1
|
Tralamazza SM, Gluck-Thaler E, Feurtey A, Croll D. Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen. Nat Commun 2024; 15:5728. [PMID: 38977688 PMCID: PMC11231334 DOI: 10.1038/s41467-024-49913-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 06/25/2024] [Indexed: 07/10/2024] Open
Abstract
Copy number variation (CNV) can drive rapid evolution in changing environments. In microbial pathogens, such adaptation is a key factor underpinning epidemics and colonization of new niches. However, the genomic determinants of such adaptation remain poorly understood. Here, we systematically investigate CNVs in a large genome sequencing dataset spanning a worldwide collection of 1104 genomes from the major wheat pathogen Zymoseptoria tritici. We found overall strong purifying selection acting on most CNVs. Genomic defense mechanisms likely accelerated gene loss over episodes of continental colonization. Local adaptation along climatic gradients was likely facilitated by CNVs affecting secondary metabolite production and gene loss in general. One of the strongest loci for climatic adaptation is a highly conserved gene of the NAD-dependent Sirtuin family. The Sirtuin CNV locus localizes to an ~68-kb Starship mobile element unique to the species carrying genes highly expressed during plant infection. The element has likely lost the ability to transpose, demonstrating how the ongoing domestication of cargo-carrying selfish elements can contribute to selectable variation within populations. Our work highlights how standing variation in gene copy numbers at the global scale can be a major factor driving climatic and metabolic adaptation in microbial species.
Collapse
Affiliation(s)
- Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Emile Gluck-Thaler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
| |
Collapse
|
2
|
Badet T, Tralamazza SM, Feurtey A, Croll D. Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen. Nucleic Acids Res 2024; 52:1226-1242. [PMID: 38142443 PMCID: PMC10853768 DOI: 10.1093/nar/gkad1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/26/2023] Open
Abstract
Transposable elements (TEs) are key drivers of genomic variation contributing to recent adaptation in most species. Yet, the evolutionary origins and insertion dynamics within species remain poorly understood. We recapitulate the spread of the pathogenicity-associated Styx element across five species that last diverged ∼11 000 years ago. We show that the element likely originated in the Zymoseptoria fungal pathogen genus and underwent multiple independent reactivation events. Using a global 900-genome panel of the wheat pathogen Zymoseptoria tritici, we assess Styx copy number variation and identify renewed transposition activity in Oceania and South America. We show that the element can mobilize to create additional Styx copies in a four-generation pedigree. Importantly, we find that new copies of the element are not affected by genomic defenses suggesting minimal control against the element. Styx copies are preferentially located in recombination breakpoints and likely triggered multiple types of large chromosomal rearrangements. Taken together, we establish the origin, diversification and reactivation of a highly active TE with likely major consequences for chromosomal integrity and the expression of disease.
Collapse
Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| |
Collapse
|
3
|
Kausar MA, Narayan J, Agarwal P, Singh P, Ahmed RME, El-Hag ABM, Khalifa AM, Mohammed NARK, Singh R, Mahfooz S. Distribution and conservation of simple sequence repeats in plant pathogenic species of Zymoseptoria and development of genomic resources for its orphaned species. Antonie Van Leeuwenhoek 2024; 117:11. [PMID: 38170404 DOI: 10.1007/s10482-023-01915-z] [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: 10/06/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
To better understand the structure and evolution of the genomes of four plant pathogenic species of Zymoseptoria, we analyzed the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) in their whole genome and transcriptome sequences. In this study, SSRs are defined as repeats of more than 12 bases in length. The genome and transcriptome sequences of Zymoseptoria ardabiliae show the highest RA (201.1 and 129.9) and RD (3229.4 and 1928.2) of SSRs, while those of Zymoseptoria pseudotritici show the lowest RA (167.2 and 118.5) and RD (2482.2 and 1687.0). The majority of SSRs in the genomic and transcriptome sequences of species were trinucleotide SSRs, while dinucleotide SSRs were the least common. The most common trinucleotide motifs in the transcriptomic sequences across all species were those that encoded the amino acid arginine. As per our motif conservation study, Zymoseptoria tritici (12.4%) possessed the most unique motifs, while Z. pseudotritici (3.9%) had the fewest. Overall, only 38.1% of the motifs were found to be conserved among the species. Gene enrichment studies reveal that three of the species, Z. ardabiliae, Zymoseptoria brevis, and Z. pseudotritici, have SSRs in their genes related to cellular metabolism, while the remaining Z. tritici harbors SSRs in genes related to DNA synthesis and gene expression. In an effort to improve the genetic resources for the orphan species of pathogenic Zymoseptoria, a total of 73,134 primers were created. The genomic resources developed in this study could help with analyses of genetic relatedness within the population and the development of species-specific markers.
Collapse
Affiliation(s)
- Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Hail, 2440, Hail, Saudi Arabia.
| | - Jitendra Narayan
- CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
| | - Preeti Agarwal
- CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
| | - Pallavi Singh
- Department of Biotechnology, Dr APJ Abdul Kalam Technical University, Lucknow, 226031, India
| | | | | | - Amany Mohammed Khalifa
- Department of Pathology, College of Medicine, University of Hail, 2440, Hail, Saudi Arabia
| | | | - Rajeev Singh
- Department of Environmental Science, Jamia Millia Islamia Central University, 110025, New Delhi, India
| | - Sahil Mahfooz
- The Academic Editors, Saryu Enclave, Awadh Vikas Yojna, Lucknow, 226002, India.
- Department of Industrial Microbiology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009, India.
| |
Collapse
|
4
|
Baril T, Croll D. A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici. BMC Res Notes 2023; 16:335. [PMID: 37974222 PMCID: PMC10652580 DOI: 10.1186/s13104-023-06613-7] [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: 09/29/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
OBJECTIVES High-quality species-specific transposable element (TE) libraries are required for studies to elucidate the evolutionary dynamics of TEs and gain an understanding of their impacts on host genomes. Such high-quality TE resources are severely lacking for species in the fungal kingdom. To facilitate future studies on the putative role of TEs in rapid adaptation observed in the fungal wheat pathogen Zymoseptoria tritici, we produced a manually curated TE library. This was generated by detecting TEs in 19 reference genome assemblies representing the global diversity of the species supplemented by multiple sister species genomes. Improvements over previous TE libraries have been made on TE boundary resolution, detection of ORFs, TE domains, terminal inverted repeats, and class-specific motifs. DATA DESCRIPTION A TE consensus library for Z. tritici formatted for use with RepeatMasker. This data is relevant to other researchers investigating TE-host evolutionary dynamics in Z. tritici or who are interested in comparative studies of the fungal kingdom. Further, this TE library can be used to improve gene annotation. Finally, this TE library increases the number of manually curated TE datasets, providing resources to further our understanding of TE diversity.
Collapse
Affiliation(s)
- Tobias Baril
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Rue -Argand 11, 2000, Neuchatel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Rue -Argand 11, 2000, Neuchatel, Switzerland.
| |
Collapse
|
5
|
Fones HN, Soanes D, Gurr SJ. Epiphytic proliferation of Zymoseptoria tritici isolates on resistant wheat leaves. Fungal Genet Biol 2023; 168:103822. [PMID: 37343618 DOI: 10.1016/j.fgb.2023.103822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 06/04/2023] [Accepted: 06/15/2023] [Indexed: 06/23/2023]
Abstract
The wheat pathogen Zymoseptoria tritici is capable of a long period of pre-invasive epiphytic growth. Studies have shown that virulent isolates vary in the extent, duration and growth form of this epiphytic growth, and the fungus has been observed to undergo behaviours such as asexual reproduction by budding and vegetative fusion of hyphae on the leaf surface. This epiphytic colonisation has been investigated very little during interactions in which an isolate of Z. tritici is unable to colonise the apoplast, as occurs during avirulence. However, avirulent isolates have been seen to undergo sexual crosses in the absense of leaf penetration, and it is widely accepted that the main point of distinction between virulent and avirulent isolates occurs at the point of attempted leaf penetration or attempted apoplastic growth, which fails in the avirulent case. In this work, we describe extensive epiphytic growth in three isolates which are unable or have very limited ability to invade the leaf, and show that growth form is as variable as for fully virulent isolates. We demonstrate that during certain interactions, Z. tritici isolates rarely invade the leaf and form pycnidia, but induce necrosis. These isolates are able to achieve higher epiphytic biomass than fully virulent isolates during asymptomatic growth, and may undergo very extensive asexual reproduction on the leaf surface. These findings have implications for open questions such as whether and how Z. tritici obtains nutrients on the leaf surface and the nature of its interaction with wheat defences.
Collapse
Affiliation(s)
- H N Fones
- Biosciences, University of Exeter, Exeter, UK
| | - D Soanes
- University of Exeter Medical School, Exeter, UK
| | - S J Gurr
- Biosciences, University of Exeter, Exeter, UK; Department of Biosciences, Utrecht University, Utrecht, the Netherlands.
| |
Collapse
|
6
|
Lainscsek X, Taher L. Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA. Brief Bioinform 2023; 24:bbad198. [PMID: 37264486 PMCID: PMC10359093 DOI: 10.1093/bib/bbad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023] Open
Abstract
Three-dimensional (3D) genome architecture is characterized by multi-scale patterns and plays an essential role in gene regulation. Chromatin conformation capturing experiments have revealed many properties underlying 3D genome architecture, such as the compartmentalization of chromatin based on transcriptional states. However, they are complex, costly and time consuming, and therefore only a limited number of cell types have been examined using these techniques. Increasing effort is being directed towards deriving computational methods that can predict chromatin conformation and associated structures. Here we present DNA-delay differential analysis (DDA), a purely sequence-based method based on chaos theory to predict genome-wide A and B compartments. We show that DNA-DDA models derived from a 20 Mb sequence are sufficient to predict genome wide compartmentalization at the scale of 100 kb in four different cell types. Although this is a proof-of-concept study, our method shows promise in elucidating the mechanisms responsible for genome folding as well as modeling the impact of genetic variation on 3D genome architecture and the processes regulated thereby.
Collapse
Affiliation(s)
- Xenia Lainscsek
- Institute of Biomedical Informatics, Graz University of Technology, Austria
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Austria
| |
Collapse
|
7
|
Meile L, Garrido-Arandia M, Bernasconi Z, Peter J, Schneller A, Bernasconi A, Alassimone J, McDonald BA, Sánchez-Vallet A. Natural variation in Avr3D1 from Zymoseptoria sp. contributes to quantitative gene-for-gene resistance and to host specificity. THE NEW PHYTOLOGIST 2023; 238:1562-1577. [PMID: 36529883 DOI: 10.1111/nph.18690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Successful host colonization by plant pathogens requires the circumvention of host defense responses, frequently through sequence modifications in secreted pathogen proteins known as avirulence factors (Avrs). Although Avr sequences are often polymorphic, the contribution of these polymorphisms to virulence diversity in natural pathogen populations remains largely unexplored. We used molecular genetic tools to determine how natural sequence polymorphisms of the avirulence factor Avr3D1 in the wheat pathogen Zymoseptoria tritici contributed to adaptive changes in virulence. We showed that there is a continuous distribution in the magnitude of resistance triggered by different Avr3D1 isoforms and demonstrated that natural variation in an Avr gene can lead to a quantitative resistance phenotype. We further showed that homologues of Avr3D1 in two nonpathogenic sister species of Z. tritici are recognized by some wheat cultivars, suggesting that Avr-R gene-for-gene interactions can contribute to nonhost resistance. We suggest that the mechanisms underlying host range, qualitative resistance, and quantitative resistance are not exclusive.
Collapse
Affiliation(s)
- Lukas Meile
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - María Garrido-Arandia
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040, Madrid, Spain
| | - Zoe Bernasconi
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Jules Peter
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Alissa Schneller
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Alessio Bernasconi
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Julien Alassimone
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Andrea Sánchez-Vallet
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
| |
Collapse
|
8
|
Rudd JJ. Effector-mediated partial and nonhost disease resistance in wheat. THE NEW PHYTOLOGIST 2023; 238:1340-1342. [PMID: 36999944 DOI: 10.1111/nph.18872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Affiliation(s)
- Jason J Rudd
- Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| |
Collapse
|
9
|
Hadimani S, De Britto S, Udayashankar AC, Geetha N, Nayaka CS, Ali D, Alarifi S, Ito SI, Jogaiah S. Genome-Wide Characterization of Effector Protein-Encoding Genes in Sclerospora graminicola and Its Validation in Response to Pearl Millet Downy Mildew Disease Stress. J Fungi (Basel) 2023; 9:jof9040431. [PMID: 37108886 PMCID: PMC10142805 DOI: 10.3390/jof9040431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Pearl millet [Pennisetum glaucum (L.) R. Br.] is the essential food crop for over ninety million people living in drier parts of India and South Africa. Pearl millet crop production is harshly hindered by numerous biotic stresses. Sclerospora graminicola causes downy mildew disease in pearl millet. Effectors are the proteins secreted by several fungi and bacteria that manipulate the host cell structure and function. This current study aims to identify genes encoding effector proteins from the S. graminicola genome and validate them through molecular techniques. In silico analyses were employed for candidate effector prediction. A total of 845 secretory transmembrane proteins were predicted, out of which 35 proteins carrying LxLFLAK (Leucine–any amino acid–Phenylalanine–Leucine–Alanine–Lysine) motif were crinkler, 52 RxLR (Arginine, any amino acid, Leucine, Arginine), and 17 RxLR-dEER putative effector proteins. Gene validation analysis of 17 RxLR-dEER effector protein-producing genes was carried out, of which 5genes were amplified on the gel. These novel gene sequences were submitted to NCBI. This study is the first report on the identification and characterization of effector genes in Sclerospora graminicola. This dataset will aid in the integration of effector classes that act independently, paving the way to investigate how pearl millet responds to effector protein interactions. These results will assist in identifying functional effector proteins involving the omic approach using newer bioinformatics tools to protect pearl millet plants against downy mildew stress. Considered together, the identified effector protein-encoding functional genes can be utilized in screening oomycetes downy mildew diseases in other crops across the globe.
Collapse
Affiliation(s)
- Shiva Hadimani
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, India
| | - Savitha De Britto
- Division of Biological Sciences, School of Science and Technology, University of Goroka, Goroka 441, Papua New Guinea
| | - Arakere C. Udayashankar
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India
| | - Nagaraj Geetha
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India
| | - Chandra S. Nayaka
- Department of Studies in Biotechnology, University of Mysore, Manasagangotri, Mysuru 570006, India
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shin-ichi Ito
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Biotechnology and Microbiology, Karnatak University, Dharwad 580003, India
- Department of Environmental Science, Central University of Kerala, Tejaswini Hills, Periye (PO) 671316, Kasaragod (DT), Kerala, India
- Correspondence: ; Tel.: +91-836-2779533; Fax: +91-836-2747884
| |
Collapse
|
10
|
Feurtey A, Lorrain C, McDonald MC, Milgate A, Solomon PS, Warren R, Puccetti G, Scalliet G, Torriani SFF, Gout L, Marcel TC, Suffert F, Alassimone J, Lipzen A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Goodwin SB, Genissel A, Seidl MF, Stukenbrock EH, Lebrun MH, Kema GHJ, McDonald BA, Croll D. A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen. Nat Commun 2023; 14:1059. [PMID: 36828814 PMCID: PMC9958100 DOI: 10.1038/s41467-023-36674-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.
Collapse
Affiliation(s)
- Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Cécile Lorrain
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Megan C McDonald
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Andrew Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia
| | - Peter S Solomon
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Rachael Warren
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Guido Puccetti
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Syngenta Crop Protection AG, CH-4332, Stein, Switzerland
| | | | | | - Lilian Gout
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Thierry C Marcel
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Frédéric Suffert
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 9472, USA
| | | | - Anne Genissel
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Michael F Seidl
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
- Utrecht University, Theoretical Biology and Bioinformatics, Utrecht, The Netherlands
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | | | - Gert H J Kema
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Bruce A McDonald
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
| |
Collapse
|
11
|
Oggenfuss U, Croll D. Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011130. [PMID: 36787337 PMCID: PMC9970103 DOI: 10.1371/journal.ppat.1011130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/27/2023] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a pathogen species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogen Zymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences, or as a consequence of insertion site preferences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that a Copia element burst was initiated from recent copies inserted substantially closer to genes compared to older copies. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation in pathogen genomes.
Collapse
Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
| |
Collapse
|
12
|
Wingfield BD, Berger DK, Coetzee MPA, Duong TA, Martin A, Pham NQ, van den Berg N, Wilken PM, Arun-Chinnappa KS, Barnes I, Buthelezi S, Dahanayaka BA, Durán A, Engelbrecht J, Feurtey A, Fourie A, Fourie G, Hartley J, Kabwe ENK, Maphosa M, Narh Mensah DL, Nsibo DL, Potgieter L, Poudel B, Stukenbrock EH, Thomas C, Vaghefi N, Welgemoed T, Wingfield MJ. IMA genome‑F17 : Draft genome sequences of an Armillaria species from Zimbabwe, Ceratocystis colombiana, Elsinoë necatrix, Rosellinia necatrix, two genomes of Sclerotinia minor, short‑read genome assemblies and annotations of four Pyrenophora teres isolates from barley grass, and a long-read genome assembly of Cercospora zeina. IMA Fungus 2022; 13:19. [PMID: 36411457 PMCID: PMC9677705 DOI: 10.1186/s43008-022-00104-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Brenda D. Wingfield
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Dave K. Berger
- grid.49697.350000 0001 2107 2298Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Martin P. A. Coetzee
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tuan A. Duong
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Anke Martin
- grid.1048.d0000 0004 0473 0844Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350 Australia
| | - Nam Q. Pham
- grid.49697.350000 0001 2107 2298Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Noelani van den Berg
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - P. Markus Wilken
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Kiruba Shankari Arun-Chinnappa
- grid.1048.d0000 0004 0473 0844Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350 Australia ,PerkinElmer Pty Ltd., Level 2, Building 5, Brandon Business Park, 530‑540, Springvale Road, Glen Waverley, VIC 3150 Australia
| | - Irene Barnes
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Sikelela Buthelezi
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Alvaro Durán
- Plant Health Program, Research and Development, Asia Pacific Resources International Holdings Ltd. (APRIL), Pangkalan Kerinci, Riau 28300 Indonesia
| | - Juanita Engelbrecht
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Alice Feurtey
- grid.419520.b0000 0001 2222 4708Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany ,grid.9764.c0000 0001 2153 9986Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Arista Fourie
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Gerda Fourie
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jesse Hartley
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Eugene N. K. Kabwe
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Mkhululi Maphosa
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Deborah L. Narh Mensah
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa ,grid.423756.10000 0004 1764 1672CSIR, Food Research Institute, Accra, Ghana
| | - David L. Nsibo
- grid.49697.350000 0001 2107 2298Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| | - Lizel Potgieter
- grid.419520.b0000 0001 2222 4708Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany ,grid.9764.c0000 0001 2153 9986Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Barsha Poudel
- grid.1048.d0000 0004 0473 0844Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350 Australia
| | - Eva H. Stukenbrock
- grid.419520.b0000 0001 2222 4708Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany ,grid.9764.c0000 0001 2153 9986Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Chanel Thomas
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Niloofar Vaghefi
- grid.1048.d0000 0004 0473 0844Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350 Australia ,grid.1008.90000 0001 2179 088XSchool of Agriculture and Food, University of Melbourne, Parkville, VIC 3010 Australia
| | - Tanya Welgemoed
- grid.49697.350000 0001 2107 2298Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J. Wingfield
- grid.49697.350000 0001 2107 2298Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028 South Africa
| |
Collapse
|
13
|
Montezano Fernandes F, Vieira de Queiroz M, Lopes da Silva L, Maria Queiroz Azevedo D, Luis Badel J, Couto Alfenas A. Chromosomal polymorphism of the Ceratocystis fimbriata species complex in Brazil. Fungal Genet Biol 2022; 162:103728. [PMID: 35932991 DOI: 10.1016/j.fgb.2022.103728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 11/04/2022]
Abstract
Ceratocystis fimbriata is an important pathogen that causes wilt in several plant species. Despite the importance of this pathogen, knowledge about its karyotypic polymorphism and genomic architecture is limited. The main objective of this study was to investigate the karyotype of isolates of the C. fimbriata species complex from different host plants and geographical origins in Brazil. First, the identity of the isolates was confirmed conducting multilocus sequence analysis (MLSA) phylogeny using β-tubulin (TUBB), translation elongation factor 1α (TEF-1α) and mating-type (MAT1 and MAT2) gene sequences. To investigate the chromosomal polymorphism, two conditions of pulsed-field gel electrophoresis (PFGE) were used and the karyotypes of the isolates obtained. The retrotransposon-microsatellite amplified polymorphism (REMAP) molecular marker was utilized to assess the genetic variability among isolates. In the MLSA utilizing the concatenated gene sequences, Ceratocystis cacaofunesta and C. fimbriata formed separate clades, but considerable variation among C. fimbriata isolates was observed. Polymorphism in chromosome number and size was found, indicating the existence of genomic differences among isolates and occurrence of chromosomal rearrangements in the species complex. The number of chromosomes varied from seven to nine and the estimated minimum chromosome sizes were estimated to be between 2.7 to 6.0 Mbp. Small polymorphic chromosomes ranging from 1.2 to 1.8 Mbp were observed in all isolates, raising the hypothesis that they could be supernumerary chromosomes. REMAP analysis revealed a high genetic variability and that isolates from the same host tend to group together in a same cluster. Our results bring new insights into the chromosomal diversity and genome organization of the C. fimbriata complex.
Collapse
Affiliation(s)
- Fernando Montezano Fernandes
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Marisa Vieira de Queiroz
- Laboratory of Molecular Genetics of Microorganisms, Department of Microbiology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Leandro Lopes da Silva
- Laboratory of Molecular Genetics of Microorganisms, Department of Microbiology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Daiana Maria Queiroz Azevedo
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Jorge Luis Badel
- Laboratory of Molecular Phytobacteriology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil
| | - Acelino Couto Alfenas
- Laboratory of Forest Pathology, Department of Plant Pathology, Universidade Federal de Viçosa, Minas Gerais State, 36570-900, Brazil.
| |
Collapse
|
14
|
Differential regulation and production of secondary metabolites among isolates of the fungal wheat pathogen Zymoseptoria tritici. Appl Environ Microbiol 2022; 88:e0229621. [PMID: 35108092 PMCID: PMC8939313 DOI: 10.1128/aem.02296-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of the wheat pathogenic fungus, Zymoseptoria tritici, represents extensive presence-absence variation in gene content. Here, we addressed variation in biosynthetic gene clusters (BGCs) content and biochemical profiles among three isolates. We analysed secondary metabolite properties based on genome, transcriptome and metabolome data. The isolates represent highly distinct genome architecture, but harbor similar repertoire of BGCs. Expression profiles for most BGCs show comparable patterns of regulation among the isolates, suggesting a conserved "biochemical infection program". For all three isolates, we observed a strong up-regulation of a putative abscisic acid (ABA) gene cluster during biotrophic host colonization, indicating that Z. tritici potentially interfere with host defenses by the biosynthesis of this phytohormone. Further, during in vitro growth the isolates show similar metabolomes congruent with the predicted BGC content. We assessed if secondary metabolite production is regulated by histone methylation using a mutant impaired in formation of facultative heterochromatin (H3K27me3). In contrast to other ascomycete fungi, chromatin modifications play a less prominent role in regulation of secondary metabolites. In summary, we show that Z. tritici has a conserved program of secondary metabolite production contrasting the immense variation in effector expression, some of these metabolites might play a key role during host colonization. Importance Zymoseptoria tritici is one of the most devastating pathogens of wheat. So far the molecular determinants of virulence and their regulation are poorly understood. Previous studies have focused on proteinasous virulence factors and their extensive diversity. In this study, we focus on secondary metabolites produced by Z. tritici. Using a comparative framework, we here characterize core and non-core metabolites produced by Z. tritici by combining genome, transcriptome and metabolome datasets. Our findings indicate highly conserved biochemical profiles contrasting genetic and phenotypic diversity of the field isolates investigated here. This discovery has relevance for future crop protection strategies.
Collapse
|
15
|
Tralamazza SM, Abraham LN, Reyes-Avila CS, Corrêa B, Croll D. Histone H3K27 methylation perturbs transcriptional robustness and underpins dispensability of highly conserved genes in fungi. Mol Biol Evol 2021; 39:6424003. [PMID: 34751371 PMCID: PMC8789075 DOI: 10.1093/molbev/msab323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications are key regulators of gene expression and underpin genome integrity. Yet, how epigenetic changes affect the evolution and transcriptional robustness of genes remains largely unknown. Here, we show how the repressive histone mark H3K27me3 underpins the trajectory of highly conserved genes in fungi. We first performed transcriptomic profiling on closely related species of the plant pathogen Fusarium graminearum species complex. We determined transcriptional responsiveness of genes across environmental conditions to determine expression robustness. To infer evolutionary conservation, we used a framework of 23 species across the Fusarium genus including three species covered with histone methylation data. Gene expression variation is negatively correlated with gene conservation confirming that highly conserved genes show higher expression robustness. In contrast, genes marked by H3K27me3 do not show such associations. Furthermore, highly conserved genes marked by H3K27me3 encode smaller proteins, exhibit weaker codon usage bias, higher levels of hydrophobicity, show lower intrinsically disordered regions, and are enriched for functions related to regulation and membrane transport. The evolutionary age of conserved genes with H3K27me3 histone marks falls typically within the origins of the Fusarium genus. We show that highly conserved genes marked by H3K27me3 are more likely to be dispensable for survival during host infection. Lastly, we show that conserved genes exposed to repressive H3K27me3 marks across distantly related Fusarium fungi are associated with transcriptional perturbation at the microevolutionary scale. In conclusion, we show how repressive histone marks are entangled in the evolutionary fate of highly conserved genes across evolutionary timescales.
Collapse
Affiliation(s)
- Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland.,Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Leen Nanchira Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland
| | | | - Benedito Corrêa
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Brazil
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, Switzerland
| |
Collapse
|
16
|
Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus. Nat Commun 2021; 12:5869. [PMID: 34620872 PMCID: PMC8497519 DOI: 10.1038/s41467-021-26108-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Mutations are the source of genetic variation and the substrate for evolution. Genome-wide mutation rates appear to be affected by selection and are probably adaptive. Mutation rates are also known to vary along genomes, possibly in response to epigenetic modifications, but causality is only assumed. In this study we determine the direct impact of epigenetic modifications and temperature stress on mitotic mutation rates in a fungal pathogen using a mutation accumulation approach. Deletion mutants lacking epigenetic modifications confirm that histone mark H3K27me3 increases whereas H3K9me3 decreases the mutation rate. Furthermore, cytosine methylation in transposable elements (TE) increases the mutation rate 15-fold resulting in significantly less TE mobilization. Also accessory chromosomes have significantly higher mutation rates. Finally, we find that temperature stress substantially elevates the mutation rate. Taken together, we find that epigenetic modifications and environmental conditions modify the rate and the location of spontaneous mutations in the genome and alter its evolutionary trajectory.
Collapse
|
17
|
Oggenfuss U, Badet T, Wicker T, Hartmann FE, Singh NK, Abraham L, Karisto P, Vonlanthen T, Mundt C, McDonald BA, Croll D. A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen. eLife 2021; 10:e69249. [PMID: 34528512 PMCID: PMC8445621 DOI: 10.7554/elife.69249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Genome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations, but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogen's center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.
Collapse
Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-SaclayOrsayFrance
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Petteri Karisto
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Tiziana Vonlanthen
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Christopher Mundt
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| |
Collapse
|
18
|
Lorrain C, Feurtey A, Möller M, Haueisen J, Stukenbrock E. Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses. G3-GENES GENOMES GENETICS 2021; 11:6173990. [PMID: 33724368 PMCID: PMC8759822 DOI: 10.1093/g3journal/jkab068] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/19/2021] [Indexed: 01/29/2023]
Abstract
Transposable elements (TEs) impact genome plasticity, architecture, and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defense mechanisms that can counter-balance TE expansion and spread. Closely related species can harbor drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here, we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and repeat-induced point mutation signatures in 26 genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The 26 genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation, and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.
Collapse
Affiliation(s)
- Cécile Lorrain
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany.,Université de Lorraine/INRAE, UMR 1136 Interactions Arbres/Microorganismes, INRAE Centre Grand Est-Nancy, Champenoux 54280, France
| | - Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Mareike Möller
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Janine Haueisen
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Eva Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| |
Collapse
|
19
|
John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. MOLECULAR PLANT PATHOLOGY 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
Collapse
Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| |
Collapse
|
20
|
Wang C, Milgate AW, Solomon PS, McDonald MC. The identification of a transposon affecting the asexual reproduction of the wheat pathogen Zymoseptoria tritici. MOLECULAR PLANT PATHOLOGY 2021; 22:800-816. [PMID: 33949756 PMCID: PMC8232023 DOI: 10.1111/mpp.13064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 05/13/2023]
Abstract
Zymoseptoria tritici, the causal agent of Septoria tritici blotch, is a fungal wheat pathogen that causes significant global yield losses. Within Z. tritici populations, quantitative differences in virulence among different isolates are commonly observed; however, the genetic components that underpin these differences remain elusive. In this study, intraspecific comparative transcriptomic analysis was used to identify candidate genes that contribute to differences in virulence on the wheat cultivar WW2449. This led to the identification of a multicopy gene that was not expressed in the high-virulence isolate when compared to the medium- and low-virulence isolates. Further investigation suggested this gene resides in a 7.9-kb transposon. Subsequent long-read sequencing of the isolates used in the transcriptomic analysis confirmed that this gene did reside in an active Class II transposon, which is composed of four genes named REP9-1 to -4. Silencing and overexpression of REP9-1 in two distinct genetic backgrounds demonstrated that its expression alone reduces the number of pycnidia produced by Z. tritici during infection. The REP9-1 gene identified within a Class II transposon is the first discovery of a gene in a transposable element that influences the virulence of Z. tritici. This discovery adds further complexity to genetic loci that contribute to quantitative virulence in this important pathogen.
Collapse
Affiliation(s)
- Chen Wang
- Division of Plant SciencesResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Andrew W. Milgate
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNSWAustralia
| | - Peter S. Solomon
- Division of Plant SciencesResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Megan C. McDonald
- Division of Plant SciencesResearch School of BiologyThe Australian National UniversityCanberraACTAustralia
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamUK
| |
Collapse
|
21
|
Soyer JL, Clairet C, Gay EJ, Lapalu N, Rouxel T, Stukenbrock EH, Fudal I. Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization. Chromosome Res 2021; 29:219-236. [PMID: 34018080 PMCID: PMC8159818 DOI: 10.1007/s10577-021-09658-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 12/25/2022]
Abstract
Leptosphaeria maculans 'brassicae' (Lmb) and Leptosphaeria maculans 'lepidii' (Lml) are closely related phytopathogenic species that exhibit a large macrosynteny but contrasting genome structure. Lmb has more than 30% of repeats clustered in large repeat-rich regions, while the Lml genome has only a small amount of evenly distributed repeats. Repeat-rich regions of Lmb are enriched in effector genes, expressed during plant infection. The distinct genome structures of Lmb and Lml provide an excellent model for comparing the organization of pathogenicity genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation (ChIP) during axenic culture, targeting histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyze the influence of chromatin organization on gene expression. In both species, we found that facultative heterochromatin is enriched with genes lacking functional annotation, including numerous effector and species-specific genes. Notably, orthologous genes located in H3K27me3 domains are enriched with effector genes. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3 domains associated with repeat-rich regions that contain numerous species-specific effector genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection and the selective advantage to the fungus to host effector genes in H3K9me3 or H3K27me3 domains.
Collapse
Affiliation(s)
- Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
| | - Colin Clairet
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| |
Collapse
|
22
|
Möller M, Habig M, Lorrain C, Feurtey A, Haueisen J, Fagundes WC, Alizadeh A, Freitag M, Stukenbrock EH. Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen. PLoS Genet 2021; 17:e1009448. [PMID: 33750960 PMCID: PMC8016269 DOI: 10.1371/journal.pgen.1009448] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 04/01/2021] [Accepted: 02/26/2021] [Indexed: 01/04/2023] Open
Abstract
DNA methylation is found throughout all domains of life, yet the extent and function of DNA methylation differ among eukaryotes. Strains of the plant pathogenic fungus Zymoseptoria tritici appeared to lack cytosine DNA methylation (5mC) because gene amplification followed by Repeat-Induced Point mutation (RIP) resulted in the inactivation of the dim2 DNA methyltransferase gene. 5mC is, however, present in closely related sister species. We demonstrate that inactivation of dim2 occurred recently as some Z. tritici isolates carry a functional dim2 gene. Moreover, we show that dim2 inactivation occurred by a different path than previously hypothesized. We mapped the genome-wide distribution of 5mC in strains with or without functional dim2 alleles. Presence of functional dim2 correlates with high levels of 5mC in transposable elements (TEs), suggesting a role in genome defense. We identified low levels of 5mC in strains carrying non-functional dim2 alleles, suggesting that 5mC is maintained over time, presumably by an active Dnmt5 DNA methyltransferase. Integration of a functional dim2 allele in strains with mutated dim2 restored normal 5mC levels, demonstrating de novo cytosine methylation activity of Dim2. To assess the importance of 5mC for genome evolution, we performed an evolution experiment, comparing genomes of strains with high levels of 5mC to genomes of strains lacking functional dim2. We found that presence of a functional dim2 allele alters nucleotide composition by promoting C to T transitions (C→T) specifically at CpA (CA) sites during mitosis, likely contributing to TE inactivation. Our results show that 5mC density at TEs is a polymorphic trait in Z. tritici populations that can impact genome evolution.
Collapse
Affiliation(s)
- Mareike Möller
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Michael Habig
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Cécile Lorrain
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Alice Feurtey
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Janine Haueisen
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Wagner C. Fagundes
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Alireza Alizadeh
- Department of Plant Protection, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States of America
| | - Eva H. Stukenbrock
- Environmental Genomics, Christian-Albrechts University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| |
Collapse
|
23
|
Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene. PHYTOPATHOLOGY 2021; 111:49-67. [PMID: 33200962 DOI: 10.1094/phyto-08-20-0358-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.
Collapse
Affiliation(s)
- Pauline Hessenauer
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
| | - Nicolas Feau
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Upinder Gill
- College of Agriculture, Food Systems, and Natural Resources, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Richard C Hamelin
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| |
Collapse
|