1
|
Rojas-Barrera IC, Flores-Núñez VM, Haueisen J, Alizadeh A, Salimi F, Stukenbrock EH. Evolution of sympatric host-specialized lineages of the fungal plant pathogen Zymoseptoria passerinii in natural ecosystems. THE NEW PHYTOLOGIST 2024. [PMID: 39686531 DOI: 10.1111/nph.20340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 11/22/2024] [Indexed: 12/18/2024]
Abstract
The barley disease Septoria Speckled Leaf Blotch, caused by the fungus Zymoseptoria passerinii, last appeared in North America in the early 2000s. Although rare in crops, field sampling of wild grasses in the Middle East revealed the disease persistence in wild barley. Identification of Z. passerinii in various wild barley species prompted us to examine genomic signatures of host specialization and trace the emergence of the domesticated-barley-infecting lineage. Furthermore, we applied virulence assays and confocal laser microscopy to evaluate whether the disease development differs between wild and domesticated barley. Wild- and domesticated-host-infecting populations have diverged, and phylogenetic relationships support the evolution of sympatric host-specialized lineages in wild hosts. Cross-virulence assays showed that Z. passerinii from domesticated hosts infect domesticated barley and its wild ancestor, Hordeum spontaneum. However, wild isolates from Iran did not infect domesticated barley. Wild and domesticated pathosystems have similar disease timing and progression, suggesting its persistence does not depend on a shorter period of incubation. The study supports that a wide range of hosts can foster the evolution of host-specialized lineages in sympatry and provide novel insights into the evolution of understudied fungal pathogens on wild hosts.
Collapse
Affiliation(s)
- Idalia C Rojas-Barrera
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-11, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Victor M Flores-Núñez
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-11, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Janine Haueisen
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-11, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Alireza Alizadeh
- Department of Plant Protection, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, 53714-161, Iran
| | - Fatemeh Salimi
- Department of Plant Protection, Faculty of Agriculture, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue Str. 13, D-60438, Frankfurt am Main, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-11, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| |
Collapse
|
2
|
Alkemade JA, Hohmann P, Messmer MM, Barraclough TG. Comparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini. MOLECULAR PLANT PATHOLOGY 2024; 25:e70039. [PMID: 39673077 PMCID: PMC11645255 DOI: 10.1111/mpp.70039] [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: 09/01/2024] [Revised: 11/21/2024] [Accepted: 11/24/2024] [Indexed: 12/15/2024]
Abstract
Fungal plant pathogens cause major crop losses worldwide, with many featuring compartmentalised genomes that include both core and accessory regions, which are believed to drive adaptation. The highly host-specific fungus Colletotrichum lupini greatly impacts lupin (Lupinus spp.) cultivation. This pathogen is part of clade 1 of the C. acutatum species complex and comprises four genetically uniform, presumably clonal, lineages (I-IV). Despite this, variation in virulence and morphology has been observed within these lineages. To investigate the potential sources of genetic variability in this asexual fungus, we compared the genomes of 16 C. lupini strains and 17 related Colletotrichum species. Phylogenomics confirmed the presence of four distinct lineages, but further examination based on genome size, gene content, transposable elements (TEs), and deletions revealed that lineage II could be split into two groups, II-A and II-B. TE content varied between lineages and correlated strongly with genome size variation, supporting a role for TEs in genome expansion in this species. Pangenome analysis revealed a highly variable accessory genome, including a minichromosome present in lineages II, III, and IV, but absent in lineage I. Accessory genes and effectors appeared to cluster in proximity to TEs. Presence/absence variation of putative effectors was lineage-specific, suggesting that these genes play a crucial role in determining host range. Notably, no effectors were found on the TE-rich minichromosome. Our findings shed light on the potential mechanisms generating genetic diversity in this asexual fungal pathogen that could aid future disease management.
Collapse
Affiliation(s)
- Joris A. Alkemade
- Department of BiologyUniversity of OxfordOxfordUK
- Calleva Research Centre for Evolution and Human ScienceMagdalen CollegeOxfordUK
- Department of Crop SciencesResearch Institute of Organic Agriculture (FiBL)FrickSwitzerland
| | - Pierre Hohmann
- Department of Crop SciencesResearch Institute of Organic Agriculture (FiBL)FrickSwitzerland
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food SciencesUniversitat de BarcelonaBarcelonaSpain
| | - Monika M. Messmer
- Department of Crop SciencesResearch Institute of Organic Agriculture (FiBL)FrickSwitzerland
| | - Timothy G. Barraclough
- Department of BiologyUniversity of OxfordOxfordUK
- Calleva Research Centre for Evolution and Human ScienceMagdalen CollegeOxfordUK
| |
Collapse
|
3
|
Urquhart A, Vogan AA, Gluck-Thaler E. Starships: a new frontier for fungal biology. Trends Genet 2024; 40:1060-1073. [PMID: 39299886 DOI: 10.1016/j.tig.2024.08.006] [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: 07/02/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Transposable elements (TEs) are semiautonomous genetic entities that proliferate in genomes. We recently discovered the Starships, a previously hidden superfamily of giant TEs found in a diverse subphylum of filamentous fungi, the Pezizomycotina. Starships are unlike other eukaryotic TEs because they have evolved mechanisms for both mobilizing entire genes, including those encoding conditionally beneficial phenotypes, and for horizontally transferring between individuals. We argue that Starships have unrivaled capacity to engage their fungal hosts as genetic parasites and mutualists, revealing unexplored terrain for investigating the ecoevolutionary dynamics of TE-eukaryote interactions. We build on existing models of fungal genome evolution by conceptualizing Starships as a distinct genomic compartment whose dynamics profoundly shape fungal biology.
Collapse
Affiliation(s)
- Andrew Urquhart
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, 752 36, Sweden
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, 752 36, Sweden
| | - Emile Gluck-Thaler
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706, USA; Wisconsin Institute for Discovery, Madison, WI 53706, USA.
| |
Collapse
|
4
|
Cornet C, Mora P, Augustijnen H, Nguyen P, Escudero M, Lucek K. Holocentric repeat landscapes: From micro-evolutionary patterns to macro-evolutionary associations with karyotype evolution. Mol Ecol 2024; 33:e17100. [PMID: 37577951 PMCID: PMC11628661 DOI: 10.1111/mec.17100] [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: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/15/2023]
Abstract
Repetitive elements can cause large-scale chromosomal rearrangements, for example through ectopic recombination, potentially promoting reproductive isolation and speciation. Species with holocentric chromosomes, that lack a localized centromere, might be more likely to retain chromosomal rearrangements that lead to karyotype changes such as fusions and fissions. This is because chromosome segregation during cell division should be less affected than in organisms with a localized centromere. The relationships between repetitive elements and chromosomal rearrangements and how they may translate to patterns of speciation in holocentric organisms are though poorly understood. Here, we use a reference-free approach based on low-coverage short-read sequencing data to characterize the repeat landscape of two independently evolved holocentric groups: Erebia butterflies and Carex sedges. We consider both micro- and macro-evolutionary scales to investigate the repeat landscape differentiation between Erebia populations and the association between repeats and karyotype changes in a phylogenetic framework for both Erebia and Carex. At a micro-evolutionary scale, we found population differentiation in repeat landscape that increases with overall intraspecific genetic differentiation among four Erebia species. At a macro-evolutionary scale, we found indications for an association between repetitive elements and karyotype changes along both Erebia and Carex phylogenies. Altogether, our results suggest that repetitive elements are associated with the level of population differentiation and chromosomal rearrangements in holocentric clades and therefore likely play a role in adaptation and potentially species diversification.
Collapse
Affiliation(s)
- Camille Cornet
- Biodiversity Genomics Laboratory, Institute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Pablo Mora
- Department of Experimental Biology, Genetics AreaUniversity of JaénJaénSpain
- University of South BohemiaFaculty of ScienceČeské BudějoviceCzech Republic
| | | | - Petr Nguyen
- University of South BohemiaFaculty of ScienceČeské BudějoviceCzech Republic
| | - Marcial Escudero
- Department of Plant Biology and EcologyUniversity of SevilleSevilleSpain
| | - Kay Lucek
- Biodiversity Genomics Laboratory, Institute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
| |
Collapse
|
5
|
Zaccaron AZ, Stergiopoulos I. The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance. J Genet Genomics 2024:S1673-8527(24)00284-4. [PMID: 39522682 DOI: 10.1016/j.jgg.2024.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 10/15/2024] [Accepted: 10/21/2024] [Indexed: 11/16/2024]
Abstract
Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions. In this review, we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance. We examine key features and the heterogeneity of genomes across different fungal species, including but not limited to their chromosome content, DNA composition, distribution and arrangement of their content across chromosomes, and other major traits. We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions. Fungal genomes exhibit large variations in size, gene content, and structural features, such as abundance of transposable elements (TEs), compartmentalization into gene-rich and TE-rich regions, and the presence or absence of dispensable chromosomes. Genomic structural variations are equally diverse in fungi, ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds, to targeted deletion of effector encoding genes that may promote virulence. Finally, the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides. Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.
Collapse
Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis (UCD), Davis, CA, USA; Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA 95616, USA
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis (UCD), Davis, CA, USA.
| |
Collapse
|
6
|
McTaggart LR, Braukmann TWA, Kus JV. Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens Blastomyces dermatitidis and Blastomyces gilchristii. G3 (BETHESDA, MD.) 2024; 14:jkae194. [PMID: 39163563 PMCID: PMC11540331 DOI: 10.1093/g3journal/jkae194] [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: 05/07/2024] [Revised: 07/12/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024]
Abstract
Blastomyces dermatitidis and Blastomyces gilchristii are cryptic species of fungi that cause blastomycosis, an often severe disease involving pulmonary infection capable of systemic dissemination. While these species appear morphologically identical, differences exist in the genetic makeup, geographical range, and possibly the clinical presentation of infection. Here, we show genetic divergence between the cryptic species through both a Blastomyces species tree constructed from orthologous protein sequences and whole genome single-nucleotide variant phylogenomic analysis. Following linked-read sequencing and de novo genome assembly, we characterized and compared the genomes of 3 B. dermatitidis and 3 B. gilchristii isolates. The B. gilchristii genomes (73.25-75.4 Mb) were ∼8 Mb larger than the B. dermatitidis genomes (64.88-66.61 Mb). Average nucleotide identity was lower between genomes of different species than genomes of the same species, yet functional classification of genes suggested similar proteomes. The most striking difference involved long terminal repeat retrotransposons. Although the same retrotransposon elements were detected in the genomes, the quantity of elements differed between the 2 species. Gypsy retrotransposon content was significantly higher in B. gilchristii (38.04-39.26 Mb) than in B. dermatitidis (30.85-32.40 Mb), accounting for the majority of genome size difference between species. Age estimation and phylogenetic analysis of the reverse transcriptase domains suggested that these retrotransposons are relatively ancient, with genome insertion predating the speciation of B. dermatitidis and B. gilchristii. We postulate that different trajectories of genome contraction led to genetic incompatibility, reproductive isolation, and speciation, highlighting the role of transposable elements in fungal evolution.
Collapse
Affiliation(s)
- Lisa R McTaggart
- Microbiology and Laboratory Services, Public Health Ontario, 661 University Avenue, Toronto, ON M5G 1M1, Canada
| | - Thomas W A Braukmann
- Microbiology and Laboratory Services, Public Health Ontario, 661 University Avenue, Toronto, ON M5G 1M1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Julianne V Kus
- Microbiology and Laboratory Services, Public Health Ontario, 661 University Avenue, Toronto, ON M5G 1M1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
7
|
Tralamazza SM, Gluck-Thaler E, Feurtey A, Croll D. Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen. Nat Commun 2024; 15:5728. [PMID: 38977688 PMCID: PMC11231334 DOI: 10.1038/s41467-024-49913-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 06/25/2024] [Indexed: 07/10/2024] Open
Abstract
Copy number variation (CNV) can drive rapid evolution in changing environments. In microbial pathogens, such adaptation is a key factor underpinning epidemics and colonization of new niches. However, the genomic determinants of such adaptation remain poorly understood. Here, we systematically investigate CNVs in a large genome sequencing dataset spanning a worldwide collection of 1104 genomes from the major wheat pathogen Zymoseptoria tritici. We found overall strong purifying selection acting on most CNVs. Genomic defense mechanisms likely accelerated gene loss over episodes of continental colonization. Local adaptation along climatic gradients was likely facilitated by CNVs affecting secondary metabolite production and gene loss in general. One of the strongest loci for climatic adaptation is a highly conserved gene of the NAD-dependent Sirtuin family. The Sirtuin CNV locus localizes to an ~68-kb Starship mobile element unique to the species carrying genes highly expressed during plant infection. The element has likely lost the ability to transpose, demonstrating how the ongoing domestication of cargo-carrying selfish elements can contribute to selectable variation within populations. Our work highlights how standing variation in gene copy numbers at the global scale can be a major factor driving climatic and metabolic adaptation in microbial species.
Collapse
Affiliation(s)
- Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Emile Gluck-Thaler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
| |
Collapse
|
8
|
Zheng R, Dunlap M, Bobkov GOM, Gonzalez-Figueroa C, Patel KJ, Lyu J, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Le Roux CA, Bartels MD, Vuong A, Flynn RA, Chang HY, Van Nostrand EL, Xiao X, Cheng C. hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing. Mol Cell 2024; 84:2087-2103.e8. [PMID: 38815579 PMCID: PMC11204102 DOI: 10.1016/j.molcel.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 01/09/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
RNA splicing is pivotal in post-transcriptional gene regulation, yet the exponential expansion of intron length in humans poses a challenge for accurate splicing. Here, we identify hnRNPM as an essential RNA-binding protein that suppresses cryptic splicing through binding to deep introns, maintaining human transcriptome integrity. Long interspersed nuclear elements (LINEs) in introns harbor numerous pseudo splice sites. hnRNPM preferentially binds at intronic LINEs to repress pseudo splice site usage for cryptic splicing. Remarkably, cryptic exons can generate long dsRNAs through base-pairing of inverted ALU transposable elements interspersed among LINEs and consequently trigger an interferon response, a well-known antiviral defense mechanism. Significantly, hnRNPM-deficient tumors show upregulated interferon-associated pathways and elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity by repressing cryptic splicing and suggest that targeting hnRNPM in tumors may be used to trigger an inflammatory immune response, thereby boosting cancer surveillance.
Collapse
Affiliation(s)
- Rong Zheng
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mikayla Dunlap
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Georg O M Bobkov
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carlos Gonzalez-Figueroa
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Khushali J Patel
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jingyi Lyu
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Samuel E Harvey
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tracey W Chan
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Charlotte A Le Roux
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mason D Bartels
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amy Vuong
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulome, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulome, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Eric L Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Chonghui Cheng
- Lester & Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
9
|
Abraham LN, Oggenfuss U, Croll D. Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen. mBio 2024; 15:e0284023. [PMID: 38349152 PMCID: PMC10936205 DOI: 10.1128/mbio.02840-23] [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: 10/20/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024] Open
Abstract
The rapid adaptive evolution of microbes is driven by strong selection pressure acting on genetic variation. How adaptive genetic variation is generated within species and how such variation influences phenotypic trait expression is often not well understood though. We focused on the recent activity of transposable elements (TEs) using deep population genomics and transcriptomics analyses of a fungal plant pathogen with a highly active content of TEs in the genome. Zymoseptoria tritici causes one of the most damaging diseases on wheat, with recent adaptation to the host and environment being facilitated by TE-associated mutations. We obtained genomic and RNA-sequencing data from 146 isolates collected from a single wheat field. We established a genome-wide map of TE insertion polymorphisms in the population by analyzing recent TE insertions among individuals. We quantified the locus-specific transcription of individual TE copies and found considerable population variation at individual TE loci in the population. About 20% of all TE copies show transcription in the genome suggesting that genomic defenses such as repressive epigenetic marks and repeat-induced polymorphisms are at least partially ineffective at preventing the proliferation of TEs in the genome. A quarter of recent TE insertions are associated with expression variation of neighboring genes providing broad potential to influence trait expression. We indeed found that TE insertions are likely responsible for variation in virulence on the host and potentially diverse components of secondary metabolite production. Our large-scale transcriptomics study emphasizes how TE-derived polymorphisms segregate even in individual microbial populations and can broadly underpin trait variation in pathogens.IMPORTANCEPathogens can rapidly adapt to new hosts, antimicrobials, or changes in the environment. Adaptation arises often from mutations in the genome; however, how such variation is generated remains poorly understood. We investigated the most dynamic regions of the genome of Zymoseptoria tritici, a major fungal pathogen of wheat. We focused on the transcription of transposable elements. A large proportion of the transposable elements not only show signatures of potential activity but are also variable within a single population of the pathogen. We find that this variation in activity is likely influencing many important traits of the pathogen. Hence, our work provides insights into how a microbial species can adapt over the shortest time periods based on the activity of transposable elements.
Collapse
Affiliation(s)
- Leen Nanchira Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
10
|
Badet T, Tralamazza SM, Feurtey A, Croll D. Recent reactivation of a pathogenicity-associated transposable element is associated with major chromosomal rearrangements in a fungal wheat pathogen. Nucleic Acids Res 2024; 52:1226-1242. [PMID: 38142443 PMCID: PMC10853768 DOI: 10.1093/nar/gkad1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/26/2023] Open
Abstract
Transposable elements (TEs) are key drivers of genomic variation contributing to recent adaptation in most species. Yet, the evolutionary origins and insertion dynamics within species remain poorly understood. We recapitulate the spread of the pathogenicity-associated Styx element across five species that last diverged ∼11 000 years ago. We show that the element likely originated in the Zymoseptoria fungal pathogen genus and underwent multiple independent reactivation events. Using a global 900-genome panel of the wheat pathogen Zymoseptoria tritici, we assess Styx copy number variation and identify renewed transposition activity in Oceania and South America. We show that the element can mobilize to create additional Styx copies in a four-generation pedigree. Importantly, we find that new copies of the element are not affected by genomic defenses suggesting minimal control against the element. Styx copies are preferentially located in recombination breakpoints and likely triggered multiple types of large chromosomal rearrangements. Taken together, we establish the origin, diversification and reactivation of a highly active TE with likely major consequences for chromosomal integrity and the expression of disease.
Collapse
Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| |
Collapse
|
11
|
Westerberg I, Ament-Velásquez SL, Vogan AA, Johannesson H. Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations. Mob DNA 2024; 15:1. [PMID: 38218923 PMCID: PMC10787394 DOI: 10.1186/s13100-023-00311-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/22/2023] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance of retrotransposons compared to other interspersed repeats. The LTR-retrotransposon family crapaud is particularly abundant in the genome, and consists of multiple diverged sequence variations specifically localized in the 5' half of both long terminal repeats (LTRs). P. anserina is part of a recently diverged species-complex, which makes the system ideal to classify the crapaud family based on the observed LTR variation and to study the evolutionary dynamics, such as the diversification and bursts of the elements over recent evolutionary time. RESULTS We developed a sequence similarity network approach to classify the crapaud repeats of seven genomes representing the P. anserina species complex into 14 subfamilies. This method does not utilize a consensus sequence, but instead it connects any copies that share enough sequence similarity over a set sequence coverage. Based on phylogenetic analyses, we found that the crapaud repeats likely diversified in the ancestor of the complex and have had activity at different time points for different subfamilies. Furthermore, while we hypothesized that the evolution into multiple subfamilies could have been a direct effect of escaping the genome defense system of repeat induced point mutations, we found this not to be the case. CONCLUSIONS Our study contributes to the development of methods to classify transposable elements in fungi, and also highlights the intricate patterns of retrotransposon evolution over short timescales and under high mutational load caused by nucleotide-altering genome defense.
Collapse
Affiliation(s)
- Ivar Westerberg
- Department of Ecology, environmental and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - S Lorena Ament-Velásquez
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden.
| | - Hanna Johannesson
- Department of Ecology, environmental and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- The Royal Swedish Academy of Sciences, Stockholm, 114 18, Sweden.
| |
Collapse
|
12
|
Chavarro-Carrero EA, Snelders NC, Torres DE, Kraege A, López-Moral A, Petti GC, Punt W, Wieneke J, García-Velasco R, López-Herrera CJ, Seidl MF, Thomma BPHJ. The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization. PLoS Pathog 2024; 20:e1011866. [PMID: 38236788 PMCID: PMC10796067 DOI: 10.1371/journal.ppat.1011866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.
Collapse
Affiliation(s)
- Edgar A. Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Nick C. Snelders
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - David E. Torres
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Anton Kraege
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Ana López-Moral
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Gabriella C. Petti
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Wilko Punt
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Jan Wieneke
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Rómulo García-Velasco
- Laboratory of Phytopathology, Tenancingo University Center, Autonomous University of the State of Mexico, Tenancingo, State of Mexico, Mexico
| | - Carlos J. López-Herrera
- CSIC, Instituto de Agricultura Sostenible, Dept. Protección de Cultivos, C/Alameda del Obispo s/n, Córdoba, Spain
| | - Michael F. Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| |
Collapse
|
13
|
Hensen N, Bonometti L, Westerberg I, Brännström IO, Guillou S, Cros-Aarteil S, Calhoun S, Haridas S, Kuo A, Mondo S, Pangilinan J, Riley R, LaButti K, Andreopoulos B, Lipzen A, Chen C, Yan M, Daum C, Ng V, Clum A, Steindorff A, Ohm RA, Martin F, Silar P, Natvig DO, Lalanne C, Gautier V, Ament-Velásquez SL, Kruys Å, Hutchinson MI, Powell AJ, Barry K, Miller AN, Grigoriev IV, Debuchy R, Gladieux P, Hiltunen Thorén M, Johannesson H. Genome-scale phylogeny and comparative genomics of the fungal order Sordariales. Mol Phylogenet Evol 2023; 189:107938. [PMID: 37820761 DOI: 10.1016/j.ympev.2023.107938] [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] [Received: 06/26/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.
Collapse
Affiliation(s)
- Noah Hensen
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden
| | - Lucas Bonometti
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | - Ivar Westerberg
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden
| | - Ioana Onut Brännström
- Oslo University, Natural History Museum, Oslo, Norway; Uppsala University, Department of Ecology and Genetics, Uppsala, Sweden
| | - Sonia Guillou
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | | | - Sara Calhoun
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Sajeet Haridas
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Stephen Mondo
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Robert Riley
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Bill Andreopoulos
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Cindy Chen
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Mi Yan
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Chris Daum
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alicia Clum
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Andrei Steindorff
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Robin A Ohm
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Philippe Silar
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | - Donald O Natvig
- University of New Mexico, Department of Biology, Albuquerque, USA
| | - Christophe Lalanne
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | - Valérie Gautier
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | | | - Åsa Kruys
- Uppsala University, Museum of Evolution, Uppsala, Sweden
| | | | - Amy Jo Powell
- Sandia National Laboratories, Dept. of Systems Design and Architecture, Albuquerque, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Andrew N Miller
- University of Illinois Urbana-Champaign, Illinois Natural History Survey, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA; University of California Berkeley, Department of Plant and Microbial Biology, Berkeley, CA, USA
| | - Robert Debuchy
- Université Paris-Saclay, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Pierre Gladieux
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | - Markus Hiltunen Thorén
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Hanna Johannesson
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Glad HM, Tralamazza SM, Croll D. The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici. Microb Genom 2023; 9. [PMID: 37991492 DOI: 10.1099/mgen.0.001136] [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] [Indexed: 11/23/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyse genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host defence signals, such as oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling future molecular genetics and functional analyses in an important pathogen.
Collapse
Affiliation(s)
- Hanna M Glad
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| |
Collapse
|
17
|
Fuselli S, Greco S, Biello R, Palmitessa S, Lago M, Meneghetti C, McDougall C, Trucchi E, Rota Stabelli O, Biscotti AM, Schmidt DJ, Roberts DT, Espinoza T, Hughes JM, Ometto L, Gerdol M, Bertorelle G. Relaxation of Natural Selection in the Evolution of the Giant Lungfish Genomes. Mol Biol Evol 2023; 40:msad193. [PMID: 37671664 PMCID: PMC10503785 DOI: 10.1093/molbev/msad193] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/16/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
Nonadaptive hypotheses on the evolution of eukaryotic genome size predict an expansion when the process of purifying selection becomes weak. Accordingly, species with huge genomes, such as lungfish, are expected to show a genome-wide relaxation signature of selection compared with other organisms. However, few studies have empirically tested this prediction using genomic data in a comparative framework. Here, we show that 1) the newly assembled transcriptome of the Australian lungfish, Neoceratodus forsteri, is characterized by an excess of pervasive transcription, or transcriptional leakage, possibly due to suboptimal transcriptional control, and 2) a significant relaxation signature in coding genes in lungfish species compared with other vertebrates. Based on these observations, we propose that the largest known animal genomes evolved in a nearly neutral scenario where genome expansion is less efficiently constrained.
Collapse
Affiliation(s)
- Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Roberto Biello
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Marta Lago
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Corrado Meneghetti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Carmel McDougall
- Australian Rivers Institute, Griffith University, Brisbane, Queensland, Australia
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Omar Rota Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, 38010 San Michele all'Adige, Italy
| | - Assunta Maria Biscotti
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Daniel J Schmidt
- Australian Rivers Institute, Griffith University, Brisbane, Queensland, Australia
| | | | | | - Jane Margaret Hughes
- Australian Rivers Institute, Griffith University, Brisbane, Queensland, Australia
| | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| |
Collapse
|
18
|
Chen J, Basting PJ, Han S, Garfinkel DJ, Bergman CM. Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast. Mob DNA 2023; 14:8. [PMID: 37452430 PMCID: PMC10347736 DOI: 10.1186/s13100-023-00296-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute, or evaluate multiple TE insertion detectors. RESULTS We previously developed the McClintock meta-pipeline to facilitate the installation, execution, and evaluation of six first-generation short-read TE detectors. Here, we report a completely re-implemented version of McClintock written in Python using Snakemake and Conda that improves its installation, error handling, speed, stability, and extensibility. McClintock 2 now includes 12 short-read TE detectors, auxiliary pre-processing and analysis modules, interactive HTML reports, and a simulation framework to reproducibly evaluate the accuracy of component TE detectors. When applied to the model microbial eukaryote Saccharomyces cerevisiae, we find substantial variation in the ability of McClintock 2 components to identify the precise locations of non-reference TE insertions, with RelocaTE2 showing the highest recall and precision in simulated data. We find that RelocaTE2, TEMP, TEMP2 and TEBreak provide consistent estimates of [Formula: see text]50 non-reference TE insertions per strain and that Ty2 has the highest number of non-reference TE insertions in a species-wide panel of [Formula: see text]1000 yeast genomes. Finally, we show that best-in-class predictors for yeast applied to resequencing data have sufficient resolution to reveal a dyad pattern of integration in nucleosome-bound regions upstream of yeast tRNA genes for Ty1, Ty2, and Ty4, allowing us to extend knowledge about fine-scale target preferences revealed previously for experimentally-induced Ty1 insertions to spontaneous insertions for other copia-superfamily retrotransposons in yeast. CONCLUSION McClintock ( https://github.com/bergmanlab/mcclintock/ ) provides a user-friendly pipeline for the identification of TEs in short-read WGS data using multiple TE detectors, which should benefit researchers studying TE insertion variation in a wide range of different organisms. Application of the improved McClintock system to simulated and empirical yeast genome data reveals best-in-class methods and novel biological insights for one of the most widely-studied model eukaryotes and provides a paradigm for evaluating and selecting non-reference TE detectors in other species.
Collapse
Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
| | | | - Shunhua Han
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Casey M. Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA USA
- Department of Genetics, University of Georgia, Athens, GA USA
| |
Collapse
|
19
|
Gupta YK, Marcelino-Guimarães FC, Lorrain C, Farmer A, Haridas S, Ferreira EGC, Lopes-Caitar VS, Oliveira LS, Morin E, Widdison S, Cameron C, Inoue Y, Thor K, Robinson K, Drula E, Henrissat B, LaButti K, Bini AMR, Paget E, Singan V, Daum C, Dorme C, van Hoek M, Janssen A, Chandat L, Tarriotte Y, Richardson J, Melo BDVA, Wittenberg AHJ, Schneiders H, Peyrard S, Zanardo LG, Holtman VC, Coulombier-Chauvel F, Link TI, Balmer D, Müller AN, Kind S, Bohnert S, Wirtz L, Chen C, Yan M, Ng V, Gautier P, Meyer MC, Voegele RT, Liu Q, Grigoriev IV, Conrath U, Brommonschenkel SH, Loehrer M, Schaffrath U, Sirven C, Scalliet G, Duplessis S, van Esse HP. Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nat Commun 2023; 14:1835. [PMID: 37005409 PMCID: PMC10067951 DOI: 10.1038/s41467-023-37551-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/22/2023] [Indexed: 04/04/2023] Open
Abstract
With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world's most economically damaging agricultural diseases. Despite P. pachyrhizi's impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.
Collapse
Affiliation(s)
- Yogesh K Gupta
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Cécile Lorrain
- Pathogen Evolutionary Ecology, ETH Zürich, Zürich, Switzerland
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Everton Geraldo Capote Ferreira
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Valéria S Lopes-Caitar
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Liliane Santana Oliveira
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | | | | | - Connor Cameron
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Yoshihiro Inoue
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kathrin Thor
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kelly Robinson
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Elodie Drula
- AFMB, Aix-Marseille Univ., INRAE, Marseille, France
- Biodiversité et Biotechnologie Fongiques, INRAE, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aline Mara Rudsit Bini
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | - Eric Paget
- Bayer SAS, Crop Science Division, Lyon, France
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tobias I Link
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | - André N Müller
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Sabine Kind
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Stefan Bohnert
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Louisa Wirtz
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Maurício Conrado Meyer
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | | | - Qingli Liu
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Uwe Conrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | - Marco Loehrer
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | | | | | - H Peter van Esse
- 2Blades, Evanston, Illinois, USA.
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
| |
Collapse
|
20
|
Chen J, Basting PJ, Han S, Garfinkel DJ, Bergman CM. Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528343. [PMID: 36824955 PMCID: PMC9948991 DOI: 10.1101/2023.02.13.528343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
BACKGROUND Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often present challenges to new users seeking to reproducibly install, execute, or evaluate multiple TE insertion detectors. RESULTS We previously developed the McClintock meta-pipeline to facilitate the installation, execution, and evaluation of six first-generation short-read TE detectors. Here, we report a completely re-implemented version of McClintock written in Python using Snakemake and Conda that improves its installation, error handling, speed, stability, and extensibility. McClintock 2 now includes 12 short-read TE detectors, auxiliary pre-processing and analysis modules, interactive HTML reports, and a simulation framework to reproducibly evaluate the accuracy of component TE detectors. When applied to the model microbial eukaryote Saccharomyces cerevisiae, we find substantial variation in the ability of McClintock 2 components to identify the precise locations of non-reference TE insertions, with RelocaTE2 showing the highest recall and precision in simulated data. We find that RelocaTE2, TEMP, TEMP2 and TEBreak provide a consistent and biologically meaningful view of non-reference TE insertions in a species-wide panel of ∼1000 yeast genomes, as evaluated by coverage-based abundance estimates and expected patterns of tRNA promoter targeting. Finally, we show that best-in-class predictors for yeast have sufficient resolution to reveal a dyad pattern of integration in nucleosome-bound regions upstream of yeast tRNA genes for Ty1, Ty2, and Ty4, allowing us to extend knowledge about fine-scale target preferences first revealed experimentally for Ty1 to natural insertions and related copia-superfamily retrotransposons in yeast. CONCLUSION McClintock (https://github.com/bergmanlab/mcclintock/) provides a user-friendly pipeline for the identification of TEs in short-read WGS data using multiple TE detectors, which should benefit researchers studying TE insertion variation in a wide range of different organisms. Application of the improved McClintock system to simulated and empirical yeast genome data reveals best-in-class methods and novel biological insights for one of the most widely-studied model eukaryotes and provides a paradigm for evaluating and selecting non-reference TE detectors for other species.
Collapse
Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA
| | | | - Shunhua Han
- Institute of Bioinformatics, University of Georgia, Athens, GA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | - Casey M. Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA
- Department of Genetics, University of Georgia, Athens, GA
| |
Collapse
|
21
|
Zheng R, Dunlap M, Lyu J, Gonzalez-Figueroa C, Bobkov G, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Vuong A, Flynn RA, Chang HY, Xiao X, Cheng C. LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529804. [PMID: 36865202 PMCID: PMC9980139 DOI: 10.1101/2023.02.23.529804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
RNA splicing plays a critical role in post-transcriptional gene regulation. Exponential expansion of intron length poses a challenge for accurate splicing. Little is known about how cells prevent inadvertent and often deleterious expression of intronic elements due to cryptic splicing. In this study, we identify hnRNPM as an essential RNA binding protein that suppresses cryptic splicing through binding to deep introns, preserving transcriptome integrity. Long interspersed nuclear elements (LINEs) harbor large amounts of pseudo splice sites in introns. hnRNPM preferentially binds at intronic LINEs and represses LINE-containing pseudo splice site usage for cryptic splicing. Remarkably, a subgroup of the cryptic exons can form long dsRNAs through base-pairing of inverted Alu transposable elements scattered in between LINEs and trigger interferon immune response, a well-known antiviral defense mechanism. Notably, these interferon-associated pathways are found to be upregulated in hnRNPM-deficient tumors, which also exhibit elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity. Targeting hnRNPM in tumors may be used to trigger an inflammatory immune response thereby boosting cancer surveillance.
Collapse
|
22
|
Feurtey A, Lorrain C, McDonald MC, Milgate A, Solomon PS, Warren R, Puccetti G, Scalliet G, Torriani SFF, Gout L, Marcel TC, Suffert F, Alassimone J, Lipzen A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Goodwin SB, Genissel A, Seidl MF, Stukenbrock EH, Lebrun MH, Kema GHJ, McDonald BA, Croll D. A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen. Nat Commun 2023; 14:1059. [PMID: 36828814 PMCID: PMC9958100 DOI: 10.1038/s41467-023-36674-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.
Collapse
Affiliation(s)
- Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Cécile Lorrain
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Megan C McDonald
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Andrew Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia
| | - Peter S Solomon
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Rachael Warren
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Guido Puccetti
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Syngenta Crop Protection AG, CH-4332, Stein, Switzerland
| | | | | | - Lilian Gout
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Thierry C Marcel
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Frédéric Suffert
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 9472, USA
| | | | - Anne Genissel
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Michael F Seidl
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
- Utrecht University, Theoretical Biology and Bioinformatics, Utrecht, The Netherlands
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | | | - Gert H J Kema
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Bruce A McDonald
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
| |
Collapse
|
23
|
Oggenfuss U, Croll D. Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011130. [PMID: 36787337 PMCID: PMC9970103 DOI: 10.1371/journal.ppat.1011130] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/27/2023] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a pathogen species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogen Zymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences, or as a consequence of insertion site preferences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that a Copia element burst was initiated from recent copies inserted substantially closer to genes compared to older copies. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation in pathogen genomes.
Collapse
Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
| |
Collapse
|
24
|
Wacker T, Helmstetter N, Wilson D, Fisher MC, Studholme DJ, Farrer RA. Two-speed genome evolution drives pathogenicity in fungal pathogens of animals. Proc Natl Acad Sci U S A 2023; 120:e2212633120. [PMID: 36595674 PMCID: PMC9926174 DOI: 10.1073/pnas.2212633120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/14/2022] [Indexed: 01/05/2023] Open
Abstract
The origins and evolution of virulence in amphibian-infecting chytrids Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are largely unknown. Here, we use deep nanopore sequencing of Bsal and comparative genomics against 21 high-quality genome assemblies that span the fungal Chytridiomycota. We discover that Bsal has the most repeat-rich genome of the Chytridiomycota, comprising 40.9% repetitive elements; this genome has expanded to more than 3× the length of its conspecific Bd, with autonomous and fully functional LTR/Gypsy elements contributing significantly to the expansion. The M36 metalloprotease virulence factors are highly expanded (n = 177) in Bsal, most of which (53%) are flanked by transposable elements, suggesting they have a repeat-associated expansion. We find enrichment upstream of M36 metalloprotease genes of three novel repeat families belonging to the repeat superfamily of LINEs that are implicated with gene copy number variations. Additionally, Bsal has a highly compartmentalized genome architecture, with virulence factors enriched in gene-sparse/repeat-rich compartments, while core conserved genes are enriched in gene-rich/repeat-poor compartments. Genes upregulated during infection are primarily found in the gene-sparse/repeat-rich compartment in both Bd and Bsal. Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting these regions are a cradle for the evolution of chytrid pathogenicity. These are the hallmarks of two-speed genome evolution, and this study provides evidence of two-speed genomes in an animal pathogen, shedding light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.
Collapse
Affiliation(s)
- Theresa Wacker
- Medical Research Council Centre for Medical Mycology at the University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Nicolas Helmstetter
- Medical Research Council Centre for Medical Mycology at the University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Duncan Wilson
- Medical Research Council Centre for Medical Mycology at the University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Matthew C. Fisher
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Imperial College London, LondonW12 0BZ, United Kingdom
| | - David J. Studholme
- Department of Biosciences, University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Rhys A. Farrer
- Medical Research Council Centre for Medical Mycology at the University of Exeter, ExeterEX4 4QD, United Kingdom
| |
Collapse
|
25
|
Blyth HR, Smith D, King R, Bayon C, Ashfield T, Walpole H, Venter E, Ray RV, Kanyuka K, Rudd JJ. Fungal plant pathogen "mutagenomics" reveals tagged and untagged mutations in Zymoseptoria tritici and identifies SSK2 as key morphogenesis and stress-responsive virulence factor. FRONTIERS IN PLANT SCIENCE 2023; 14:1140824. [PMID: 37206970 PMCID: PMC10190600 DOI: 10.3389/fpls.2023.1140824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/29/2023] [Indexed: 05/21/2023]
Abstract
"Mutagenomics" is the combination of random mutagenesis, phenotypic screening, and whole-genome re-sequencing to uncover all tagged and untagged mutations linked with phenotypic changes in an organism. In this study, we performed a mutagenomics screen on the wheat pathogenic fungus Zymoseptoria tritici for altered morphogenetic switching and stress sensitivity phenotypes using Agrobacterium-mediated "random" T-DNA mutagenesis (ATMT). Biological screening identified four mutants which were strongly reduced in virulence on wheat. Whole genome re-sequencing defined the positions of the T-DNA insertion events and revealed several unlinked mutations potentially affecting gene functions. Remarkably, two independent reduced virulence mutant strains, with similarly altered stress sensitivities and aberrant hyphal growth phenotypes, were found to have a distinct loss of function mutations in the ZtSSK2 MAPKKK gene. One mutant strain had a direct T-DNA insertion affecting the predicted protein's N-terminus, while the other possessed an unlinked frameshift mutation towards the C-terminus. We used genetic complementation to restore both strains' wild-type (WT) function (virulence, morphogenesis, and stress response). We demonstrated that ZtSSK2 has a non-redundant function with ZtSTE11 in virulence through the biochemical activation of the stress-activated HOG1 MAPK pathway. Moreover, we present data suggesting that SSK2 has a unique role in activating this pathway in response to specific stresses. Finally, dual RNAseq-based transcriptome profiling of WT and SSK2 mutant strains revealed many HOG1-dependent transcriptional changes in the fungus during early infection and suggested that the host response does not discriminate between WT and mutant strains during this early phase. Together these data define new genes implicated in the virulence of the pathogen and emphasise the importance of a whole genome sequencing step in mutagenomic discovery pipelines.
Collapse
Affiliation(s)
- Hannah R. Blyth
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, United Kingdom
| | - Dan Smith
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, United Kingdom
| | - Robert King
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, United Kingdom
| | - Carlos Bayon
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, United Kingdom
| | - Tom Ashfield
- Crop Health and Protection (CHAP), Rothamsted Research, Harpenden, United Kingdom
| | - Hannah Walpole
- Bioimaging Unit, Rothamsted Research, Harpenden, United Kingdom
| | - Eudri Venter
- Bioimaging Unit, Rothamsted Research, Harpenden, United Kingdom
| | - Rumiana V. Ray
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Kostya Kanyuka
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, United Kingdom
| | - Jason J. Rudd
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, United Kingdom
- *Correspondence: Jason J. Rudd,
| |
Collapse
|
26
|
Hiltunen M, Ament-Velásquez SL, Ryberg M, Johannesson H. Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades. Proc Natl Acad Sci U S A 2022; 119:e2208575119. [PMID: 36343254 PMCID: PMC9674265 DOI: 10.1073/pnas.2208575119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/02/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic variability can be generated by different mechanisms, and across the life cycle. Many basidiomycete fungi have an extended somatic stage, during which each cell carries two genetically distinct haploid nuclei (dikaryosis), resulting from fusion of two compatible monokaryotic individuals. Recent findings have revealed remarkable genome stability at the nucleotide level during dikaryotic growth in these organisms, but whether this pattern extends to mutations affecting large genomic regions remains unknown. Furthermore, despite high genome integrity during dikaryosis, basidiomycete populations are not devoid of genetic diversity, begging the question of when this diversity is introduced. Here, we used a Marasmius oreades fairy ring to investigate the rise of large-scale variants during mono- and dikaryosis. By separating the two nuclear genotypes from four fruiting bodies and generating complete genome assemblies, we gained access to investigate genomic changes of any size. We found that during dikaryotic growth in nature the genome stayed intact, but after separating the nucleotypes into monokaryons, a considerable amount of structural variation started to accumulate, driven to large extent by transposons. Transposon insertions were also found in monokaryotic single-meiospore isolates. Hence, we show that genome integrity in basidiomycetes can be interrupted during monokaryosis, leading to genomic rearrangements and increased activity of transposable elements. We suggest that genetic diversification is disproportionate between life cycle stages in mushroom-forming fungi, so that the short-lived monokaryotic growth stage is more prone to genetic changes than the dikaryotic stage.
Collapse
Affiliation(s)
- Markus Hiltunen
- Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | | | - Martin Ryberg
- Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| |
Collapse
|
27
|
Depotter JRL, Ökmen B, Ebert MK, Beckers J, Kruse J, Thines M, Doehlemann G. High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens. Microbiol Spectr 2022; 10:e0034922. [PMID: 35972267 PMCID: PMC9603552 DOI: 10.1128/spectrum.00349-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated with the mating-type locus sizes, which is up to ~560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results in substitutions that often lead to amino acid alterations. IMPORTANCE Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. They also impact genome evolution as their repetitive nature facilitates nonhomologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, Ustilago hordei. This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. We hypothesize that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.
Collapse
Affiliation(s)
- J. R. L. Depotter
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - B. Ökmen
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - M. K. Ebert
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Beckers
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Kruse
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - G. Doehlemann
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| |
Collapse
|
28
|
Cong Y, Ye X, Mei Y, He K, Li F. Transposons and non-coding regions drive the intrafamily differences of genome size in insects. iScience 2022; 25:104873. [PMID: 36039293 PMCID: PMC9418806 DOI: 10.1016/j.isci.2022.104873] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 07/29/2022] [Indexed: 11/02/2022] Open
Abstract
Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand the specific evolutionary factors that determine GS in insects, we examined flow cytometry-based published GS data from 1,326 insect species, spanning 700 genera, 155 families, and 21 orders. Model fitting showed that GS generally followed an Ornstein-Uhlenbeck adaptive evolutionary model in Insecta overall. Ancestral reconstruction indicated a likely GS of 1,069 Mb, suggesting that most insect clades appeared to undergo massive genome expansions or contractions. Quantification of genomic components in 56 species from nine families in four insect orders revealed that the proliferation of transposable elements contributed to high variation in GS between close species, such as within Coleoptera. This study sheds lights on the pattern of GS variation in insects and provides a better understanding of insect GS evolution.
Collapse
Affiliation(s)
- Yuyang Cong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
29
|
McDonald BA, Suffert F, Bernasconi A, Mikaberidze A. How large and diverse are field populations of fungal plant pathogens? The case of Zymoseptoria tritici. Evol Appl 2022; 15:1360-1373. [PMID: 36187182 PMCID: PMC9488677 DOI: 10.1111/eva.13434] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 12/02/2022] Open
Abstract
Pathogen populations differ in the amount of genetic diversity they contain. Populations carrying higher genetic diversity are thought to have a greater evolutionary potential than populations carrying less diversity. We used published studies to estimate the range of values associated with two critical components of genetic diversity, the number of unique pathogen genotypes and the number of spores produced during an epidemic, for the septoria tritici blotch pathogen Zymoseptoria tritici. We found that wheat fields experiencing typical levels of infection are likely to carry between 3.1 and 14.0 million pathogen genotypes per hectare and produce at least 2.1-9.9 trillion pycnidiospores per hectare. Given the experimentally derived mutation rate of 3 × 10-10 substitutions per site per cell division, we estimate that between 27 and 126 million pathogen spores carrying adaptive mutations to counteract fungicides and resistant cultivars will be produced per hectare during a growing season. This suggests that most of the adaptive mutations that have been observed in Z. tritici populations can emerge through local selection from standing genetic variation that already exists within each field. The consequences of these findings for disease management strategies are discussed.
Collapse
Affiliation(s)
- Bruce A. McDonald
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZurichSwitzerland
| | | | - Alessio Bernasconi
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Alexey Mikaberidze
- School of Agriculture, Policy and DevelopmentUniversity of ReadingReadingUK
| |
Collapse
|
30
|
Huang Y, Shukla H, Lee YCG. Species-specific chromatin landscape determines how transposable elements shape genome evolution. eLife 2022; 11:81567. [PMID: 35997258 PMCID: PMC9398452 DOI: 10.7554/elife.81567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic parasites that increase their copy number at the expense of host fitness. The ‘success’, or genome-wide abundance, of TEs differs widely between species. Deciphering the causes for this large variety in TE abundance has remained a central question in evolutionary genomics. We previously proposed that species-specific TE abundance could be driven by the inadvertent consequences of host-direct epigenetic silencing of TEs—the spreading of repressive epigenetic marks from silenced TEs into adjacent sequences. Here, we compared this TE-mediated local enrichment of repressive marks, or ‘the epigenetic effect of TEs’, in six species in the Drosophila melanogaster subgroup to dissect step-by-step the role of such effect in determining genomic TE abundance. We found that TE-mediated local enrichment of repressive marks is prevalent and substantially varies across and even within species. While this TE-mediated effect alters the epigenetic states of adjacent genes, we surprisingly discovered that the transcription of neighboring genes could reciprocally impact this spreading. Importantly, our multi-species analysis provides the power and appropriate phylogenetic resolution to connect species-specific host chromatin regulation, TE-mediated epigenetic effects, the strength of natural selection against TEs, and genomic TE abundance unique to individual species. Our findings point toward the importance of host chromatin landscapes in shaping genome evolution through the epigenetic effects of a selfish genetic parasite. All the instructions required for life are encoded in the set of DNA present in a cell. It therefore seems natural to think that every bit of this genetic information should serve the organism. And yet most species carry parasitic ‘transposable’ sequences, or transposons, whose only purpose is to multiply and insert themselves at other positions in the genome. It is possible for cells to suppress these selfish elements. Chemical marks can be deposited onto the DNA to temporarily ‘silence’ transposons and prevent them from being able to move and replicate. However, this sometimes comes at a cost: the repressive chemical modifications can spread to nearby genes that are essential for the organism and perturb their function. Strangely, the prevalence of transposons varies widely across the tree of life. These sequences form the majority of the genome of certain species – in fact, they represent about half of the human genetic information. But their abundance is much lower in other organisms, forming a measly 6% of the genome of puffer fish for instance. Even amongst fruit fly species, the prevalence of transposable elements can range between 2% and 25%. What explains such differences? Huang et al. set out to examine this question through the lens of transposon silencing, systematically comparing how this process impacts nearby regions in six species of fruit flies. This revealed variations in the strength of the side effects associated with transposon silencing, resulting in different levels of perturbation on neighbouring genes. A stronger impact was associated with the species having fewer transposons in its genome, suggesting that an evolutionary pressure is at work to keep the abundance of transposons at a low level in these species. Further analyses showed that the genes which determine how silencing marks are distributed may also be responsible for the variations in the impact of transposon silencing. They could therefore be the ones driving differences in the abundance of transposons between species. Overall, this work sheds light on the complex mechanisms shaping the evolution of genomes, and it may help to better understand how transposons are linked to processes such as aging and cancer.
Collapse
Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Harsh Shukla
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| |
Collapse
|
31
|
Poudel B, Purushotham N, Jones A, Nasim J, Adorada DL, Sparks AH, Schwessinger B, Vaghefi N. The First Annotated Genome Assembly of Macrophomina tecta Associated with Charcoal Rot of Sorghum. Genome Biol Evol 2022; 14:evac081. [PMID: 35647618 PMCID: PMC9185371 DOI: 10.1093/gbe/evac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/14/2022] Open
Abstract
Charcoal rot is an important soilborne disease caused by a range of Macrophomina species, which affects a broad range of commercially important crops worldwide. Even though Macrophomina species are fungal pathogens of substantial economic importance, their mechanism of pathogenicity and host spectrum are poorly understood. There is an urgent need to better understand the biology, epidemiology, and evolution of Macrophomina species, which, in turn, will aid in improving charcoal rot management strategies. Here, we present the first high-quality genome assembly and annotation of Macrophomina tecta strain BRIP 70781 associated with charcoal rot symptoms on sorghum. Hybrid assembly integrating long reads generated by Oxford Nanopore Technology and short Illumina paired-end reads resulted in 43 contigs with a total assembly size of ∼54 Mb, and an N50 of 3.4 Mb. In total, 12,926 protein-coding genes and 7,036 repeats were predicted. Genome comparisons detected accumulation of DNA transposons in Macrophomina species associated with sorghum. The first reference genome of M. tecta generated in this study will contribute to more comparative and population genomics studies of Macrophomina species.
Collapse
Affiliation(s)
- Barsha Poudel
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Neeraj Purushotham
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
- Loam Bio, Orange, NSW, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australia
| | - Jamila Nasim
- Loam Bio, Orange, NSW, Australia
- Research School of Biology, Australian National University, Canberra, Australia
| | - Dante L. Adorada
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Adam H. Sparks
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
- Department of Primary Industries and Regional Development, Perth, WA, Australia
| | | | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
- School of Agriculture and Food, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
32
|
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.
Collapse
Affiliation(s)
- Fanny E Hartmann
- Ecologie Systematique Evolution, Batiment 360, Universite Paris-Saclay, CNRS, AgroParisTech, Orsay, 91400, France
| |
Collapse
|
33
|
Stalder L, Oggenfuss U, Mohd‐Assaad N, Croll D. The population genetics of adaptation through copy‐number variation in a fungal plant pathogen. Mol Ecol 2022; 32:2443-2460. [PMID: 35313056 DOI: 10.1111/mec.16435] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/28/2022]
Abstract
Microbial pathogens can adapt rapidly to changing environments such as the application of pesticides or host resistance. Copy number variations (CNVs) are a major source of adaptive genetic variation for recent adaptation. Here, we analyse how a major fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. We screen the genomes of 125 isolates sampled across a worldwide set of populations and identify a total of 7,879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. Although CNVs are generally under negative selection, we find that genes affected by CNVs are enriched in functions related to host exploitation (i.e., effectors and cell-wall-degrading enzymes). We perform genome-wide association studies (GWAS) and identify a large segmental duplication of CYP51A that has contributed to the emergence of azole resistance and a duplication encompassing an effector gene affecting virulence. We show that the adaptive CNVs were probably created by recently active transposable element families. Moreover, we find that specific transposable element families are important drivers of recent gene CNV. Finally, we use a genome-wide single nucleotide polymorphism data set to replicate the GWAS and contrast it with the CNV-focused analysis. Together, our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.
Collapse
Affiliation(s)
- Luzia Stalder
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
| | - Norfarhan Mohd‐Assaad
- Plant Pathology Institute of Integrative Biology ETH, Zurich 8092 Zurich Switzerland
- Department of Applied Physics Faculty of Science and Technology Universiti Kebangsaan Malaysia 43600 Bangi Selangor Malaysia
| | - Daniel Croll
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
| |
Collapse
|
34
|
Stress Reactivity, Susceptibility to Hypertension, and Differential Expression of Genes in Hypertensive Compared to Normotensive Patients. Int J Mol Sci 2022; 23:ijms23052835. [PMID: 35269977 PMCID: PMC8911431 DOI: 10.3390/ijms23052835] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022] Open
Abstract
Although half of hypertensive patients have hypertensive parents, known hypertension-related human loci identified by genome-wide analysis explain only 3% of hypertension heredity. Therefore, mainstream transcriptome profiling of hypertensive subjects addresses differentially expressed genes (DEGs) specific to gender, age, and comorbidities in accordance with predictive preventive personalized participatory medicine treating patients according to their symptoms, individual lifestyle, and genetic background. Within this mainstream paradigm, here, we determined whether, among the known hypertension-related DEGs that we could find, there is any genome-wide hypertension theranostic molecular marker applicable to everyone, everywhere, anytime. Therefore, we sequenced the hippocampal transcriptome of tame and aggressive rats, corresponding to low and high stress reactivity, an increase of which raises hypertensive risk; we identified stress-reactivity-related rat DEGs and compared them with their known homologous hypertension-related animal DEGs. This yielded significant correlations between stress reactivity-related and hypertension-related fold changes (log2 values) of these DEG homologs. We found principal components, PC1 and PC2, corresponding to a half-difference and half-sum of these log2 values. Using the DEGs of hypertensive versus normotensive patients (as the control), we verified the correlations and principal components. This analysis highlighted downregulation of β-protocadherins and hemoglobin as whole-genome hypertension theranostic molecular markers associated with a wide vascular inner diameter and low blood viscosity, respectively.
Collapse
|
35
|
Dal Grande F, Jamilloux V, Choisne N, Calchera A, Rolshausen G, Petersen M, Schulz M, Nilsson MA, Schmitt I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. BIOLOGY 2021; 11:biology11010024. [PMID: 35053022 PMCID: PMC8773270 DOI: 10.3390/biology11010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
Collapse
Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)69-7542-1856
| | - Véronique Jamilloux
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Nathalie Choisne
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Gregor Rolshausen
- Senckenberg Center for Wildlife Genetics, Clamecystrasse 12, 63571 Gelnhausen, Germany;
| | - Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany;
| | - Meike Schulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Strasse. 9, 60438 Frankfurt am Main, Germany
| |
Collapse
|
36
|
Pereira D, Oggenfuss U, McDonald BA, Croll D. Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen. Microb Genom 2021; 7:000540. [PMID: 34424154 PMCID: PMC8549362 DOI: 10.1099/mgen.0.000540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.
Collapse
Affiliation(s)
- Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Present address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, D-24306 Plön, Germany
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|