1
|
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.
Collapse
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
| |
Collapse
|
3
|
Perlin MH, Amselem J, Fontanillas E, Toh SS, Chen Z, Goldberg J, Duplessis S, Henrissat B, Young S, Zeng Q, Aguileta G, Petit E, Badouin H, Andrews J, Razeeq D, Gabaldón T, Quesneville H, Giraud T, Hood ME, Schultz DJ, Cuomo CA. Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics 2015; 16:461. [PMID: 26076695 PMCID: PMC4469406 DOI: 10.1186/s12864-015-1660-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 05/28/2015] [Indexed: 12/11/2022] Open
Abstract
Background The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. Results We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14 % of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions. Conclusions The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1660-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | - Joelle Amselem
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Versailles, France. .,Institut National de la Recherche Agronomique (INRA), Biologie et gestion des risques en agriculture (BIOGER), Thiverval-Grignon, France.
| | - Eric Fontanillas
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. .,CNRS, F-91405, Orsay, France.
| | - Su San Toh
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | | | - Sebastien Duplessis
- INRA, UMR 1136, Interactions Arbres-Microorganismes, Champenoux, France. .,UMR 1136, Université de Lorraine, Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, France.
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 13288, Marseille, France. .,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Sarah Young
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | | | - Elsa Petit
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. .,CNRS, F-91405, Orsay, France. .,Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 13288, Marseille, France.
| | - Helene Badouin
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. .,CNRS, F-91405, Orsay, France.
| | - Jared Andrews
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | - Dominique Razeeq
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institució Catalana d'Estudis Avançats (ICREA), Barcelona, Spain.
| | - Hadi Quesneville
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Versailles, France.
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. .,CNRS, F-91405, Orsay, France.
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, 01002, USA.
| | - David J Schultz
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA.
| | | |
Collapse
|