1
|
Zaccaron AZ, Stergiopoulos I. Analysis of five near-complete genome assemblies of the tomato pathogen Cladosporium fulvum uncovers additional accessory chromosomes and structural variations induced by transposable elements effecting the loss of avirulence genes. BMC Biol 2024; 22:25. [PMID: 38281938 PMCID: PMC10823647 DOI: 10.1186/s12915-024-01818-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Fungal plant pathogens have dynamic genomes that allow them to rapidly adapt to adverse conditions and overcome host resistance. One way by which this dynamic genome plasticity is expressed is through effector gene loss, which enables plant pathogens to overcome recognition by cognate resistance genes in the host. However, the exact nature of these loses remains elusive in many fungi. This includes the tomato pathogen Cladosporium fulvum, which is the first fungal plant pathogen from which avirulence (Avr) genes were ever cloned and in which loss of Avr genes is often reported as a means of overcoming recognition by cognate tomato Cf resistance genes. A recent near-complete reference genome assembly of C. fulvum isolate Race 5 revealed a compartmentalized genome architecture and the presence of an accessory chromosome, thereby creating a basis for studying genome plasticity in fungal plant pathogens and its impact on avirulence genes. RESULTS Here, we obtained near-complete genome assemblies of four additional C. fulvum isolates. The genome assemblies had similar sizes (66.96 to 67.78 Mb), number of predicted genes (14,895 to 14,981), and estimated completeness (98.8 to 98.9%). Comparative analysis that included the genome of isolate Race 5 revealed high levels of synteny and colinearity, which extended to the density and distribution of repetitive elements and of repeat-induced point (RIP) mutations across homologous chromosomes. Nonetheless, structural variations, likely mediated by transposable elements and effecting the deletion of the avirulence genes Avr4E, Avr5, and Avr9, were also identified. The isolates further shared a core set of 13 chromosomes, but two accessory chromosomes were identified as well. Accessory chromosomes were significantly smaller in size, and one carried pseudogenized copies of two effector genes. Whole-genome alignments further revealed genomic islands of near-zero nucleotide diversity interspersed with islands of high nucleotide diversity that co-localized with repeat-rich regions. These regions were likely generated by RIP, which generally asymmetrically affected the genome of C. fulvum. CONCLUSIONS Our results reveal new evolutionary aspects of the C. fulvum genome and provide new insights on the importance of genomic structural variations in overcoming host resistance in fungal plant pathogens.
Collapse
Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616-8751, USA
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, CA, 95616-8751, USA.
| |
Collapse
|
2
|
Bellah H, Gazeau G, Gélisse S, Amezrou R, Marcel TC, Croll D. A highly multiplexed assay to monitor pathogenicity, fungicide resistance and gene flow in the fungal wheat pathogen Zymoseptoria tritici. PLoS One 2023; 18:e0281181. [PMID: 36745583 PMCID: PMC9901794 DOI: 10.1371/journal.pone.0281181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/17/2023] [Indexed: 02/07/2023] Open
Abstract
Crop pathogens pose severe risks to global food production due to the rapid rise of resistance to pesticides and host resistance breakdowns. Predicting future risks requires monitoring tools to identify changes in the genetic composition of pathogen populations. Here we report the design of a microfluidics-based amplicon sequencing assay to multiplex 798 loci targeting virulence and fungicide resistance genes, and randomly selected genome-wide markers for the fungal pathogen Zymoseptoria tritici. The fungus causes one of the most devastating diseases on wheat showing rapid adaptation to fungicides and host resistance. We optimized the primer design by integrating polymorphism data from 632 genomes of the same species. To test the performance of the assay, we genotyped 192 samples in two replicates. Analysis of the short-read sequence data generated by the assay showed a fairly stable success rate across samples to amplify a large number of loci. The performance was consistent between samples originating from pure genomic DNA as well as material extracted directly from infected wheat leaves. In samples with mixed genotypes, we found that the assay recovers variations in allele frequencies. We also explored the potential of the amplicon assay to recover transposable element insertion polymorphism relevant for fungicide resistance. As a proof-of-concept, we show that the assay recovers the pathogen population structure across French wheat fields. Genomic monitoring of crop pathogens contributes to more sustainable crop protection and yields.
Collapse
Affiliation(s)
- Hadjer Bellah
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Gwilherm Gazeau
- INRAE, UR BIOGER, Université Paris-Saclay, Thiverval-Grignon, France
| | - Sandrine Gélisse
- INRAE, UR BIOGER, Université Paris-Saclay, Thiverval-Grignon, France
| | - Reda Amezrou
- INRAE, UR BIOGER, Université Paris-Saclay, Thiverval-Grignon, France
| | - Thierry C. Marcel
- INRAE, UR BIOGER, Université Paris-Saclay, Thiverval-Grignon, France
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
3
|
Chen H, King R, Smith D, Bayon C, Ashfield T, Torriani S, Kanyuka K, Hammond-Kosack K, Bieri S, Rudd J. Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen. BMC Biol 2023; 21:24. [PMID: 36747219 PMCID: PMC9903594 DOI: 10.1186/s12915-023-01520-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Studying genomic variation in rapidly evolving pathogens potentially enables identification of genes supporting their "core biology", being present, functional and expressed by all strains or "flexible biology", varying between strains. Genes supporting flexible biology may be considered to be "accessory", whilst the "core" gene set is likely to be important for common features of a pathogen species biology, including virulence on all host genotypes. The wheat-pathogenic fungus Zymoseptoria tritici represents one of the most rapidly evolving threats to global food security and was the focus of this study. RESULTS We constructed a pangenome of 18 European field isolates, with 12 also subjected to RNAseq transcription profiling during infection. Combining this data, we predicted a "core" gene set comprising 9807 sequences which were (1) present in all isolates, (2) lacking inactivating polymorphisms and (3) expressed by all isolates. A large accessory genome, consisting of 45% of the total genes, was also defined. We classified genetic and genomic polymorphism at both chromosomal and individual gene scales. Proteins required for essential functions including virulence had lower-than average sequence variability amongst core genes. Both core and accessory genomes encoded many small, secreted candidate effector proteins that likely interact with plant immunity. Viral vector-mediated transient in planta overexpression of 88 candidates failed to identify any which induced leaf necrosis characteristic of disease. However, functional complementation of a non-pathogenic deletion mutant lacking five core genes demonstrated that full virulence was restored by re-introduction of the single gene exhibiting least sequence polymorphism and highest expression. CONCLUSIONS These data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.
Collapse
Affiliation(s)
- Hongxin Chen
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
- Present address: School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Guangming District, Shenzhen, Guangdong People’s Republic of China
| | - Robert King
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| | - Dan Smith
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| | - Carlos Bayon
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| | - Tom Ashfield
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
- Crop Health and Protection (CHaP), Rothamsted Research, Harpenden, Herts UK
| | - Stefano Torriani
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Kostya Kanyuka
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
- Present address: National Institute for Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, UK
| | - Kim Hammond-Kosack
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| | - Stephane Bieri
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Jason Rudd
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| |
Collapse
|
4
|
Petersen C, Sørensen T, Nielsen MR, Sondergaard TE, Sørensen JL, Fitzpatrick DA, Frisvad JC, Nielsen KL. Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events. IMA Fungus 2023; 14:3. [PMID: 36726175 PMCID: PMC9893605 DOI: 10.1186/s43008-023-00108-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
The Penicillia are known to produce a wide range natural products-some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.
Collapse
Affiliation(s)
- Celine Petersen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Ålborg, Denmark
| | - Trine Sørensen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Ålborg, Denmark
| | - Mikkel R. Nielsen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Niels-Bohrs Vej 8, 6700 Esbjerg, Denmark
| | - Teis E. Sondergaard
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Ålborg, Denmark
| | - Jens L. Sørensen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Niels-Bohrs Vej 8, 6700 Esbjerg, Denmark
| | - David A. Fitzpatrick
- grid.95004.380000 0000 9331 9029Department of Biology, Maynooth University, Maynooth, W23 F2K8 Ireland
| | - Jens C. Frisvad
- grid.5170.30000 0001 2181 8870Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads B221, 2800 Kgs, Lyngby, Denmark
| | - Kåre L. Nielsen
- grid.5117.20000 0001 0742 471XDepartment of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Ålborg, Denmark
| |
Collapse
|
5
|
Wei X, Zheng J, Evans JD, Huang Q. Transgenerational genomic analyses reveal allelic oscillation and purifying selection in a gut parasite Nosema ceranae. Front Microbiol 2022; 13:927892. [PMID: 36386715 PMCID: PMC9664190 DOI: 10.3389/fmicb.2022.927892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Standing genetic variation is the predominant source acted on by selection. Organisms with high genetic diversity generally show faster responses toward environmental change. Nosema ceranae is a microsporidian parasite of honey bees, infecting midgut epithelial cells. High genetic diversity has been found in this parasite, but the mechanism for the parasite to maintain this diversity remains unclear. This study involved continuous inoculation of N. ceranae to honey bees. We found that the parasites slowly increased genetic diversity over three continuous inoculations. The number of lost single nucleotide variants (SNVs) was balanced with novel SNVs, which were mainly embedded in coding regions. Classic allele frequency oscillation was found at the regional level along the genome, and the associated genes were enriched in apoptosis regulation and ATP binding. The ratio of synonymous and non-synonymous substitution suggests a purifying selection, and our results provide novel insights into the evolutionary dynamics in microsporidian parasites.
Collapse
Affiliation(s)
- Xiuxiu Wei
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang, China,Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Jialan Zheng
- College of Forestry, Jiangxi Agricultural University, Nanchang, China
| | - Jay D. Evans
- USDA-ARS Bee Research Laboratory, Beltsville, MD, United States
| | - Qiang Huang
- Jiangxi Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang, China,Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China,*Correspondence: Qiang Huang,
| |
Collapse
|