Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
- Cereal Crops Research Unit, Edward T. Schaefer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
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27
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Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, Giraud T. Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:431-457. [PMID: 31337277 DOI: 10.1146/annurev-phyto-082718-095947] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Anther-smut fungi provide a powerful system to study host-pathogen specialization and coevolution, with hundreds of Microbotryum species specialized on diverse Caryophyllaceae plants, castrating their hosts through manipulation of the hosts' reproductive organs to facilitate disease transmission. Microbotryum fungi have exceptional genomic characteristics, including dimorphic mating-type chromosomes, that make this genus anexcellent model for studying the evolution of mating systems and their influence on population genetics structure and adaptive potential. Important insights into adaptation, coevolution, host specialization, and mating system evolution have been gained using anther-smut fungi, with new insights made possible by the recent advent of genomic approaches. We illustrate with Microbotryum case studies how using a combination of comparative genomics, population genomics, and transcriptomics approaches enables the integration of different evolutionary perspectives across different timescales. We also highlight current challenges and suggest future studies that will contribute to advancing our understanding of the mechanisms underlying adaptive processes in populations of fungal pathogens.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| | | | - Fantin Carpentier
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| | - Pierre Gladieux
- UMR BGPI, Univ. Montpellier, INRA, CIRAD, Montpellier SupAgro, 34398 Montpellier, France
| | - Amandine Cornille
- Génétique Quantitative et Evolution-Le Moulon, INRA; Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, Massachusetts 01002-5000, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
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28
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Zuo W, Ökmen B, Depotter JRL, Ebert MK, Redkar A, Misas Villamil J, Doehlemann G. Molecular Interactions Between Smut Fungi and Their Host Plants. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:411-430. [PMID: 31337276 DOI: 10.1146/annurev-phyto-082718-100139] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Smut fungi are a large group of biotrophic plant pathogens that infect mostly monocot species, including economically relevant cereal crops. For years, Ustilago maydis has stood out as the model system to study the genetics and cell biology of smut fungi as well as the pathogenic development of biotrophic plant pathogens. The identification and functional characterization of secreted effectors and their role in virulence have particularly been driven forward using the U. maydis-maize pathosystem. Today, advancing tools for additional smut fungi such as Ustilago hordei and Sporisorium reilianum, as well as an increasing number of available genome sequences, provide excellent opportunities to investigate in parallel the effector function and evolution associated with different lifestyles and host specificities. In addition, genome analyses revealed similarities in the genomic signature between pathogenic smuts and epiphytic Pseudozyma species. This review elaborates on how knowledge about fungal lifestyles, genome biology, and functional effector biology has helped in understanding the biology of this important group of fungal pathogens. We highlight the contribution of the U. maydis model system but also discuss the differences from other smut fungi, which raises the importance of comparative genomic and genetic analyses in future research.
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Affiliation(s)
- Weiliang Zuo
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany;
| | - Bilal Ökmen
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany;
| | - Jasper R L Depotter
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany;
| | - Malaika K Ebert
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany;
| | - Amey Redkar
- Current affiliation: Department of Genetics, University of Córdoba, 14071 Córdoba, Spain
| | - Johana Misas Villamil
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany;
| | - Gunther Doehlemann
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany;
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Kobmoo N, Mongkolsamrit S, Arnamnart N, Luangsa-Ard JJ, Giraud T. Population genomics revealed cryptic species within host-specific zombie-ant fungi (Ophiocordyceps unilateralis). Mol Phylogenet Evol 2019; 140:106580. [PMID: 31419479 DOI: 10.1016/j.ympev.2019.106580] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023]
Abstract
The identification and delimitation of species boundaries are essential for understanding speciation and adaptation processes and for the management of biodiversity as well as development for applications. Ophiocordyceps unilateralis sensu lato is a complex of fungal pathogens parasitizing Formicine ants, inducing zombie behaviors in their hosts. Previous taxonomic works with limited numbers of samples and markers led to the "one ant-one fungus" paradigm, resulting in the use of ant species as a proxy for fungal identification. Here, a population genomics study with sampling on three ant species across Thailand supported the existence of host-specific species in O. unilateralis s.l. with no footprints of long term introgression despite occasional host shifts and first-generation hybrids. We further detected genetic clusters within the previously delimited fungal species, with each little footprints of recombination, suggesting high levels of inbreeding. The clusters within each of O. camponoti-leonardi and O. camponoti-saundersi were supported by differentiation throughout the genome, suggesting they may constitute further cryptic species parasitizing the same host, challenging the one ant-one fungus paradigm. These genetic clusters had different geographical ranges, supporting different biogeographic influences between the north/center and the south of Thailand, reinforcing the scenario in which Thailand endured compartmentation during the latest Pleistocene glacial cycles.
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Affiliation(s)
- Noppol Kobmoo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France.
| | - Suchada Mongkolsamrit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Nuntanat Arnamnart
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Janet Jennifer Luangsa-Ard
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
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30
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Saville BJ, Perlin MH. "When worlds collide and smuts converge": Tales from the 1st International Ustilago/Smut Convergence. Fungal Genet Biol 2019; 132:103260. [PMID: 31394176 DOI: 10.1016/j.fgb.2019.103260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 11/15/2022]
Abstract
From the evening of March 12, till dinner on March 13, 2017, the 1st International Ustilago/Smut Convergence took place as a workshop prior to the start of the 29th Fungal Genetics Conference, in Asilomar, California. The overall goals of the meeting were to expand the smut model systems being used and to expand participation by the next generations of scientists with these fungi. These goals were implemented through a combination of emphasis on student and post-doc presentations, mentoring of such individuals, and active recruitment of participation by groups under-represented at such meetings in recent years in the US, especially those from Latin America and other Spanish-speaking countries. Work was presented at the first workshop on U. maydis, Sporosorium reilianum, Microbotryum violaceum, U. esculenta, and Thecaphora thlaspeos. Students and post-doctoral researchers were encouraged to present their "just-in-time," as-yet-unpublished data, in a safe environment, with the understanding of those attending the meeting that this early access was a privilege not to be taken advantage of. The result was lively and constructive discussion, including a variety of presentations by these young scientists on putative and characterized smut effector proteins, clearly at the forefront of such research, even considering the advances presented later that week at the Fungal Genetics Conference. This review also briefly compares the first meeting with the events of the recent 2nd International Ustilago/Smut Convergence (March 11-12, 2019), which ended with a tribute to Prof. Dr. Regine Kahmann, in honor of her career, and especially for her contributions to the field of smut genetics.
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Affiliation(s)
- Barry J Saville
- Forensic Science Program, Trent University, Peterborough, Canada
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA.
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31
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Legras JL, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, Franco-Duarte R, Marcet-Houben M, Gabaldon T, Schuller D, Sampaio JP, Dequin S. Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication. Mol Biol Evol 2019; 35:1712-1727. [PMID: 29746697 PMCID: PMC5995190 DOI: 10.1093/molbev/msy066] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries, and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups. Most of these strains, compared with the reference genome, possessed additional genetic elements acquired by introgression or horizontal transfer, several of which were population-specific. In addition, several genomic regions in each population showed evidence of nonneutral evolution, as shown by high differentiation, or of selective sweeps including genes with key functions in these environments (e.g., amino acid transport for wine yeast). Linking genetics to lifestyle differences and metabolite traits has enabled us to elucidate the genetic basis of several niche-specific population traits, such as growth on galactose for cheese strains. These data indicate that yeast has been subjected to various divergent selective pressures depending on its niche, requiring the development of customized genomes for better survival in these environments. These striking genome dynamics associated with local adaptation and domestication reveal the remarkable plasticity of the S. cerevisiae genome, revealing this species to be an amazing complex of specialized populations.
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Affiliation(s)
- Jean-Luc Legras
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Virginie Galeote
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Frédéric Bigey
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Carole Camarasa
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Souhir Marsit
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Thibault Nidelet
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Arnaud Couloux
- Centre National de Séquençage, Institut de Genomique, Genoscope, Evry Cedex, France
| | - Julie Guy
- Centre National de Séquençage, Institut de Genomique, Genoscope, Evry Cedex, France
| | - Ricardo Franco-Duarte
- CBMA, Department of Biology, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Toni Gabaldon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona, Spain
| | - Dorit Schuller
- CBMA, Department of Biology, Universidade do Minho, Campus de Gualtar, Braga, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Sylvie Dequin
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
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33
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Derbyshire MC, Denton-Giles M, Hane JK, Chang S, Mousavi-Derazmahalleh M, Raffaele S, Buchwaldt L, Kamphuis LG. A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum. PLoS One 2019; 14:e0214201. [PMID: 30921376 PMCID: PMC6438532 DOI: 10.1371/journal.pone.0214201] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 03/10/2019] [Indexed: 01/08/2023] Open
Abstract
The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking. We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents–Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps. Among the 25 isolates, there was evidence for two major population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), and the other consisted of nine isolates from Australia and one from Morocco (population 2). The rest of the isolates were genotypic outliers. We found that there was evidence of outcrossing in these two populations based on linkage disequilibrium decay. However, only a single candidate selective sweep was observed, and it was present in population 2. This sweep was close to a Major Facilitator Superfamily transporter gene, and we speculate that this gene may have a role in nutrient uptake from the host. The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens. This may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction.
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Affiliation(s)
- Mark Charles Derbyshire
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
- * E-mail:
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Steven Chang
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Mahsa Mousavi-Derazmahalleh
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes-Micro-organismes (LIPM), Université de Toulouse, INRA, Toulouse, France
| | - Lone Buchwaldt
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatchewan, Saskatoon, Canada
| | - Lars G. Kamphuis
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
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34
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Saumitou-Laprade P, Vernet P, Dowkiw A, Bertrand S, Billiard S, Albert B, Gouyon PH, Dufay M. Polygamy or subdioecy? The impact of diallelic self-incompatibility on the sexual system in Fraxinus excelsior (Oleaceae). Proc Biol Sci 2019; 285:rspb.2018.0004. [PMID: 29467269 DOI: 10.1098/rspb.2018.0004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/30/2018] [Indexed: 01/02/2023] Open
Abstract
How flowering plants have recurrently evolved from hermaphroditism to separate sexes (dioecy) is a central question in evolutionary biology. Here, we investigate whether diallelic self-incompatibility (DSI) is associated with sexual specialization in the polygamous common ash (Fraxinus excelsior), which would ultimately facilitate the evolution towards dioecy. Using interspecific crosses, we provide evidence of strong relationships between the DSI system and sexual phenotype. The reproductive system in F. excelsior that was previously viewed as polygamy (co-occurrence of unisexuals and hermaphrodites with varying degrees of allocation to the male and female functions) and thus appears to actually behave as a subdioecious system. Hermaphrodites and females belong to one SI group and functionally reproduce as females, whereas males and male-biased hermaphrodites belong to the other SI group and are functionally males. Our results offer an alternative mechanism for the evolution of sexual specialization in flowering plants.
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Affiliation(s)
| | - Philippe Vernet
- CNRS, UMR 8198-Evo-Eco-Paléo, Univ Lille, 59000 Lille, France
| | - Arnaud Dowkiw
- INRA, UR 0588, Amélioration Génétique et Physiologie Forestières, INRA, 45075 Orléans, France
| | - Sylvain Bertrand
- CNRS, UMR 8198-Evo-Eco-Paléo, Univ Lille, 59000 Lille, France.,INRA, UR 0588, Amélioration Génétique et Physiologie Forestières, INRA, 45075 Orléans, France
| | | | - Béatrice Albert
- Ecologie Systématique et Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91405 Orsay cedex, France
| | - Pierre-Henri Gouyon
- UMR MNHN CNRS 7205, Dept Systemat and Evolut, Museum Natl Hist Nat, 75005 Paris, France
| | - Mathilde Dufay
- CNRS, UMR 8198-Evo-Eco-Paléo, Univ Lille, 59000 Lille, France.,CEFE, Université Montpellier, CNRS, Université Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
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35
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Liu L, Xu L, Jia Q, Pan R, Oelmüller R, Zhang W, Wu C. Arms race: diverse effector proteins with conserved motifs. PLANT SIGNALING & BEHAVIOR 2019; 14:1557008. [PMID: 30621489 PMCID: PMC6351098 DOI: 10.1080/15592324.2018.1557008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Effector proteins play important roles in the infection by pathogenic oomycetes and fungi or the colonization by endophytic and mycorrhizal fungi. They are either translocated into the host plant cells via specific translocation mechanisms and function in the host's cytoplasm or nucleus, or they reside in the apoplast of the plant cells and act at the extracellular host-microbe interface. Many effector proteins possess conserved motifs (such as the RXLR, CRN, LysM, RGD, DELD, EAR, RYWT, Y/F/WXC or CFEM motifs) localized in their N- or C-terminal regions. Analysis of the functions of effector proteins, especially so-called "core effectors", is crucial for the understanding of pathogenicity/symbiosis mechanisms and plant defense strategies, and helps to develop breeding strategies for pathogen-resistant cultivars, and to increase crop yield and quality as well as abiotic stress resistance. This review summarizes current knowledge about these effector proteins with the conversed motifs and their involvement in pathogenic or mutualistic plant/fungal interactions.
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Affiliation(s)
- Liping Liu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Le Xu
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Qie Jia
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Ralf Oelmüller
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
- CONTACT Wenying Zhang Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou 434025, China; Chu Wu College of Horticulture & Gardening, Yangtze University, Jingzhou 434025, China
| | - Chu Wu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
- Institute of Plant Ecology and Environmental Restoration, Yangtze University, Jingzhou, China
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Giraud T, Koskella B, Laine AL. Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution. Mol Ecol 2018; 26:1703-1710. [PMID: 28409900 DOI: 10.1111/mec.14091] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 02/14/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
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37
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Kobmoo N, Wichadakul D, Arnamnart N, Rodríguez De La Vega RC, Luangsa-ard JJ, Giraud T. A genome scan of diversifying selection inOphiocordycepszombie-ant fungi suggests a role for enterotoxins in co-evolution and host specificity. Mol Ecol 2018; 27:3582-3598. [DOI: 10.1111/mec.14813] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 07/13/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Noppol Kobmoo
- Ecologie Systématique Evolution; Université Paris-Sud; CNRS; AgroParisTech; Université Paris-Saclay; Orsay France
- National Center for Genetic Engineering and Biotechnology (BIOTEC); National Science and Development Agency (NSTDA); Klhong Luang Thailand
| | - Duangdao Wichadakul
- Chulalongkorn University Big Data Analytics and IoT Center (CUBIC); Department of Computer Engineering; Faculty of Engineering; Chulalongkorn University; Bangkok Thailand
- Center of Excellence in Systems Biology; Faculty of Medicine; Chulalongkorn University; Bangkok Thailand
| | - Nuntanat Arnamnart
- National Center for Genetic Engineering and Biotechnology (BIOTEC); National Science and Development Agency (NSTDA); Klhong Luang Thailand
| | | | - Janet J. Luangsa-ard
- National Center for Genetic Engineering and Biotechnology (BIOTEC); National Science and Development Agency (NSTDA); Klhong Luang Thailand
| | - Tatiana Giraud
- Ecologie Systématique Evolution; Université Paris-Sud; CNRS; AgroParisTech; Université Paris-Saclay; Orsay France
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38
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Sánchez-Vallet A, Fouché S, Fudal I, Hartmann FE, Soyer JL, Tellier A, Croll D. The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:21-40. [PMID: 29768136 DOI: 10.1146/annurev-phyto-080516-035303] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Filamentous pathogens, including fungi and oomycetes, pose major threats to global food security. Crop pathogens cause damage by secreting effectors that manipulate the host to the pathogen's advantage. Genes encoding such effectors are among the most rapidly evolving genes in pathogen genomes. Here, we review how the major characteristics of the emergence, function, and regulation of effector genes are tightly linked to the genomic compartments where these genes are located in pathogen genomes. The presence of repetitive elements in these compartments is associated with elevated rates of point mutations and sequence rearrangements with a major impact on effector diversification. The expression of many effectors converges on an epigenetic control mediated by the presence of repetitive elements. Population genomics analyses showed that rapidly evolving pathogens show high rates of turnover at effector loci and display a mosaic in effector presence-absence polymorphism among strains. We conclude that effective pathogen containment strategies require a thorough understanding of the effector genome biology and the pathogen's potential for rapid adaptation.
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Affiliation(s)
- Andrea Sánchez-Vallet
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Isabelle Fudal
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, AgroParisTech, Université Paris-Sud, CNRS, Université Paris-Saclay, 91400 Orsay, France
| | - Jessica L Soyer
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Aurélien Tellier
- Section of Population Genetics, Technical University of Munich, 85354 Freising, Germany
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland;
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Rajaraman J, Douchkov D, Lück S, Hensel G, Nowara D, Pogoda M, Rutten T, Meitzel T, Brassac J, Höfle C, Hückelhoven R, Klinkenberg J, Trujillo M, Bauer E, Schmutzer T, Himmelbach A, Mascher M, Lazzari B, Stein N, Kumlehn J, Schweizer P. Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance. Genome Biol 2018; 19:116. [PMID: 30111359 PMCID: PMC6092874 DOI: 10.1186/s13059-018-1472-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/04/2018] [Indexed: 11/11/2022] Open
Abstract
Background The large and highly repetitive genomes of the cultivated species Hordeum vulgare (barley), Triticum aestivum (wheat), and Secale cereale (rye) belonging to the Triticeae tribe of grasses appear to be particularly rich in gene-like sequences including partial duplicates. Most of them have been classified as putative pseudogenes. In this study we employ transient and stable gene silencing- and over-expression systems in barley to study the function of HvARM1 (for H. vulgare Armadillo 1), a partial gene duplicate of the U-box/armadillo-repeat E3 ligase HvPUB15 (for H. vulgare Plant U-Box 15). Results The partial ARM1 gene is derived from a gene-duplication event in a common ancestor of the Triticeae and contributes to quantitative host as well as nonhost resistance to the biotrophic powdery mildew fungus Blumeria graminis. In barley, allelic variants of HvARM1 but not of HvPUB15 are significantly associated with levels of powdery mildew infection. Both HvPUB15 and HvARM1 proteins interact in yeast and plant cells with the susceptibility-related, plastid-localized barley homologs of THF1 (for Thylakoid formation 1) and of ClpS1 (for Clp-protease adaptor S1) of Arabidopsis thaliana. A genome-wide scan for partial gene duplicates reveals further events in barley resulting in stress-regulated, potentially neo-functionalized, genes. Conclusion The results suggest neo-functionalization of the partial gene copy HvARM1 increases resistance against powdery mildew infection. It further links plastid function with susceptibility to biotrophic pathogen attack. These findings shed new light on a novel mechanism to employ partial duplication of protein-protein interaction domains to facilitate the expansion of immune signaling networks. Electronic supplementary material The online version of this article (10.1186/s13059-018-1472-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeyaraman Rajaraman
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany.
| | - Dimitar Douchkov
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany.
| | - Stefanie Lück
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Götz Hensel
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Daniela Nowara
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Maria Pogoda
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Twan Rutten
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Tobias Meitzel
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jonathan Brassac
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Caroline Höfle
- Technische Universität München, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Ralph Hückelhoven
- Technische Universität München, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Jörn Klinkenberg
- Leibniz Institut für Pflanzenbiochemie, Weinberg 3, D-06120, Halle (Saale), Germany
| | - Marco Trujillo
- Leibniz Institut für Pflanzenbiochemie, Weinberg 3, D-06120, Halle (Saale), Germany.,Albert-Ludwigs-Universität Freiburg, Institut für Biologie II, Zellbiologie, D-79104, Freiburg, Germany
| | - Eva Bauer
- Technische Universität München, Liesel-Beckmann-Straße 2, D-85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Barbara Lazzari
- Parco Technologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy
| | - Nils Stein
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
| | - Patrick Schweizer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK Gatersleben), Corrensstrasse 3, D-06466, Stadt Seeland, Germany
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40
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Abbate JL, Gladieux P, Hood ME, de Vienne DM, Antonovics J, Snirc A, Giraud T. Co-occurrence among three divergent plant-castrating fungi in the same Silene host species. Mol Ecol 2018; 27:10.1111/mec.14805. [PMID: 30030861 PMCID: PMC6340787 DOI: 10.1111/mec.14805] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 06/21/2018] [Accepted: 07/05/2018] [Indexed: 01/04/2023]
Abstract
The competitive exclusion principle postulates that different species can only coexist in sympatry if they occupy distinct ecological niches. The goal of this study was to understand the geographical distribution of three species of Microbotryum anther-smut fungi that are distantly related but infect the same host plants, the sister species Silene vulgaris and S. uniflora, in Western Europe. We used microsatellite markers to investigate pathogen distribution in relation to host specialization and ecological factors. Microbotryum violaceo-irregulare was only found on S. vulgaris at high elevations in the Alps. Microbotryum lagerheimii could be subdivided into two genetically differentiated clusters, one on S. uniflora in the UK and the second on S. vulgaris in the Alps and Pyrenees. The most abundant pathogen species, M. silenes-inflatae, could be subdivided into four genetic clusters, co-occurring in the Alps, the UK and the Pyrenees, and was found on both S. vulgaris and S. uniflora. All three fungal species had high levels of homozygosity, in agreement with the selfing mating system generally observed in anther-smut fungi. The three pathogen species and genetic clusters had large range overlaps, but occurred at sites with different elevations, temperatures and precipitation levels. The three Microbotryum species thus do not appear to be maintained by host specialization or geographic allopatry, but instead may occupy different ecological niches in terms of environmental conditions.
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Affiliation(s)
- Jessica L. Abbate
- UMR MIVEGEC, IRD 224, CNRS, Université de Montpellier, F-34394 Montpellier, France
- UMR UMMISCO, IRD 209, UPMC, F-93143 Bondy, France
| | - Pierre Gladieux
- Laboratoire Ecologie Systématique et Evolution, Univ. Paris Sud, CNRS, AgroParisTech, Université Paris Saclay, Orsay, F-91400 France
- INRA, UMR BGPI, Bâtiment K; Campus International de Baillarguet, F-34398, Montpellier, France
| | - Michael E. Hood
- Biology Department, McGuire Life Sciences Building, Amherst College, Rts 9 & 116, Amherst, MA USA 01002-5000
| | - Damien M. de Vienne
- Laboratoire Ecologie Systématique et Evolution, Univ. Paris Sud, CNRS, AgroParisTech, Université Paris Saclay, Orsay, F-91400 France
- Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France
- Université de Lyon, F-69000 Lyon, France
| | - Janis Antonovics
- University of Virginia, Dept. of Biology, Gilmer Hall, Charlottesville, VA 22904, USA
| | - Alodie Snirc
- Laboratoire Ecologie Systématique et Evolution, Univ. Paris Sud, CNRS, AgroParisTech, Université Paris Saclay, Orsay, F-91400 France
| | - Tatiana Giraud
- Laboratoire Ecologie Systématique et Evolution, Univ. Paris Sud, CNRS, AgroParisTech, Université Paris Saclay, Orsay, F-91400 France
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41
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Avia K, Lipinska AP, Mignerot L, Montecinos AE, Jamy M, Ahmed S, Valero M, Peters AF, Cock JM, Roze D, Coelho SM. Genetic Diversity in the UV Sex Chromosomes of the Brown Alga Ectocarpus. Genes (Basel) 2018; 9:E286. [PMID: 29882839 PMCID: PMC6027523 DOI: 10.3390/genes9060286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/30/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Three types of sex chromosome system exist in nature: diploid XY and ZW systems and haploid UV systems. For many years, research has focused exclusively on XY and ZW systems, leaving UV chromosomes and haploid sex determination largely neglected. Here, we perform a detailed analysis of DNA sequence neutral diversity levels across the U and V sex chromosomes of the model brown alga Ectocarpus using a large population dataset. We show that the U and V non-recombining regions of the sex chromosomes (SDR) exhibit about half as much neutral diversity as the autosomes. This difference is consistent with the reduced effective population size of these regions compared with the rest of the genome, suggesting that the influence of additional factors such as background selection or selective sweeps is minimal. The pseudoautosomal region (PAR) of this UV system, in contrast, exhibited surprisingly high neutral diversity and there were several indications that genes in this region may be under balancing selection. The PAR of Ectocarpus is known to exhibit unusual genomic features and our results lay the foundation for further work aimed at understanding whether, and to what extent, these structural features underlie the high level of genetic diversity. Overall, this study fills a gap between available information on genetic diversity in XY/ZW systems and UV systems and significantly contributes to advancing our knowledge of the evolution of UV sex chromosomes.
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Affiliation(s)
- Komlan Avia
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Laure Mignerot
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Alejandro E Montecinos
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
| | - Mahwash Jamy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Sophia Ahmed
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Myriam Valero
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | | | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
| | - Denis Roze
- Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, University of Paris VI, UC, UACH, UMI 3614, 29688 Roscoff, France.
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France.
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42
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Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Abstract
Pneumocystis species are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivable in vitro Human Pneumocystis infections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations of Pneumocystis infecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate that Pneumocystis species diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation of Pneumocystis populations during their spread across mammals.IMPORTANCE Understanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology. Pneumocystis, a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans, Pneumocystis can cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of different Pneumocystis species infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest that Pneumocystis may have undergone recent host shifts. The results demonstrate that Pneumocystis strains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens.
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Schirrmann MK, Zoller S, Croll D, Stukenbrock EH, Leuchtmann A, Fior S. Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization. Mol Ecol 2018; 27:3070-3086. [PMID: 29633410 DOI: 10.1111/mec.14585] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022]
Abstract
Host specialization is a key process in ecological divergence and speciation of plant-associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass-endophytic fungi from the Epichloë typhina complex: subsp. typhina and clarkii. The life cycle of these fungi entails unrestricted dispersal of gametes and sexual reproduction before infection of a new host, implying that the host imposes a selective barrier on viability of the progeny. We aimed to detect genes under divergent selection between subspecies, experiencing restricted gene flow due to adaptation to different hosts. Using pooled whole-genome sequencing data, we combined FST and DXY population statistics in genome scans and detected 57 outlier genes showing strong differentiation between the two subspecies. Genomewide analyses of nucleotide diversity (π), Tajima's D and dN/dS ratios indicated that these genes have evolved under positive selection. Genes encoding secreted proteins were enriched among the genes showing evidence of positive selection, suggesting that molecular plant-fungus interactions are strong drivers of endophyte divergence. We focused on five genes encoding secreted proteins, which were further sequenced in 28 additional isolates collected across Europe to assess genetic variation in a larger sample size. Signature of positive selection in these isolates and putative identification of pathogenic function supports our findings that these genes represent strong candidates for host specialization determinants in Epichloë endophytes. Our results highlight the role of secreted proteins as key determinants of host specialization.
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Affiliation(s)
- Melanie K Schirrmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.,Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Adrian Leuchtmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
| | - Simone Fior
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
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45
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LeBlanc N, Salgado-Salazar C, Crouch JA. Boxwood blight: an ongoing threat to ornamental and native boxwood. Appl Microbiol Biotechnol 2018; 102:4371-4380. [PMID: 29610965 PMCID: PMC5932091 DOI: 10.1007/s00253-018-8936-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 12/02/2022]
Abstract
Boxwood blight is an emerging disease of ornamental and native boxwood plants in the family Buxaceae. First documented in the 1990s at a single location in England, the disease is now reported throughout Europe, Asia, New Zealand, and North America. To address the growing concern over boxwood blight, ongoing research focuses on multiple biological and genetic aspects of the causal pathogens and susceptible host plants. Characterization of genetic variation among the Calonectria fungi that cause boxwood blight shows that two unique sister species with different geographic distributions incite the disease. Studies of the pathogen life cycle show the formation of long-lived survival structures and that host infection is dependent on inoculum density, temperature, and humidity. Host range investigations detail high levels of susceptibility among boxwood as well as the potential for asymptomatic boxwood infection and for other plants in the family Buxaceae to serve as additional hosts. Multiple DNA-based diagnostic assays are available, ranging from probe-based quantitative PCR assays to the use of comparative genomics to develop robust diagnostic markers or provide whole genome-scale identifications. Though many questions remain, the research that continues to address boxwood blight demonstrates the importance of applying a multidisciplinary approach to understand and control emerging plant diseases.
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Affiliation(s)
- Nicholas LeBlanc
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD, USA.,Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN, USA
| | - Catalina Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD, USA.,Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN, USA
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD, USA.
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46
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Mohd-Assaad N, McDonald BA, Croll D. Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen. Genome Biol Evol 2018; 10:1315-1332. [PMID: 29722810 PMCID: PMC5972619 DOI: 10.1093/gbe/evy087] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2018] [Indexed: 12/29/2022] Open
Abstract
Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abiotic factors could lead to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. Rhynchosporium commune, the pathogen causing barley scald disease, interacts at least partially in a gene-for-gene manner with its host. We analyzed global field populations of 125 R. commune isolates to identify candidate genes for local adaptation. Whole genome sequencing data showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded protein functions related to biotic and abiotic stress responses. Selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
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47
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Hartmann FE, Rodríguez de la Vega RC, Brandenburg JT, Carpentier F, Giraud T. Gene Presence-Absence Polymorphism in Castrating Anther-Smut Fungi: Recent Gene Gains and Phylogeographic Structure. Genome Biol Evol 2018; 10:1298-1314. [PMID: 29722826 PMCID: PMC5967549 DOI: 10.1093/gbe/evy089] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2018] [Indexed: 12/14/2022] Open
Abstract
Gene presence-absence polymorphisms segregating within species are a significant source of genetic variation but have been little investigated to date in natural populations. In plant pathogens, the gain or loss of genes encoding proteins interacting directly with the host, such as secreted proteins, probably plays an important role in coevolution and local adaptation. We investigated gene presence-absence polymorphism in populations of two closely related species of castrating anther-smut fungi, Microbotryum lychnidis-dioicae (MvSl) and M. silenes-dioicae (MvSd), from across Europe, on the basis of Illumina genome sequencing data and high-quality genome references. We observed presence-absence polymorphism for 186 autosomal genes (2% of all genes) in MvSl, and only 51 autosomal genes in MvSd. Distinct genes displayed presence-absence polymorphism in the two species. Genes displaying presence-absence polymorphism were frequently located in subtelomeric and centromeric regions and close to repetitive elements, and comparison with outgroups indicated that most were present in a single species, being recently acquired through duplications in multiple-gene families. Gene presence-absence polymorphism in MvSl showed a phylogeographic structure corresponding to clusters detected based on SNPs. In addition, gene absence alleles were rare within species and skewed toward low-frequency variants. These findings are consistent with a deleterious or neutral effect for most gene presence-absence polymorphism. Some of the observed gene loss and gain events may however be adaptive, as suggested by the putative functions of the corresponding encoded proteins (e.g., secreted proteins) or their localization within previously identified selective sweeps. The adaptive roles in plant and anther-smut fungi interactions of candidate genes however need to be experimentally tested in future studies.
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Affiliation(s)
- Fanny E Hartmann
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Jean-Tristan Brandenburg
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Fantin Carpentier
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Tatiana Giraud
- Department Génétique et Ecologie Evolutives, Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
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48
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Kelly AC, Ward TJ. Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen. PLoS One 2018; 13:e0194616. [PMID: 29584736 PMCID: PMC5870968 DOI: 10.1371/journal.pone.0194616] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/06/2018] [Indexed: 12/30/2022] Open
Abstract
The cereal pathogen Fusarium graminearum is the primary cause of Fusarium head blight (FHB) and a significant threat to food safety and crop production. To elucidate population structure and identify genomic targets of selection within major FHB pathogen populations in North America we sequenced the genomes of 60 diverse F. graminearum isolates. We also assembled the first pan-genome for F. graminearum to clarify population-level differences in gene content potentially contributing to pathogen diversity. Bayesian and phylogenomic analyses revealed genetic structure associated with isolates that produce the novel NX-2 mycotoxin, suggesting a North American population that has remained genetically distinct from other endemic and introduced cereal-infecting populations. Genome scans uncovered distinct signatures of selection within populations, focused in high diversity, frequently recombining regions. These patterns suggested selection for genomic divergence at the trichothecene toxin gene cluster and thirteen additional regions containing genes potentially involved in pathogen specialization. Gene content differences further distinguished populations, in that 121 genes showed population-specific patterns of conservation. Genes that differentiated populations had predicted functions related to pathogenesis, secondary metabolism and antagonistic interactions, though a subset had unique roles in temperature and light sensitivity. Our results indicated that F. graminearum populations are distinguished by dozens of genes with signatures of selection and an array of dispensable accessory genes, suggesting that FHB pathogen populations may be equipped with different traits to exploit the agroecosystem. These findings provide insights into the evolutionary processes and genomic features contributing to population divergence in plant pathogens, and highlight candidate genes for future functional studies of pathogen specialization across evolutionarily and ecologically diverse fungi.
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Affiliation(s)
- Amy C. Kelly
- United States Department of Agriculture, Agricultural Research Service, Peoria, Illinois, United States of America
| | - Todd J. Ward
- United States Department of Agriculture, Agricultural Research Service, Peoria, Illinois, United States of America
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49
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Abstract
The successful interaction between pathogen/parasite and host requires a delicate balance between fitness of the former and survival of the latter. To optimize fitness a parasite/pathogen must effectively create an environment conducive to reproductive success, while simultaneously avoiding or minimizing detrimental host defense response. The association between Microbotryum lychnidis-dioicae and its host Silene latifolia serves as an excellent model to examine such interactions. This fungus is part of a species complex that infects species of the Caryophyllaceae, replacing pollen with the fungal spores. In the current study, transcriptome analyses of the fungus and its host were conducted during discrete stages of bud development so as to identify changes in fungal gene expression that lead to spore development and to identify changes associated with infection in the host plant. In contrast to early biotrophic phase stages of infection for the fungus, the latter stages involve tissue necrosis and in the case of infected female flowers, further changes in the developmental program in which the ovary aborts and a pseudoanther is produced. Transcriptome analysis via Illumina RNA sequencing revealed enrichment of fungal genes encoding small secreted proteins, with hallmarks of effectors and genes found to be relatively unique to the Microbotryum species complex. Host gene expression analyses also identified interesting sets of genes up-regulated, including those involving stress response, host defense response, and several agamous-like MADS-box genes (AGL61 and AGL80), predicted to interact and be involved in male gametophyte development.
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