1
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Dhakal U, Kim HS, Toomajian C. The landscape and predicted roles of structural variants in Fusarium graminearum genomes. G3 (BETHESDA, MD.) 2024; 14:jkae065. [PMID: 38546739 DOI: 10.1093/g3journal/jkae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/22/2024] [Indexed: 06/06/2024]
Abstract
Structural rearrangements, such as inversions, translocations, duplications, and large insertions and deletions, are large-scale genomic variants that can play an important role in shaping phenotypic variation and in genome adaptation and evolution. We used chromosomal-level assemblies from eight Fusarium graminearum isolates to study structural variants and their role in fungal evolution. We generated the assemblies of four of these genomes after Oxford Nanopore sequencing. A total of 87 inversions, 159 translocations, 245 duplications, 58,489 insertions, and 34,102 deletions were detected. Regions of high recombination rate are associated with structural rearrangements, and a significant proportion of inversions, translocations, and duplications overlap with the repeat content of the genome, suggesting recombination and repeat elements are major factors in the origin of structural rearrangements in F. graminearum. Large insertions and deletions introduce presence-absence polymorphisms for many genes, including secondary metabolite biosynthesis cluster genes and predicted effectors genes. Translocation events were found to be shuffling predicted effector-rich regions of the genomes and are likely contributing to the gain and loss of effectors facilitated by recombination. Breakpoints of some structural rearrangements fall within coding sequences and are likely altering the protein products. Structural rearrangements in F. graminearum thus have an important role to play in shaping pathogen-host interactions and broader evolution through genome reorganization, the introduction of presence-absence polymorphisms, and changing protein products and gene regulation.
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Affiliation(s)
- Upasana Dhakal
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Hye-Seon Kim
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N University St., Peoria, IL 61604, USA
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2
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Kusch S, Qian J, Loos A, Kümmel F, Spanu PD, Panstruga R. Long-term and rapid evolution in powdery mildew fungi. Mol Ecol 2024; 33:e16909. [PMID: 36862075 DOI: 10.1111/mec.16909] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
The powdery mildew fungi (Erysiphaceae) are globally distributed plant pathogens with a range of more than 10,000 plant hosts. In this review, we discuss the long- and short-term evolution of these obligate biotrophic fungi and outline their diversity with respect to morphology, lifestyle, and host range. We highlight their remarkable ability to rapidly overcome plant immunity, evolve fungicide resistance, and broaden their host range, for example, through adaptation and hybridization. Recent advances in genomics and proteomics, particularly in cereal powdery mildews (genus Blumeria), provided first insights into mechanisms of genomic adaptation in these fungi. Transposable elements play key roles in shaping their genomes, where even close relatives exhibit diversified patterns of recent and ongoing transposon activity. These transposons are ubiquitously distributed in the powdery mildew genomes, resulting in a highly adaptive genome architecture lacking obvious regions of conserved gene space. Transposons can also be neofunctionalized to encode novel virulence factors, particularly candidate secreted effector proteins, which may undermine the plant immune system. In cereals like barley and wheat, some of these effectors are recognized by plant immune receptors encoded by resistance genes with numerous allelic variants. These effectors determine incompatibility ("avirulence") and evolve rapidly through sequence diversification and copy number variation. Altogether, powdery mildew fungi possess plastic genomes that enable their fast evolutionary adaptation towards overcoming plant immunity, host barriers, and chemical stress such as fungicides, foreshadowing future outbreaks, host range shifts and expansions as well as potential pandemics by these pathogens.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Jiangzhao Qian
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Anne Loos
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Florian Kümmel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Pietro D Spanu
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
- Imperial College, London, UK
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
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3
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Baudin M, Le Naour‐Vernet M, Gladieux P, Tharreau D, Lebrun M, Lambou K, Leys M, Fournier E, Césari S, Kroj T. Pyricularia oryzae: Lab star and field scourge. MOLECULAR PLANT PATHOLOGY 2024; 25:e13449. [PMID: 38619508 PMCID: PMC11018116 DOI: 10.1111/mpp.13449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/16/2024]
Abstract
Pyricularia oryzae (syn. Magnaporthe oryzae), is a filamentous ascomycete that causes a major disease called blast on cereal crops, as well as on a wide variety of wild and cultivated grasses. Blast diseases have a tremendous impact worldwide particularly on rice and on wheat, where the disease emerged in South America in the 1980s, before spreading to Asia and Africa. Its economic importance, coupled with its amenability to molecular and genetic manipulation, have inspired extensive research efforts aiming at understanding its biology and evolution. In the past 40 years, this plant-pathogenic fungus has emerged as a major model in molecular plant-microbe interactions. In this review, we focus on the clarification of the taxonomy and genetic structure of the species and its host range determinants. We also discuss recent molecular studies deciphering its lifecycle. TAXONOMY Kingdom: Fungi, phylum: Ascomycota, sub-phylum: Pezizomycotina, class: Sordariomycetes, order: Magnaporthales, family: Pyriculariaceae, genus: Pyricularia. HOST RANGE P. oryzae has the ability to infect a wide range of Poaceae. It is structured into different host-specialized lineages that are each associated with a few host plant genera. The fungus is best known to cause tremendous damage to rice crops, but it can also attack other economically important crops such as wheat, maize, barley, and finger millet. DISEASE SYMPTOMS P. oryzae can cause necrotic lesions or bleaching on all aerial parts of its host plants, including leaf blades, sheaths, and inflorescences (panicles, spikes, and seeds). Characteristic symptoms on leaves are diamond-shaped silver lesions that often have a brown margin and whose appearance is influenced by numerous factors such as the plant genotype and environmental conditions. USEFUL WEBSITES Resources URL Genomic data repositories http://genome.jouy.inra.fr/gemo/ Genomic data repositories http://openriceblast.org/ Genomic data repositories http://openwheatblast.net/ Genome browser for fungi (including P. oryzae) http://fungi.ensembl.org/index.html Comparative genomics database https://mycocosm.jgi.doe.gov/mycocosm/home T-DNA mutant database http://atmt.snu.kr/ T-DNA mutant database http://www.phi-base.org/ SNP and expression data https://fungidb.org/fungidb/app/.
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Affiliation(s)
- Maël Baudin
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
- Present address:
Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Marie Le Naour‐Vernet
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
- CIRAD, UMR PHIMMontpellierFrance
| | - Marc‐Henri Lebrun
- UMR 1290 BIOGER – Campus Agro Paris‐Saclay – INRAE‐AgroParisTechPalaiseauFrance
| | - Karine Lambou
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Marie Leys
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Stella Césari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
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Liang X, Yu W, Meng Y, Shang S, Tian H, Zhang Z, Rollins JA, Zhang R, Sun G. Genome comparisons reveal accessory genes crucial for the evolution of apple Glomerella leaf spot pathogenicity in Colletotrichum fungi. MOLECULAR PLANT PATHOLOGY 2024; 25:e13454. [PMID: 38619507 PMCID: PMC11018114 DOI: 10.1111/mpp.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/16/2024]
Abstract
Apple Glomerella leaf spot (GLS) is an emerging fungal disease caused by Colletotrichum fructicola and other Colletotrichum species. These species are polyphyletic and it is currently unknown how these pathogens convergently evolved to infect apple. We generated chromosome-level genome assemblies of a GLS-adapted isolate and a non-adapted isolate in C. fructicola using long-read sequencing. Additionally, we resequenced 17 C. fructicola and C. aenigma isolates varying in GLS pathogenicity using short-read sequencing. Genome comparisons revealed a conserved bipartite genome architecture involving minichromosomes (accessory chromosomes) shared by C. fructicola and other closely related species within the C. gloeosporioides species complex. Moreover, two repeat-rich genomic regions (1.61 Mb in total) were specifically conserved among GLS-pathogenic isolates in C. fructicola and C. aenigma. Single-gene deletion of 10 accessory genes within the GLS-specific regions of C. fructicola identified three that were essential for GLS pathogenicity. These genes encoded a putative non-ribosomal peptide synthetase, a flavin-binding monooxygenase and a small protein with unknown function. These results highlight the crucial role accessory genes play in the evolution of Colletotrichum pathogenicity and imply the significance of an unidentified secondary metabolite in GLS pathogenesis.
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Affiliation(s)
- Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Wei Yu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Yanan Meng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Shengping Shang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Huanhuan Tian
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Zhaohui Zhang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | | | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
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5
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Narayanan A, Reza MH, Sanyal K. Behind the scenes: Centromere-driven genomic innovations in fungal pathogens. PLoS Pathog 2024; 20:e1012080. [PMID: 38547101 PMCID: PMC10977804 DOI: 10.1371/journal.ppat.1012080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Affiliation(s)
- Aswathy Narayanan
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Md. Hashim Reza
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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6
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Liu S, Lin G, Ramachandran SR, Daza LC, Cruppe G, Tembo B, Singh PK, Cook D, Pedley KF, Valent B. Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia. THE NEW PHYTOLOGIST 2024; 241:1266-1276. [PMID: 37984076 DOI: 10.1111/nph.19402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023]
Abstract
The fungal pathogen, Magnaporthe oryzae Triticum pathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Magnaporthe oryzae strains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole-genome sequences. We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini-chromosome. Genome assembly of a Zambian strain revealed that its mini-chromosome was similar to the B71 mini-chromosome but with a high level of structural variation. Our findings show that while core genomes of the multiple introductions are highly similar, the mini-chromosomes have undergone marked diversification. The maintenance of the mini-chromosome and rapid genomic changes suggest the mini-chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Sowmya R Ramachandran
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, 21702-9253, USA
| | - Lidia Calderon Daza
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Giovana Cruppe
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Batiseba Tembo
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, 10101, Zambia
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, 56237, Mexico
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Kerry F Pedley
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, 21702-9253, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
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7
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Nakamoto AA, Joubert PM, Krasileva KV. Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes. Genome Biol Evol 2023; 15:evad206. [PMID: 37975814 PMCID: PMC10691877 DOI: 10.1093/gbe/evad206] [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: 04/27/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.
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Affiliation(s)
- Anne A Nakamoto
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Pierre M Joubert
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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8
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Asuke S, Horie A, Komatsu K, Mori R, Vy TTP, Inoue Y, Jiang Y, Tatematsu Y, Shimizu M, Tosa Y. Loss of PWT7, Located on a Supernumerary Chromosome, Is Associated with Parasitic Specialization of Pyricularia oryzae on Wheat. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:716-725. [PMID: 37432132 DOI: 10.1094/mpmi-06-23-0078-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: 07/12/2023]
Abstract
Pyricularia oryzae, a blast fungus of gramineous plants, is composed of various host genus-specific pathotypes. The avirulence of an Avena isolate on wheat is conditioned by PWT3 and PWT4. We isolated the third avirulence gene from the Avena isolate and designated it as PWT7. PWT7 was effective as an avirulence gene only at the seedling stage or on leaves. PWT7 homologs were widely distributed in a subpopulation of the Eleusine pathotype and the Lolium pathotype but completely absent in the Triticum pathotype (the wheat blast fungus). The PWT7 homolog found in the Eleusine pathotype was one of the five genes involved in its avirulence on wheat. A comparative analysis of distribution of PWT7 and the other two genes previously identified in the Eleusine pathotype suggested that, in the course of parasitic specialization toward the wheat blast fungus, a common ancestor of the Eleusine, Lolium, Avena, and Triticum pathotypes first lost PWT6, secondly PWT7, and, finally, the function of PWT3. PWT7 or its homologs were located on core chromosomes in Setaria and Eleusine isolates but on supernumerary chromosomes in Lolium and Avena isolates. This is an example of interchromosomal translocations of effector genes between core and supernumerary chromosomes. [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)
- Soichiro Asuke
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Akiko Horie
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Kaori Komatsu
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Ryota Mori
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Trinh Thi Phuong Vy
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yoshihiro Inoue
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yushan Jiang
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Yuna Tatematsu
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan
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9
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Dutta A, McDonald BA, Croll D. Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011801. [PMID: 37972199 PMCID: PMC10688896 DOI: 10.1371/journal.ppat.1011801] [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: 05/10/2023] [Revised: 11/30/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping. We performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., k-mer) approach using raw whole-genome sequencing data in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the k-mer approach explained a higher proportion of phenotypic variation than a reference genome-based approach and revealed functionally confirmed loci that classic GWAS approaches failed to map. The power of GWAS in microbial pathogens can be significantly enhanced by comprehensively capturing structural genetic variation. Our approach is generalizable to a large number of species and will uncover novel mechanisms driving rapid adaptation of pathogens.
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Affiliation(s)
- Anik Dutta
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - 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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10
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Weisberg AJ, Chang JH. Mobile Genetic Element Flexibility as an Underlying Principle to Bacterial Evolution. Annu Rev Microbiol 2023; 77:603-624. [PMID: 37437216 DOI: 10.1146/annurev-micro-032521-022006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Mobile genetic elements are key to the evolution of bacteria and traits that affect host and ecosystem health. Here, we use a framework of a hierarchical and modular system that scales from genes to populations to synthesize recent findings on mobile genetic elements (MGEs) of bacteria. Doing so highlights the role that emergent properties of flexibility, robustness, and genetic capacitance of MGEs have on the evolution of bacteria. Some of their traits can be stored, shared, and diversified across different MGEs, taxa of bacteria, and time. Collectively, these properties contribute to maintaining functionality against perturbations while allowing changes to accumulate in order to diversify and give rise to new traits. These properties of MGEs have long challenged our abilities to study them. Implementation of new technologies and strategies allows for MGEs to be analyzed in new and powerful ways.
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Affiliation(s)
- Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
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11
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Ebrahimzadegan R, Fuchs J, Chen J, Schubert V, Meister A, Houben A, Mirzaghaderi G. Meiotic segregation and post-meiotic drive of the Festuca pratensis B chromosome. Chromosome Res 2023; 31:26. [PMID: 37658970 PMCID: PMC10474989 DOI: 10.1007/s10577-023-09728-6] [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: 05/11/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023]
Abstract
In many species, the transmission of B chromosomes (Bs) does not follow the Mendelian laws of equal segregation and independent assortment. This deviation results in transmission rates of Bs higher than 0.5, a process known as "chromosome drive". Here, we studied the behavior of the 103 Mbp-large B chromosome of Festuca pratensis during all meiotic and mitotic stages of microsporogenesis. Mostly, the B chromosome of F. pratensis segregates during meiosis like standard A chromosomes (As). In some cases, the B passes through meiosis in a non-Mendelian segregation leading to their accumulation already in meiosis. However, a true drive of the B happens during the first pollen mitosis, by which the B preferentially migrates to the generative nucleus. During second pollen mitosis, B divides equally between the two sperms. Despite some differences in the frequency of drive between individuals with different numbers of Bs, at least 82% of drive was observed. Flow cytometry-based quantification of B-containing sperm nuclei agrees with the FISH data.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj, 66177-15175, Iran
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Jianyong Chen
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Armin Meister
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
| | - Ghader Mirzaghaderi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj, 66177-15175, Iran.
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Kobayashi N, Dang TA, Pham KTM, Gómez Luciano LB, Van Vu B, Izumitsu K, Shimizu M, Ikeda KI, Li WH, Nakayashiki H. Horizontally Transferred DNA in the Genome of the Fungus Pyricularia oryzae is Associated With Repressive Histone Modifications. Mol Biol Evol 2023; 40:msad186. [PMID: 37595132 PMCID: PMC10473863 DOI: 10.1093/molbev/msad186] [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: 02/05/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023] Open
Abstract
Horizontal gene transfer (HGT) is a means of exchanging genetic material asexually. The process by which horizontally transferred genes are domesticated by the host genome is of great interest but is not well understood. In this study, we determined the telomere-to-telomere genome sequence of the wheat-infecting Pyricularia oryzae strain Br48. SNP analysis indicated that the Br48 strain is a hybrid of wheat- and Brachiaria-infecting strains by a sexual or parasexual cross. Comparative genomic analysis identified several megabase-scale "insertions" in the Br48 genome, some of which were possibly gained by HGT-related events from related species, such as P. pennisetigena or P. grisea. Notably, the mega-insertions often contained genes whose phylogeny is not congruent with the species phylogeny. Moreover, some of the genes have a close homolog even in distantly related organisms, such as basidiomycetes or prokaryotes, implying the involvement of multiple HGT events. Interestingly, the levels of the silent epigenetic marks H3K9me3 and H3K27me3 in a genomic region tended to be negatively correlated with the phylogenetic concordance of genes in the same region, suggesting that horizontally transferred DNA is preferentially targeted for epigenetic silencing. Indeed, the putative HGT-derived genes were activated when MoKmt6, the gene responsible for H3K27me3 modification, was deleted. Notably, these genes also tended to be up-regulated during infection, suggesting that they are now under host control and have contributed to establishing a fungal niche. In conclusion, this study suggests that epigenetic modifications have played an important role in the domestication of HGT-derived genes in the P. oryzae genome.
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Affiliation(s)
- Natsuki Kobayashi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Thach An Dang
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kieu Thi Minh Pham
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Luis B Gómez Luciano
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Ba Van Vu
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kosuke Izumitsu
- Graduate School of Environmental Science, The University of Shiga Prefecture, Hikone, Japan
| | - Motoki Shimizu
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
| | - Ken-ichi Ikeda
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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13
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Wang H, Huang R, Ren J, Tang L, Huang S, Chen X, Fan J, Li B, Wang Q, Hsiang T, Liu H, Li Q. The evolution of mini-chromosomes in the fungal genus Colletotrichum. mBio 2023; 14:e0062923. [PMID: 37283539 PMCID: PMC10470602 DOI: 10.1128/mbio.00629-23] [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: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 06/08/2023] Open
Abstract
Anthracnose diseases caused by Colletotrichum species are among the most common fungal diseases. These symptoms typically manifest as dark, sunken lesions on leaves, stems, and fruit. In China, mango anthracnose seriously affects fruit yield and quality. Genome sequencing of several species shows the presence of mini-chromosomes. These are thought to contribute to virulence, but their formation and activity remain to be fully elucidated. Here, we assembled 17 Colletotrichum genomes (16 isolated from mango plus one from persimmon) through PacBio long-read sequencing. Half of the assembled scaffolds had telomeric repeats at both ends indicating full-length chromosomes. Based on comparative genomics analysis at interspecies and intraspecies levels, we identified extensive chromosomal rearrangements events. We analyzed mini-chromosomes of Colletotrichum spp. and found large variation among close relatives. In C. fructicola, homology between core chromosomes and mini-chromosomes suggested that some mini-chromosomes were generated by recombination of core chromosomes. In C. musae GZ23-3, we found 26 horizontally transferred genes arranged in clusters on mini-chromosomes. In C. asianum FJ11-1, several potential pathogenesis-related genes on mini-chromosomes were upregulated, especially in strains with highly pathogenic phenotypes. Mutants of these upregulated genes showed obvious defects in virulence. Our findings provide insights into the evolution and potential relationships to virulence associated with mini-chromosomes. IMPORTANCE Colletotrichum is a cosmopolitan fungal genus that seriously affects fruit yield and quality of many plant species. Mini-chromosomes have been found to be related to virulence in Colletotrichum. Further examination of mini-chromosomes can help us elucidate some pathogenic mechanisms of Colletotrichum. In this study, we generated novel assemblies of several Colletotrichum strains. Comparative genomic analyses within and between Colletotrichum species were conducted. We then identified mini-chromosomes in our sequenced strains systematically. The characteristics and generation of mini-chromosomes were investigated. Transcriptome analysis and gene knockout revealed pathogenesis-related genes located on mini-chromosomes of C. asianum FJ11-1. This study represents the most comprehensive investigation of chromosome evolution and potential pathogenicity of mini-chromosomes in the Colletotrichum genus.
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Affiliation(s)
- Haoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Rong Huang
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
| | - Jingyi Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Lihua Tang
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
| | - Suiping Huang
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
| | - Xiaolin Chen
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
| | - Jun Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Bintao Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qili Li
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
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14
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Ma W, Yang J, Ding J, Duan C, Zhao W, Peng YL, Bhadauria V. CRISPR/Cas9-mediated deletion of large chromosomal segments identifies a minichromosome modulating the Colletotrichum graminicola virulence on maize. Int J Biol Macromol 2023; 245:125462. [PMID: 37336378 DOI: 10.1016/j.ijbiomac.2023.125462] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
Colletotrichum graminicola causes anthracnose on maize, an economically significant disease worldwide. To decipher how the pathogen controls its virulence/pathogenicity on maize at the minichromosomal level, we sequenced the genome and transcriptome of the C. graminicola strain T1-3-3. The 61.91 Mb genome contains three transcriptionally repressed, full-length strain-specific minichromosomes (<1 Mb; Chr11 through Chr13). A CRISPR/Cas9-based system was developed to knock out large chromosomal segments; it involved the generation of multiple simultaneous DNA double-strand breaks across a targeted genomic region, followed by homology-directed replacement thereof with a donor DNA template carrying the selectable marker hygromycin phosphotransferase gene flanked by homologous sequence arms of the targeted region. Using this system, we obtained distinct mutants functionally nullisomic for individual minichromosomes. Only the ΔChr12 mutant lacking the 498.44 Kb genomic region carrying all of the 31 genes of Chr12 exhibited attenuated virulence on maize and was indistinguishable from T1-3-3 in fungal growth and conidiation, indicating that Chr12 is a conditionally dispensable minichromosome and imparts full virulence to C. graminicola on maize. The CRISPR/Cas9-mediated genome editing system developed in this study will enable the determination of the biological functions of minichromosomes or large chromosomal segments in fungal plant pathogens.
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Affiliation(s)
- Wendi Ma
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; Ministry of Agriculture and Rural Affairs-Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wensheng Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; Ministry of Agriculture and Rural Affairs-Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China
| | - You-Liang Peng
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; Ministry of Agriculture and Rural Affairs-Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China
| | - Vijai Bhadauria
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; Ministry of Agriculture and Rural Affairs-Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China.
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Disentangling the complex gene interaction networks between rice and the blast fungus identifies a new pathogen effector. PLoS Biol 2023; 21:e3001945. [PMID: 36656825 PMCID: PMC9851567 DOI: 10.1371/journal.pbio.3001945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023] Open
Abstract
Studies focused solely on single organisms can fail to identify the networks underlying host-pathogen gene-for-gene interactions. Here, we integrate genetic analyses of rice (Oryza sativa, host) and rice blast fungus (Magnaporthe oryzae, pathogen) and uncover a new pathogen recognition specificity of the rice nucleotide-binding domain and leucine-rich repeat protein (NLR) immune receptor Pik, which mediates resistance to M. oryzae expressing the avirulence effector gene AVR-Pik. Rice Piks-1, encoded by an allele of Pik-1, recognizes a previously unidentified effector encoded by the M. oryzae avirulence gene AVR-Mgk1, which is found on a mini-chromosome. AVR-Mgk1 has no sequence similarity to known AVR-Pik effectors and is prone to deletion from the mini-chromosome mediated by repeated Inago2 retrotransposon sequences. AVR-Mgk1 is detected by Piks-1 and by other Pik-1 alleles known to recognize AVR-Pik effectors; recognition is mediated by AVR-Mgk1 binding to the integrated heavy metal-associated (HMA) domain of Piks-1 and other Pik-1 alleles. Our findings highlight how complex gene-for-gene interaction networks can be disentangled by applying forward genetics approaches simultaneously to the host and pathogen. We demonstrate dynamic coevolution between an NLR integrated domain and multiple families of effector proteins.
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Rajpal VR, Sharma S, Sehgal D, Sharma P, Wadhwa N, Dhakate P, Chandra A, Thakur RK, Deb S, Rama Rao S, Mir BA, Raina SN. Comprehending the dynamism of B chromosomes in their journey towards becoming unselfish. Front Cell Dev Biol 2023; 10:1072716. [PMID: 36684438 PMCID: PMC9846793 DOI: 10.3389/fcell.2022.1072716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Investigated for more than a century now, B chromosomes (Bs) research has come a long way from Bs being considered parasitic or neutral to becoming unselfish and bringing benefits to their hosts. B chromosomes exist as accessory chromosomes along with the standard A chromosomes (As) across eukaryotic taxa. Represented singly or in multiple copies, B chromosomes are largely heterochromatic but also contain euchromatic and organellar segments. Although B chromosomes are derived entities, they follow their species-specific evolutionary pattern. B chromosomes fail to pair with the standard chromosomes during meiosis and vary in their number, size, composition and structure across taxa and ensure their successful transmission through non-mendelian mechanisms like mitotic, pre-meiotic, meiotic or post-meiotic drives, unique non-disjunction, self-pairing or even imparting benefits to the host when they lack drive. B chromosomes have been associated with cellular processes like sex determination, pathogenicity, resistance to pathogens, phenotypic effects, and differential gene expression. With the advancements in B-omics research, novel insights have been gleaned on their functions, some of which have been associated with the regulation of gene expression of A chromosomes through increased expression of miRNAs or differential expression of transposable elements located on them. The next-generation sequencing and emerging technologies will further likely unravel the cellular, molecular and functional behaviour of these enigmatic entities. Amidst the extensive fluidity shown by B chromosomes in their structural and functional attributes, we perceive that the existence and survival of B chromosomes in the populations most likely seem to be a trade-off between the drive efficiency and adaptive significance versus their adverse effects on reproduction.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India,*Correspondence: Vijay Rani Rajpal, , ; Soom Nath Raina,
| | - Suman Sharma
- Department of Botany, Ramjas College, University of Delhi, Delhi, India
| | - Deepmala Sehgal
- Syngenta, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Prashansa Sharma
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Rakesh Kr. Thakur
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Sohini Deb
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Bilal Ahmad Mir
- Department of Botany, University of Kashmir, Srinagar, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India,*Correspondence: Vijay Rani Rajpal, , ; Soom Nath Raina,
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Becerra S, Baroncelli R, Boufleur TR, Sukno SA, Thon MR. Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes. Front Microbiol 2023; 14:1129319. [PMID: 37032845 PMCID: PMC10076810 DOI: 10.3389/fmicb.2023.1129319] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
The fungal pathogen Colletotrichum graminicola causes the anthracnose of maize (Zea mays) and is responsible for significant yield losses worldwide. The genome of C. graminicola was sequenced in 2012 using Sanger sequencing, 454 pyrosequencing, and an optical map to obtain an assembly of 13 pseudochromosomes. We re-sequenced the genome using a combination of short-read (Illumina) and long-read (PacBio) technologies to obtain a chromosome-level assembly. The new version of the genome sequence has 13 chromosomes with a total length of 57.43 Mb. We detected 66 (23.62 Mb) structural rearrangements in the new assembly with respect to the previous version, consisting of 61 (21.98 Mb) translocations, 1 (1.41 Mb) inversion, and 4 (221 Kb) duplications. We annotated the genome and obtained 15,118 predicted genes and 3,614 new gene models compared to the previous version of the assembly. We show that 25.88% of the new assembly is composed of repetitive DNA elements (13.68% more than the previous assembly version), which are mostly found in gene-sparse regions. We describe genomic compartmentalization consisting of repeat-rich and gene-poor regions vs. repeat-poor and gene-rich regions. A total of 1,140 secreted proteins were found mainly in repeat-rich regions. We also found that ~75% of the three smallest chromosomes (minichromosomes, between 730 and 551 Kb) are strongly affected by repeat-induced point mutation (RIP) compared with 28% of the larger chromosomes. The gene content of the minichromosomes (MCs) comprises 121 genes, of which 83.6% are hypothetical proteins with no predicted function, while the mean percentage of Chr1-Chr10 is 36.5%. No predicted secreted proteins are present in the MCs. Interestingly, only 2% of the genes in Chr11 have homologs in other strains of C. graminicola, while Chr12 and 13 have 58 and 57%, respectively, raising the question as to whether Chrs12 and 13 are dispensable. The core chromosomes (Chr1-Chr10) are very different with respect to the MCs (Chr11-Chr13) in terms of the content and sequence features. We hypothesize that the higher density of repetitive elements and RIPs in the MCs may be linked to the adaptation and/or host co-evolution of this pathogenic fungus.
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Affiliation(s)
- Sioly Becerra
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
| | - Riccardo Baroncelli
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Thaís R. Boufleur
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Serenella A. Sukno
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- *Correspondence: Serenella A. Sukno
| | - Michael R. Thon
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- Michael R. Thon
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Syauqi J, Chen RK, Cheng AH, Wu YF, Chung CL, Lin CC, Chou HP, Wu HY, Jian JY, Liao CT, Kuo CC, Chu SC, Tsai YC, Liao DJ, Wu YP, Abadi AL, Sulistyowati L, Shen WC. Surveillance of Rice Blast Resistance Effectiveness and Emerging Virulent Isolates in Taiwan. PLANT DISEASE 2022; 106:3187-3197. [PMID: 35581907 DOI: 10.1094/pdis-12-21-2806-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Rice blast caused by Magnaporthe oryzae is a dangerous threat to rice production and food security worldwide. Breeding and proper deployment of resistant varieties are effective and environmentally friendly strategies to manage this notorious disease. However, a highly dynamic and quickly evolved rice blast pathogen population in the field has made disease control with resistance germplasms more challenging. Therefore, continued monitoring of pathogen dynamics and application of effective resistance varieties are critical tasks to prolong or sustain field resistance. Here, we report a team project that involved evaluation of rice blast resistance genes and surveillance of M. oryzae field populations in Taiwan. A set of International Rice Research Institute-bred blast-resistant lines (IRBLs) carrying single blast resistance genes was utilized to monitor the field effectiveness of rice blast resistance. Resistance genes such as Ptr (formerly Pita2) and Pi9 exhibited the best and most durable resistance against the rice blast fungus population in Taiwan. Interestingly, line IRBLb-B harboring the Pib gene with good field protection has recently shown susceptible lesions in some locations. To dissect the genotypic features of virulent isolates against the Pib resistance gene, M. oryzae isolates were collected and analyzed. Screening of the AvrPib locus revealed that the majority of field isolates still maintained the wild-type AvrPib status but eight virulent genotypes were found. Pot3 insertion appeared to be a major way to disrupt the AvrPib avirulence function. Interestingly, a novel AvrPib double-allele genotype among virulent isolates was first identified. Pot2 repetitive element-based polymerase chain reaction (rep-PCR) fingerprinting analysis indicated that mutation events may occur independently among different lineages in different geographic locations of Taiwan. This study provides our surveillance experience of rice blast disease and serves as the foundation to sustain rice production.
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Affiliation(s)
- Jauhar Syauqi
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 106216, Taiwan
- Department of Plant Pathology, University of Brawijaya, Lowokwaru, Malang City, Jawa Timur 65145, Indonesia
| | - Rong-Kuen Chen
- Tainan District Agricultural Research and Extension Station, Hsinhua District, Tainan 712009, Taiwan
| | - An-Hsiu Cheng
- Tainan District Agricultural Research and Extension Station, Hsinhua District, Tainan 712009, Taiwan
| | - Yea-Fang Wu
- Tainan District Agricultural Research and Extension Station, Hsinhua District, Tainan 712009, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 106216, Taiwan
| | - Chun-Chi Lin
- Taidung District Agricultural Research and Extension Station, Taidung City 950244, Taiwan
| | - Hau-Ping Chou
- Kaohsiung District Agricultural Research and Extension Station, Pingtung County 908126, Taiwan
| | - Hsin-Yuh Wu
- Taoyuan District Agricultural Research and Extension Station, Xinwu District, Taoyuan City 327005, Taiwan
| | - Jen-You Jian
- Taoyuan District Agricultural Research and Extension Station, Xinwu District, Taoyuan City 327005, Taiwan
| | - Chung-Ta Liao
- Taichung District Agricultural Research and Extension Station, Changhua County 515008, Taiwan
| | - Chien-Chih Kuo
- Taichung District Agricultural Research and Extension Station, Changhua County 515008, Taiwan
| | - Sheng-Chi Chu
- Miaoli District Agricultural Research and Extension Station, Gongguan Township, Miaoli County 363201, Taiwan
| | - Yi-Chen Tsai
- Hualien District Agricultural Research and Extension Station, Hualien County 973044, Taiwan
| | - Dah-Jing Liao
- Department of Agronomy, Chiayi Agricultural Experiment Branch, Taiwan Agricultural Research Institute, Chiayi City 600015, Taiwan
| | - Yong-Pei Wu
- Department of Agronomy, Chiayi Agricultural Experiment Branch, Taiwan Agricultural Research Institute, Chiayi City 600015, Taiwan
| | - Abdul Latief Abadi
- Department of Plant Pathology, University of Brawijaya, Lowokwaru, Malang City, Jawa Timur 65145, Indonesia
| | - Liliek Sulistyowati
- Department of Plant Pathology, University of Brawijaya, Lowokwaru, Malang City, Jawa Timur 65145, Indonesia
| | - Wei-Chiang Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 106216, Taiwan
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Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae. J Fungi (Basel) 2022; 8:jof8121238. [PMID: 36547571 PMCID: PMC9785059 DOI: 10.3390/jof8121238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
(1) Background: Pyricularia oryzae, the causal agent of rice blast disease, is one of the major rice pathogens. The complex population structure of P. oryzae facilitates the rapid virulence variations, which make the blast disease a serious challenge for global food security. There is a large body of existing genomics research on P. oryzae, however the population structure at the pan-genome level is not clear, and the mechanism of genetic divergence and virulence variations of different sub-populations is also unknown. (2) Methods: Based on the genome data published in the NCBI, we constructed a pan-genome database of P. oryzae, which consisted of 156 strains (117 isolated from rice and 39 isolated from other hosts). (3) Results: The pan-genome contained a total of 24,100 genes (12,005 novel genes absent in the reference genome 70-15), including 16,911 (~70%) core genes (population frequency ≥95%) and 1378 (~5%) strain-specific genes (population frequency ≤5%). Gene presence-absence variation (PAV) based clustering analysis of the population structure of P. oryzae revealed four subgroups (three from rice and one from other hosts). Interestingly, the cloned avirulence genes and conventional secreted proteins (SPs, with signal peptides) were enriched in the high-frequency regions and significantly associated with transposable elements (TEs), while the unconventional SPs (without signal peptides) were enriched in the low-frequency regions and not associated significantly with TEs. This pan-genome will expand the breadth and depth of the rice blast fungus reference genome, and also serve as a new blueprint for scientists to further study the pathogenic mechanism and virulence variation of the rice blast fungus.
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Joubert PM, Krasileva KV. The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors. BMC Biol 2022; 20:260. [PMID: 36424609 PMCID: PMC9694575 DOI: 10.1186/s12915-022-01457-2] [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: 10/04/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND One of the ways genomes respond to stress is by producing extrachromosomal circular DNAs (eccDNAs). EccDNAs can contain genes and dramatically increase their copy number. They can also reinsert into the genome, generating structural variation. They have been shown to provide a source of phenotypic and genotypic plasticity in several species. However, whole circularome studies have so far been limited to a few model organisms. Fungal plant pathogens are a serious threat to global food security in part because of their rapid adaptation to disease prevention strategies. Understanding the mechanisms fungal pathogens use to escape disease control is paramount to curbing their threat. RESULTS We present a whole circularome sequencing study of the rice blast pathogen, Magnaporthe oryzae. We find that M. oryzae has a highly diverse circularome that contains many genes and shows evidence of large LTR retrotransposon activity. We find that genes enriched on eccDNAs in M. oryzae occur in genomic regions prone to presence-absence variation and that disease-associated genes are frequently on eccDNAs. Finally, we find that a subset of genes is never present on eccDNAs in our data, which indicates that the presence of these genes on eccDNAs is selected against. CONCLUSIONS Our study paves the way to understanding how eccDNAs contribute to adaptation in M. oryzae. Our analysis also reveals how M. oryzae eccDNAs differ from those of other species and highlights the need for further comparative characterization of eccDNAs across species to gain a better understanding of these molecules.
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Affiliation(s)
- Pierre M Joubert
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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21
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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.
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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.
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22
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Komluski J, Stukenbrock EH, Habig M. Non-Mendelian transmission of accessory chromosomes in fungi. Chromosome Res 2022; 30:241-253. [PMID: 35881207 PMCID: PMC9508043 DOI: 10.1007/s10577-022-09691-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
Non-Mendelian transmission has been reported for various genetic elements, ranging from small transposons to entire chromosomes. One prime example of such a transmission pattern are B chromosomes in plants and animals. Accessory chromosomes in fungi are similar to B chromosomes in showing presence/absence polymorphism and being non-essential. How these chromosomes are transmitted during meiosis is however poorly understood—despite their often high impact on the fitness of the host. For several fungal organisms, a non-Mendelian transmission or a mechanistically unique meiotic drive of accessory chromosomes have been reported. In this review, we provide an overview of the possible mechanisms that can cause the non-Mendelian transmission or meiotic drives of fungal accessory chromosomes. We compare processes responsible for the non-Mendelian transmission of accessory chromosomes for different fungal eukaryotes and discuss the structural traits of fungal accessory chromosomes affecting their meiotic transmission. We conclude that research on fungal accessory chromosomes, due to their small size, ease of sequencing, and epigenetic profiling, can complement the study of B chromosomes in deciphering factors that influence and regulate the non-Mendelian transmission of entire chromosomes.
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Affiliation(s)
- Jovan Komluski
- 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.
| | - Michael Habig
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
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23
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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24
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Understanding the Dynamics of Blast Resistance in Rice-Magnaporthe oryzae Interactions. J Fungi (Basel) 2022; 8:jof8060584. [PMID: 35736067 PMCID: PMC9224618 DOI: 10.3390/jof8060584] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/03/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.
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25
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Hartmann FE. Using structural variants to understand the ecological and evolutionary dynamics of fungal plant pathogens. THE NEW PHYTOLOGIST 2022; 234:43-49. [PMID: 34873717 DOI: 10.1111/nph.17907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Deletions, duplications, insertions, inversions and translocations are commonly referred to as structural variants (SVs). Fungal plant pathogens have compact genomes, facilitating the generation of accurate maps of SVs for these species in recent studies. Structural variants have been found to constitute a significant proportion of the standing genetic variation in fungal plant pathogen populations, potentially leading to the generation of accessory genes, regions or chromosomes enriched in pathogenicity factors. Structural variants are involved in the rapid adaptation and ecological traits of pathogens, including host specialization and mating. Long-read sequencing techniques coupled with theoretical and experimental approaches have considerable potential for elucidating the phenotypic effects of SVs and deciphering the evolutionary and genomic mechanisms underlying the formation of SVs in fungal plant pathogens.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systematique Evolution, Batiment 360, Universite Paris-Saclay, CNRS, AgroParisTech, Orsay, 91400, France
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26
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Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions. BIOLOGY 2022; 11:biology11030421. [PMID: 35336795 PMCID: PMC8945218 DOI: 10.3390/biology11030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022]
Abstract
Simple Summary Plants, unlike animals, do not have defender cells or an adaptive immune system. Instead, plants rely on each cell’s innate immunity and systemic signals emitted from infection sites. On the other hand, not all plants, even within the same species, are genetically identical, and their genetic backgrounds determine how well they respond to stress factors. Through evolution, plants have acquired various defense mechanisms that play important roles in the never-ending fight between plants and pathogens. Genetic variation in relation to plant disease resistance can thus be contextualized to provide new insights into these defense mechanisms and evolutionary processes that lead to resistance to pathogens. By focusing on genetic variations and mutational events linked with plant–pathogen interactions, the paper explores how genome compartments facilitate plant and pathogen evolutionary processes. Abstract Phytopathologists are actively researching the molecular basis of plant–pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant–microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant–pathogen interactions and discusses how these genome compartments enhance plants’ and pathogens’ evolutionary processes.
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27
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Pasin F, Daròs JA, Tzanetakis IE. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6534904. [PMID: 35195244 PMCID: PMC9249622 DOI: 10.1093/femsre/fuac011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Potyviridae, the largest family of known RNA viruses (realm Riboviria), belongs to the picorna-like supergroup and has important agricultural and ecological impacts. Potyvirid genomes are translated into polyproteins, which are in turn hydrolyzed to release mature products. Recent sequencing efforts revealed an unprecedented number of potyvirids with a rich variability in gene content and genomic layouts. Here, we review the heterogeneity of non-core modules that expand the structural and functional diversity of the potyvirid proteomes. We provide a family-wide classification of P1 proteinases into the functional Types A and B, and discuss pretty interesting sweet potato potyviral ORF (PISPO), putative zinc fingers, and alkylation B (AlkB)—non-core modules found within P1 cistrons. The atypical inosine triphosphate pyrophosphatase (ITPase/HAM1), as well as the pseudo tobacco mosaic virus-like coat protein (TMV-like CP) are discussed alongside homologs of unrelated virus taxa. Family-wide abundance of the multitasking helper component proteinase (HC-pro) is revised. Functional connections between non-core modules are highlighted to support host niche adaptation and immune evasion as main drivers of the Potyviridae evolutionary radiation. Potential biotechnological and synthetic biology applications of potyvirid leader proteinases and non-core modules are finally explored.
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Affiliation(s)
- Fabio Pasin
- Corresponding author: Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), UPV Building 8E, Ingeniero Fausto Elio, 46011 Valencia, Spain. E-mail:
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València (CSIC-UPV), 46011 Valencia, Spain
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, 72701 Fayetteville, AR, USA
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28
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Bentham AR, Petit-Houdenot Y, Win J, Chuma I, Terauchi R, Banfield MJ, Kamoun S, Langner T. A single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum. PLoS Pathog 2021; 17:e1009957. [PMID: 34758051 PMCID: PMC8608293 DOI: 10.1371/journal.ppat.1009957] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/22/2021] [Accepted: 09/14/2021] [Indexed: 12/14/2022] Open
Abstract
Accelerated gene evolution is a hallmark of pathogen adaptation and specialization following host-jumps. However, the molecular processes associated with adaptive evolution between host-specific lineages of a multihost plant pathogen remain poorly understood. In the blast fungus Magnaporthe oryzae (Syn. Pyricularia oryzae), host specialization on different grass hosts is generally associated with dynamic patterns of gain and loss of virulence effector genes that tend to define the distinct genetic lineages of this pathogen. Here, we unravelled the biochemical and structural basis of adaptive evolution of APikL2, an exceptionally conserved paralog of the well-studied rice-lineage specific effector AVR-Pik. Whereas AVR-Pik and other members of the six-gene AVR-Pik family show specific patterns of presence/absence polymorphisms between grass-specific lineages of M. oryzae, APikL2 stands out by being ubiquitously present in all blast fungus lineages from 13 different host species. Using biochemical, biophysical and structural biology methods, we show that a single aspartate to asparagine polymorphism expands the binding spectrum of APikL2 to host proteins of the heavy-metal associated (HMA) domain family. This mutation maps to one of the APikL2-HMA binding interfaces and contributes to an altered hydrogen-bonding network. By combining phylogenetic ancestral reconstruction with an analysis of the structural consequences of allelic diversification, we revealed a common mechanism of effector specialization in the AVR-Pik/APikL2 family that involves two major HMA-binding interfaces. Together, our findings provide a detailed molecular evolution and structural biology framework for diversification and adaptation of a fungal pathogen effector family following host-jumps.
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Affiliation(s)
- Adam R. Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Yohann Petit-Houdenot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Thiverval-Grignon, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Izumi Chuma
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Ryohei Terauchi
- Kyoto University, Kyoto, Japan
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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29
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Maroilley T, Li X, Oldach M, Jean F, Stasiuk SJ, Tarailo-Graovac M. Deciphering complex genome rearrangements in C. elegans using short-read whole genome sequencing. Sci Rep 2021; 11:18258. [PMID: 34521941 PMCID: PMC8440550 DOI: 10.1038/s41598-021-97764-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic rearrangements cause congenital disorders, cancer, and complex diseases in human. Yet, they are still understudied in rare diseases because their detection is challenging, despite the advent of whole genome sequencing (WGS) technologies. Short-read (srWGS) and long-read WGS approaches are regularly compared, and the latter is commonly recommended in studies focusing on genomic rearrangements. However, srWGS is currently the most economical, accurate, and widely supported technology. In Caenorhabditis elegans (C. elegans), such variants, induced by various mutagenesis processes, have been used for decades to balance large genomic regions by preventing chromosomal crossover events and allowing the maintenance of lethal mutations. Interestingly, those chromosomal rearrangements have rarely been characterized on a molecular level. To evaluate the ability of srWGS to detect various types of complex genomic rearrangements, we sequenced three balancer strains using short-read Illumina technology. As we experimentally validated the breakpoints uncovered by srWGS, we showed that, by combining several types of analyses, srWGS enables the detection of a reciprocal translocation (eT1), a free duplication (sDp3), a large deletion (sC4), and chromoanagenesis events. Thus, applying srWGS to decipher real complex genomic rearrangements in model organisms may help designing efficient bioinformatics pipelines with systematic detection of complex rearrangements in human genomes.
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Affiliation(s)
- Tatiana Maroilley
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Xiao Li
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Matthew Oldach
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Francesca Jean
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Susan J Stasiuk
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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30
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CEM, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:e66961. [PMID: 34288868 PMCID: PMC8294853 DOI: 10.7554/elife.66961] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 12/17/2022] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Clare EM Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research CentreIwateJapan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto UniversityKyotoJapan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
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31
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CE, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:66961. [PMID: 34288868 DOI: 10.1101/2021.01.26.428286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 05/21/2023] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Clare Em Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Centre, Iwate, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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32
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Badet T, Fouché S, Hartmann FE, Zala M, Croll D. Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen. Nat Commun 2021; 12:3551. [PMID: 34112792 PMCID: PMC8192914 DOI: 10.1038/s41467-021-23862-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere genome assemblies of a fungal pathogen of wheat to establish a nucleotide-level map of structural variation. We show that the recent emergence of pesticide resistance has been disproportionally driven by rearrangements. We use machine learning to train a model on structural variation events based on 30 chromosomal sequence features. We show that base composition and gene density are the major determinants of structural variation. Retrotransposons explain most inversion, indel and duplication events. We apply our model to Arabidopsis thaliana and show that our approach extends to more complex genomes. Finally, we analyze complete genomes of haploid offspring in a four-generation pedigree. Meiotic crossover locations are enriched for new rearrangements consistent with crossovers being mutational hotspots. The model trained on species-wide structural variation accurately predicts the position of >74% of newly generated variants along the pedigree. The predictive power highlights causality between specific sequence features and the induction of chromosomal rearrangements. Our work demonstrates that training sequence-derived models can accurately identify regions of intrinsic DNA instability in eukaryotic genomes.
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Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Simone Fouché
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Marcello Zala
- 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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33
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Eseola AB, Ryder LS, Osés-Ruiz M, Findlay K, Yan X, Cruz-Mireles N, Molinari C, Garduño-Rosales M, Talbot NJ. Investigating the cell and developmental biology of plant infection by the rice blast fungus Magnaporthe oryzae. Fungal Genet Biol 2021; 154:103562. [PMID: 33882359 DOI: 10.1016/j.fgb.2021.103562] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/18/2023]
Abstract
Magnaporthe oryzae is the causal agent of rice blast disease, the most widespread and serious disease of cultivated rice. Live cell imaging and quantitative 4D image analysis have provided new insight into the mechanisms by which the fungus infects host cells and spreads rapidly in plant tissue. In this video review article, we apply live cell imaging approaches to understanding the cell and developmental biology of rice blast disease. To gain entry to host plants, M. oryzae develops a specialised infection structure called an appressorium, a unicellular dome-shaped cell which generates enormous turgor, translated into mechanical force to rupture the leaf cuticle. Appressorium development is induced by perception of the hydrophobic leaf surface and nutrient deprivation. Cargo-independent autophagy in the three-celled conidium, controlled by cell cycle regulation, is essential for appressorium morphogenesis. Appressorium maturation involves turgor generation and melanin pigment deposition in the appressorial cell wall. Once a threshold of turgor has been reached, this triggers re-polarisation which requires regulated generation of reactive oxygen species, to facilitate septin GTPase-dependent cytoskeletal re-organisation and re-polarisation of the appressorium to form a narrow, rigid penetration peg. Infection of host tissue requires a further morphogenetic transition to a pseudohyphal-type of growth within colonised rice cells. At the same time the fungus secretes an arsenal of effector proteins to suppress plant immunity. Many effectors are secreted into host cells directly, which involves a specific secretory pathway and a specialised structure called the biotrophic interfacial complex. Cell-to-cell spread of the fungus then requires development of a specialised structure, the transpressorium, that is used to traverse pit field sites, allowing the fungus to maintain host cell membrane integrity as new living plant cells are invaded. Thereafter, the fungus rapidly moves through plant tissue and host cells begin to die, as the fungus switches to necrotrophic growth and disease symptoms develop. These morphogenetic transitions are reviewed in the context of live cell imaging studies.
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Affiliation(s)
- Alice Bisola Eseola
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR47UH, United Kingdom
| | - Lauren S Ryder
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR47UH, United Kingdom
| | - Míriam Osés-Ruiz
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR47UH, United Kingdom
| | - Kim Findlay
- The John Innes Centre, Norwich Research Park, NR47UH, United Kingdom
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR47UH, United Kingdom
| | - Neftaly Cruz-Mireles
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR47UH, United Kingdom
| | - Camilla Molinari
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR47UH, United Kingdom
| | - Marisela Garduño-Rosales
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR47UH, United Kingdom
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR47UH, United Kingdom.
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