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Cohen AB, Cai G, Price DC, Molnar TJ, Zhang N, Hillman BI. The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut. BMC Genomics 2024; 25:347. [PMID: 38580927 PMCID: PMC10998396 DOI: 10.1186/s12864-024-10198-1] [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: 05/12/2023] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome. RESULTS The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors. CONCLUSIONS This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen's life cycle and a solid foundation for studying EFB.
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Affiliation(s)
- Alanna B Cohen
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Guohong Cai
- Crop Production and Pest Control Research Unit, USDA-ARS, West Lafayette, IN, 47907, USA.
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Dana C Price
- Department of Entomology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Center for Vector Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Thomas J Molnar
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Biochemistry and Microbiology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Bradley I Hillman
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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2
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Liang X, Yu W, Meng Y, Shang S, Tian H, Zhang Z, Rollins JA, Zhang R, Sun G. Genome comparisons reveal accessory genes crucial for the evolution of apple Glomerella leaf spot pathogenicity in Colletotrichum fungi. MOLECULAR PLANT PATHOLOGY 2024; 25:e13454. [PMID: 38619507 PMCID: PMC11018114 DOI: 10.1111/mpp.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/16/2024]
Abstract
Apple Glomerella leaf spot (GLS) is an emerging fungal disease caused by Colletotrichum fructicola and other Colletotrichum species. These species are polyphyletic and it is currently unknown how these pathogens convergently evolved to infect apple. We generated chromosome-level genome assemblies of a GLS-adapted isolate and a non-adapted isolate in C. fructicola using long-read sequencing. Additionally, we resequenced 17 C. fructicola and C. aenigma isolates varying in GLS pathogenicity using short-read sequencing. Genome comparisons revealed a conserved bipartite genome architecture involving minichromosomes (accessory chromosomes) shared by C. fructicola and other closely related species within the C. gloeosporioides species complex. Moreover, two repeat-rich genomic regions (1.61 Mb in total) were specifically conserved among GLS-pathogenic isolates in C. fructicola and C. aenigma. Single-gene deletion of 10 accessory genes within the GLS-specific regions of C. fructicola identified three that were essential for GLS pathogenicity. These genes encoded a putative non-ribosomal peptide synthetase, a flavin-binding monooxygenase and a small protein with unknown function. These results highlight the crucial role accessory genes play in the evolution of Colletotrichum pathogenicity and imply the significance of an unidentified secondary metabolite in GLS pathogenesis.
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Affiliation(s)
- Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Wei Yu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Yanan Meng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Shengping Shang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Huanhuan Tian
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Zhaohui Zhang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | | | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingChina
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3
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Benson CW, Sheltra MR, Huff DR. The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss. G3 (BETHESDA, MD.) 2024; 14:jkad238. [PMID: 37847611 PMCID: PMC10849329 DOI: 10.1093/g3journal/jkad238] [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: 05/28/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023]
Abstract
To complete its parasitic lifecycle, Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloëana's ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloëana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloëana is nested within the genus Tilletia and diverged from Tilletia caries and Tilletia walkeri ∼40 MYA. We find that S. buchloëana contains a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes, and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloëana's evolution and host specificity. Salmacisia buchloëana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation, and that S. buchloëana has a unique bias for the serine codon UCG. Finally, we identify 3 inteins within the S. buchloëana genome, 2 of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.
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Affiliation(s)
- Christopher W Benson
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Matthew R Sheltra
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
- Intercollegiate Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - David R Huff
- Department of Plant Science, Pennsylvania State University, University Park, PA 16801, USA
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4
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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.
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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.
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5
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Hybrid de novo genome assembly and comparative genomics of three different isolates of Gnomoniopsis castaneae. Sci Rep 2023; 13:3356. [PMID: 36849528 PMCID: PMC9971261 DOI: 10.1038/s41598-023-30496-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/24/2023] [Indexed: 03/01/2023] Open
Abstract
The first genome assemblies of Gnomoniopsis castaneae (syn. G. smithogilvyi), the causal agent of chestnut brown rot of kernels, shoot blight and cankers, are provided here. Specifically, the complete genome of the Italian ex-type MUT401 isolate was compared to the draft genome of a second Italian isolate (GN01) and to the ICMP 14040 isolate from New Zealand. The three genome sequences were obtained through a hybrid assembly using both short Illumina reads and long Nanopore reads, their coding sequences were annotated and compared with each other and with other Diaporthales. The information offered by the genome assembly of the three isolates represents the base of data for further application related to -omics strategies of the fungus and to develop markers for population studies at a local and global scale.
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Lustig AJ. Investigating the origin of subtelomeric and centromeric AT-rich elements in Aspergillus flavus. PLoS One 2023; 18:e0279148. [PMID: 36758027 PMCID: PMC9910759 DOI: 10.1371/journal.pone.0279148] [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: 11/30/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
An in silico study of Aspergillus flavus genome stability uncovered significant variations in both coding and non-coding regions. The non-coding insertions uniformly consisted of AT-rich sequences that are evolutionarily maintained, albeit distributed at widely different sites in an array of A. flavus strains. A survey of ≥ 2kb AT-rich elements (AT ≥ 70%; ATEs) in non-centromeric regions uncovered two major categories of ATEs. The first category is composed of homologous insertions at ectopic, non-allelic sites that contain homology to transposable elements (TEs; Classes B, C, D, and E). Strains differed significantly in frequency, position, and TE type, but displayed a common enrichment in subtelomeric regions. The TEs were heavily mutated, with patterns consistent with the ancestral activity of repeat-induced point mutations (RIP). The second category consists of a conserved set of novel subtelomeric ATE repeats (Classes A, G, G, H, I and J) which lack discernible TEs and, unlike TEs, display a constant polarity relative to the telomere. Members of one of these classes are derivatives of a progenitor ATE that is predicted to have undergone extensive homologous recombination during evolution. A third category of ATEs consists of ~100 kb regions at each centromere. Centromeric ATEs and TE clusters within these centromeres display a high level of sequence identity between strains. These studies suggest that transposition and RIP are forces in the evolution of subtelomeric and centromeric structure and function.
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Affiliation(s)
- Arthur J. Lustig
- Department of Biochemistry and Molecular Biology, Tulane University Medical School, New Orleans, LA, United States of America
- * E-mail:
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7
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De Miccolis Angelini RM, Landi L, Raguseo C, Pollastro S, Faretra F, Romanazzi G. Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa. Front Microbiol 2022; 13:854852. [PMID: 35356516 PMCID: PMC8959702 DOI: 10.3389/fmicb.2022.854852] [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: 01/14/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.
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Affiliation(s)
| | - Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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8
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Severn-Ellis AA, Schoeman MH, Bayer PE, Hane JK, Rees DJG, Edwards D, Batley J. Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. FRONTIERS IN PLANT SCIENCE 2022; 13:811152. [PMID: 35283890 PMCID: PMC8914235 DOI: 10.3389/fpls.2022.811152] [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: 11/08/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Guava wilt disease is caused by the fungus Nalanthamala psidii. The wilt disease results in large-scale destruction of orchards in South Africa, Taiwan, and several Southeast Asian countries. De novo assembly, annotation, and in-depth analysis of the N. psidii genome were carried out to facilitate the identification of characteristics associated with pathogenicity and pathogen evolution. The predicted secretome revealed a range of CAZymes, proteases, lipases and peroxidases associated with plant cell wall degradation, nutrient acquisition, and disease development. Further analysis of the N. psidii carbohydrate-active enzyme profile exposed the broad-spectrum necrotrophic lifestyle of the pathogen, which was corroborated by the identification of putative effectors and secondary metabolites with the potential to induce tissue necrosis and cell surface-dependent immune responses. Putative regulatory proteins including transcription factors and kinases were identified in addition to transporters potentially involved in the secretion of secondary metabolites. Transporters identified included important ABC and MFS transporters involved in the efflux of fungicides. Analysis of the repetitive landscape and the detection of mechanisms linked to reproduction such as het and mating genes rendered insights into the biological complexity and evolutionary potential of N. psidii as guava pathogen. Hence, the assembly and annotation of the N. psidii genome provided a valuable platform to explore the pathogenic potential and necrotrophic lifestyle of the guava wilt pathogen.
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Affiliation(s)
- Anita A. Severn-Ellis
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
- Aquaculture Research and Development, Department of Primary Industries and Regional Development, Indian Ocean Marine Research Centre, Watermans Bay, WA, Australia
| | - Maritha H. Schoeman
- Institute for Tropical and Subtropical Crops, Agricultural Research Council, Nelspruit, South Africa
| | - Philipp E. Bayer
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - D. Jasper G. Rees
- Agricultural Research Council, Biotechnology Platform, Pretoria, South Africa
- Botswana University of Agriculture and Natural Resources, Gaborone, Botswana
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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McTaggart AR, James TY, Shivas RG, Drenth A, Wingfield BD, Summerell BA, Duong TA. Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex. Stud Mycol 2022; 99:100132. [PMID: 35027981 PMCID: PMC8693468 DOI: 10.1016/j.simyco.2021.100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Fusarium oxysporum species complex (FOSC) is a group of closely related plant pathogens long-considered strictly clonal, as sexual stages have never been recorded. Several studies have questioned whether recombination occurs in FOSC, and if it occurs its nature and frequency are unknown. We analysed 410 assembled genomes to answer whether FOSC diversified by occasional sexual reproduction interspersed with numerous cycles of asexual reproduction akin to a model of predominant clonal evolution (PCE). We tested the hypothesis that sexual reproduction occurred in the evolutionary history of FOSC by examining the distribution of idiomorphs at the mating locus, phylogenetic conflict and independent measures of recombination from genome-wide SNPs and genes. A phylogenomic dataset of 40 single copy orthologs was used to define structure a priori within FOSC based on genealogical concordance. Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from assembled genomes using a k-mer approach and tested for significant linkage disequilibrium as an indication of PCE. We clone-corrected and tested whether SNPs were randomly associated as an indication of recombination. Our analyses provide evidence for sexual or parasexual reproduction within, but not between, clades of FOSC that diversified from a most recent common ancestor about 500 000 years ago. There was no evidence of substructure based on geography or host that might indicate how clades diversified. Competing evolutionary hypotheses for FOSC are discussed in the context of our results.
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Affiliation(s)
- A R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, 4102, Queensland, Australia
| | - T Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - R G Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, 4350, Australia
| | - A Drenth
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, 4102, Queensland, Australia
| | - B D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - B A Summerell
- Australian Institute of Botanical Science, Royal Botanic Gardens & Domain Trust, Sydney, Australia
| | - T A Duong
- Department of Biochemistry, Genetics and Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
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10
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Liu Q, Xu Y, Zhang X, Li K, Li X, Wang F, Xu F, Dong C. Infection Process and Genome Assembly Provide Insights into the Pathogenic Mechanism of Destructive Mycoparasite Calcarisporium cordycipiticola with Host Specificity. J Fungi (Basel) 2021; 7:918. [PMID: 34829206 PMCID: PMC8620734 DOI: 10.3390/jof7110918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 11/21/2022] Open
Abstract
Calcarisporium cordycipiticola is the pathogen in the white mildew disease of Cordyceps militaris, one of the popular mushrooms. This disease frequently occurs and there is no effective method for disease prevention and control. In the present study, C. militaris is found to be the only host of C. cordycipiticola, indicating strict host specificity. The infection process was monitored by fluorescent labeling and scanning and transmission electron microscopes. C. cordycipiticola can invade into the gaps among hyphae of the fruiting bodies of the host and fill them gradually. It can degrade the hyphae of the host by both direct contact and noncontact. The parasitism is initially biotrophic, and then necrotrophic as mycoparasitic interaction progresses. The approximate chromosome-level genome assembly of C. cordycipiticola yielded an N50 length of 5.45 Mbp and a total size of 34.51 Mbp, encoding 10,443 proteins. Phylogenomic analysis revealed that C. cordycipiticola is phylogenetically close to its specific host, C. militaris. A comparative genomic analysis showed that the number of CAZymes of C. cordycipiticola was much less than in other mycoparasites, which might be attributed to its host specificity. Secondary metabolite cluster analysis disclosed the great biosynthetic capabilities and potential mycotoxin production capability. This study provides insights into the potential pathogenesis and interaction between mycoparasite and its host.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Kuan Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Xiao Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fen Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
| | - Fangxu Xu
- Experimental Teaching Center, Shenyang Normal University, Shenyang 110034, China;
| | - Caihong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Q.L.); (Y.X.); (X.Z.); (K.L.); (X.L.); (F.W.)
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11
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Fouché S, Oggenfuss U, Chanclud E, Croll D. A devil's bargain with transposable elements in plant pathogens. Trends Genet 2021; 38:222-230. [PMID: 34489138 DOI: 10.1016/j.tig.2021.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 02/08/2023]
Abstract
Transposable elements (TEs) spread in genomes through self-copying mechanisms and are a major cause of genome expansions. Plant pathogens have finely tuned the expression of virulence factors to rely on epigenetic control targeted at nearby TEs. Stress experienced during the plant infection process leads to derepression of TEs and concurrently allows the expression of virulence factors. We argue that the derepression of TEs elements causes an evolutionary conflict by favoring TEs that can be reactivated. Active TEs and recent genome size expansions indicate that plant pathogens could face long-term consequences from the short-term benefit of fine-tuning the infection process. Hence, encoding key virulence factors close to TEs under epigenetic control constitutes a devil's bargain for pathogens.
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Affiliation(s)
- Simone Fouché
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland; Department of Organismal Biology - Systematic Biology, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Emilie Chanclud
- 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.
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12
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Porquier A, Tisserant C, Salinas F, Glassl C, Wange L, Enard W, Hauser A, Hahn M, Weiberg A. Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea. Genome Biol 2021; 22:225. [PMID: 34399815 PMCID: PMC8365987 DOI: 10.1186/s13059-021-02446-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/26/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Retrotransposons are genetic elements inducing mutations in all domains of life. Despite their detrimental effect, retrotransposons can become temporarily active during epigenetic reprogramming and cellular stress response, which may accelerate host genome evolution. In fungal pathogens, a positive role has been attributed to retrotransposons when shaping genome architecture and expression of genes encoding pathogenicity factors; thus, retrotransposons are known to influence pathogenicity. RESULTS We uncover a hitherto unknown role of fungal retrotransposons as being pathogenicity factors, themselves. The aggressive fungal plant pathogen, Botrytis cinerea, is known to deliver some long-terminal repeat (LTR) deriving regulatory trans-species small RNAs (BcsRNAs) into plant cells to suppress host gene expression for infection. We find that naturally occurring, less aggressive B. cinerea strains possess considerably lower copy numbers of LTR retrotransposons and had lost retrotransposon BcsRNA production. Using a transgenic proof-of-concept approach, we reconstitute retrotransposon expression in a BcsRNA-lacking B. cinerea strain, which results in enhanced aggressiveness in a retrotransposon and BcsRNA expression-dependent manner. Moreover, retrotransposon expression in B. cinerea leads to suppression of plant defence-related genes during infection. CONCLUSIONS We propose that retrotransposons are pathogenicity factors that manipulate host plant gene expression by encoding trans-species BcsRNAs. Taken together, the novelty that retrotransposons are pathogenicity factors will have a broad impact on studies of host-microbe interactions and pathology.
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Affiliation(s)
| | | | | | - Carla Glassl
- Faculty of Biology, Genetics, LMU Munich, Martinsried, Germany
| | - Lucas Wange
- Faculty of Biology, Anthropology & Human Genomics, LMU Munich, Martinsried, Germany
| | - Wolfgang Enard
- Faculty of Biology, Anthropology & Human Genomics, LMU Munich, Martinsried, Germany
| | - Andreas Hauser
- Gene Center, Laboratory for Functional Genome Analysis, LMU Munich, Martinsried, Germany
| | - Matthias Hahn
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Arne Weiberg
- Faculty of Biology, Genetics, LMU Munich, Martinsried, Germany.
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13
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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: 2] [Impact Index Per Article: 0.7] [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.
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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
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14
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Nielsen KN, Salgado JFM, Natsopoulou ME, Kristensen T, Stajich JE, De Fine Licht HH. Diploidy within a Haploid Genus of Entomopathogenic Fungi. Genome Biol Evol 2021; 13:evab158. [PMID: 34247231 PMCID: PMC8325562 DOI: 10.1093/gbe/evab158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/28/2022] Open
Abstract
Fungi in the genus Metarhizium are soil-borne plant-root endophytes and rhizosphere colonizers, but also potent insect pathogens with highly variable host ranges. These ascomycete fungi are predominantly asexually reproducing and ancestrally haploid, but two independent origins of persistent diploidy within the Coleoptera-infecting Metarhizium majus species complex are known and has been attributed to incomplete chromosomal segregation following meiosis during the sexual cycle. There is also evidence for infrequent sexual cycles in the locust-specific pathogenic fungus Metarhizium acridum (Hypocreales: Clavicipitaceae), which is an important entomopathogenic biocontrol agent used for the control of grasshoppers in agricultural systems as an alternative to chemical control. Here, we show that the genome of the M. acridum isolate ARSEF 324, which is formulated and commercially utilized is functionally diploid. We used single-molecule real-time sequencing technology to complete a high-quality assembly of ARSEF 324. K-mer frequencies, intragenomic collinearity between contigs and single nucleotide variant read depths across the genome revealed the first incidence of diploidy described within the species M. acridum. The haploid assembly of 44.7 Mb consisted of 20.8% repetitive elements, which is the highest proportion described of any Metarhizium species. The long-read diploid genome assembly sheds light on past research on this strain, such as unusual high UVB tolerance. The data presented here could fuel future investigation into the fitness landscape of fungi with infrequent sexual reproduction and aberrant ploidy levels, not least in the context of biocontrol agents.
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Affiliation(s)
- Knud Nor Nielsen
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - João Felipe Moreira Salgado
- Department of Microbiology and Plant Pathology, University of California Riverside, California, USA
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Brazil
| | - Myrsini Eirini Natsopoulou
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Thea Kristensen
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, California, USA
| | - Henrik H De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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15
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Yow AG, Zhang Y, Bansal K, Eacker SM, Sullivan S, Liachko I, Cubeta MA, Rollins JA, Ashrafi H. Genome sequence of Monilinia vaccinii-corymbosi sheds light on mummy berry disease infection of blueberry and mating type. G3-GENES GENOMES GENETICS 2021; 11:6062400. [PMID: 33598705 PMCID: PMC8022979 DOI: 10.1093/g3journal/jkaa052] [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: 05/08/2020] [Accepted: 10/29/2020] [Indexed: 11/22/2022]
Abstract
Mummy berry disease, caused by the fungal pathogen Monilinia vaccinii-corymbosi (Mvc), is one of the most economically important diseases of blueberries in North America. Mvc is capable of inducing two separate blighting stages during its life cycle. Infected fruits are rendered mummified and unmarketable. Genomic data for this pathogen is lacking, but could be useful in understanding the reproductive biology of Mvc and the mechanisms it deploys to facilitate host infection. In this study, PacBio sequencing and Hi-C interaction data were utilized to create a chromosome-scale reference genome for Mvc. The genome comprises nine chromosomes with a total length of 30 Mb, an N50 length of 4.06 Mb, and an average 413X sequence coverage. A total of 9399 gene models were predicted and annotated, and BUSCO analysis revealed that 98% of 1,438 searched conserved eukaryotic genes were present in the predicted gene set. Potential effectors were identified, and the mating-type (MAT) locus was characterized. Biotrophic effectors allow the pathogen to avoid recognition by the host plant and evade or mitigate host defense responses during the early stages of fruit infection. Following locule colonization, necrotizing effectors promote the mummification of host tissues. Potential biotrophic effectors utilized by Mvc include chorismate mutase for reducing host salicylate and necrotrophic effectors include necrosis-inducing proteins and hydrolytic enzymes for macerating host tissue. The MAT locus sequences indicate the potential for homothallism in the reference genome, but a deletion allele of the MAT locus, characterized in a second isolate, indicates heterothallism. Further research is needed to verify the roles of individual effectors in virulence and to determine the role of the MAT locus in outcrossing and population genotypic diversity.
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Affiliation(s)
- Ashley G Yow
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Yucheng Zhang
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Kamaldeep Bansal
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | | | | | | | - Marc A Cubeta
- Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27606, USA
| | - Jeffrey A Rollins
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
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16
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Peck LD, Nowell RW, Flood J, Ryan MJ, Barraclough TG. Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides. BMC Genomics 2021; 22:404. [PMID: 34082717 PMCID: PMC8176585 DOI: 10.1186/s12864-021-07700-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Nearly 50% of crop yields are lost to pests and disease, with plants and pathogens locked in an amplified co-evolutionary process of disease outbreaks. Coffee wilt disease, caused by Fusarium xylarioides, decimated coffee production in west and central Africa following its initial outbreak in the 1920s. After successful management, it later re-emerged and by the 2000s comprised two separate epidemics on arabica coffee in Ethiopia and robusta coffee in east and central Africa. RESULTS Here, we use genome sequencing of six historical culture collection strains spanning 52 years to identify the evolutionary processes behind these repeated outbreaks. Phylogenomic reconstruction using 13,782 single copy orthologs shows that the robusta population arose from the initial outbreak, whilst the arabica population is a divergent sister clade to the other strains. A screen for putative effector genes involved in pathogenesis shows that the populations have diverged in gene content and sequence mainly by vertical processes within lineages. However, 15 putative effector genes show evidence of horizontal acquisition, with close homology to genes from F. oxysporum. Most occupy small regions of homology within wider scaffolds, whereas a cluster of four genes occupy a 20Kb scaffold with strong homology to a region on a mobile pathogenicity chromosome in F. oxysporum that houses known effector genes. Lacking a match to the whole mobile chromosome, we nonetheless found close associations with DNA transposons, especially the miniature impala type previously proposed to facilitate horizontal transfer of pathogenicity genes in F. oxysporum. These findings support a working hypothesis that the arabica and robusta populations partly acquired distinct effector genes via transposition-mediated horizontal transfer from F. oxysporum, which shares coffee as a host and lives on other plants intercropped with coffee. CONCLUSION Our results show how historical genomics can help reveal mechanisms that allow fungal pathogens to keep pace with our efforts to resist them. Our list of putative effector genes identifies possible future targets for fungal control. In turn, knowledge of horizontal transfer mechanisms and putative donor taxa might help to design future intercropping strategies that minimize the risk of transfer of effector genes between closely-related Fusarium taxa.
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Affiliation(s)
- Lily D Peck
- Science and Solutions for a Changing Planet Doctoral Training Partnership, Grantham Institute, Imperial College London, South Kensington, London, SW7 2AZ, UK. .,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.,Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Julie Flood
- CABI, Bakeham Lane, Egham, Surrey, TW20 9TY, UK
| | | | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK.,Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
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17
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Bertazzoni S, Jones DAB, Phan HT, Tan KC, Hane JK. Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome. BMC Genomics 2021; 22:382. [PMID: 34034667 PMCID: PMC8146201 DOI: 10.1186/s12864-021-07699-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Background The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised – ToxA, Tox1 and Tox3. Results A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions. Conclusions We present an updated series of genomic resources for P. nodorum Sn15 – an important reference isolate and model necrotroph – with a comprehensive survey of its predicted pathogenicity content. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07699-8.
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Affiliation(s)
| | - Darcy A B Jones
- Centre for Crop & Disease Management, Curtin University, Perth, Australia
| | - Huyen T Phan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - James K Hane
- Centre for Crop & Disease Management, Curtin University, Perth, Australia. .,Curtin Institute for Computation, Curtin University, Perth, Australia.
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18
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Evolutionary and genomic comparisons of hybrid uninucleate and nonhybrid Rhizoctonia fungi. Commun Biol 2021; 4:201. [PMID: 33589695 PMCID: PMC7884421 DOI: 10.1038/s42003-021-01724-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
The basidiomycetous fungal genus, Rhizoctonia, can cause severe damage to many plants and is composed of multinucleate, binucleate, and uninucleate species differing in pathogenicity. Here we generated chromosome-scale genome assemblies of the three nuclear types of Rhizoctonia isolates. The genomic comparisons revealed that the uninucleate JN strain likely arose by somatic hybridization of two binucleate isolates, and maintained a diploid nucleus. Homeolog gene pairs in the JN genome have experienced both decelerated or accelerated evolution. Homeolog expression dominance occurred between JN subgenomes, in which differentially expressed genes show potentially less evolutionary constraint than the genes without. Analysis of mating-type genes suggested that Rhizoctonia maintains the ancestral tetrapolarity of the Basidiomycota. Long terminal repeat-retrotransposons displayed a reciprocal correlation with the chromosomal GC content in the three chromosome-scale genomes. The more aggressive multinucleate XN strain had more genes encoding enzymes for host cell wall decomposition. These findings demonstrate some evolutionary changes of a recently derived hybrid and in multiple nuclear types of Rhizoctonia.
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19
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van Wyk S, Wingfield BD, De Vos L, van der Merwe NA, Steenkamp ET. Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota. Front Microbiol 2021; 11:622368. [PMID: 33597932 PMCID: PMC7882544 DOI: 10.3389/fmicb.2020.622368] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/29/2020] [Indexed: 11/17/2022] Open
Abstract
The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach. Using genome-wide RIP data and two sets of control groups, the association between RIP, TEs, and GC content were contrasted in organisms capable and incapable of RIP. Based on these data, we then set out to determine the extent and occurrence of RIP in 58 representatives of the Ascomycota. The findings were summarized by placing each of the fungi investigated in one of six categories based on the extent of genome-wide RIP. In silico RIP analyses, using a sliding-window approach with stringent RIP parameters, implemented simultaneously within the same genetic context, on high quality genome assemblies, yielded superior results in determining the genome-wide RIP among the Ascomycota. Most Ascomycota had RIP and these mutations were particularly widespread among classes of the Pezizomycotina, including the early diverging Orbiliomycetes and the Pezizomycetes. The most extreme cases of RIP were limited to representatives of the Dothideomycetes and Sordariomycetes. By contrast, the genomes of the Taphrinomycotina and Saccharomycotina contained no detectable evidence of RIP. Also, recent losses in RIP combined with controlled TE proliferation in the Pezizomycotina subphyla may promote substantial genome enlargement as well as the formation of sub-genomic compartments. These findings have broadened our understanding of the taxonomic range and extent of RIP in Ascomycota and how this pathway affects the genomes of fungi harboring it.
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Affiliation(s)
| | | | | | | | - Emma T. Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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20
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RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics. IMA Fungus 2020; 11:18. [PMID: 32974122 PMCID: PMC7493409 DOI: 10.1186/s43008-020-00040-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/01/2020] [Indexed: 11/23/2022] Open
Abstract
Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.
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21
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Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14. G3-GENES GENOMES GENETICS 2020; 10:2131-2140. [PMID: 32345704 PMCID: PMC7341154 DOI: 10.1534/g3.120.401265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.
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22
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Crouch JA, Dawe A, Aerts A, Barry K, Churchill ACL, Grimwood J, Hillman BI, Milgroom MG, Pangilinan J, Smith M, Salamov A, Schmutz J, Yadav JS, Grigoriev IV, Nuss DL. Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen. PHYTOPATHOLOGY 2020; 110:1180-1188. [PMID: 32207662 DOI: 10.1094/phyto-12-19-0478-a] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cryphonectria parasitica is the causal agent of chestnut blight, a fungal disease that almost entirely eliminated mature American chestnut from North America over a 50-year period. Here, we formally report the genome of C. parasitica EP155 using a Sanger shotgun sequencing approach. After finishing and integration with simple-sequence repeat markers, the assembly was 43.8 Mb in 26 scaffolds (L50 = 5; N50 = 4.0Mb). Eight chromosomes are predicted: five scaffolds have two telomeres and six scaffolds have one telomere sequence. In total, 11,609 gene models were predicted, of which 85% show similarities to other proteins. This genome resource has already increased the utility of a fundamental plant pathogen experimental system through new understanding of the fungal vegetative incompatibility system, with significant implications for enhancing mycovirus-based biological control.
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Affiliation(s)
- Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture-Agricultural Research Service, 10300 Baltimore Avenue, Building 010A, Beltsville, MD, U.S.A
| | - Angus Dawe
- Department of Biological Sciences, Mississippi State University, 295 Lee Boulevard, Mississippi State, MS, U.S.A
| | - Andrea Aerts
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Alice C L Churchill
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, U.S.A
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, U.S.A
| | - Bradley I Hillman
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, U.S.A
| | - Michael G Milgroom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, U.S.A
| | - Jasmyn Pangilinan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Myron Smith
- Department of Biology, Carleton University, 1125 Colonel by Drive, Ottawa, ON, Canada
| | - Asaf Salamov
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Jeremy Schmutz
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, U.S.A
| | - Jagjit S Yadav
- Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, U.S.A
| | - Igor V Grigoriev
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, U.S.A
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, U.S.A
| | - Donald L Nuss
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, U.S.A
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, U.S.A
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Ji X, Yu Z, Yang J, Xu J, Zhang Y, Liu S, Zou C, Li J, Liang L, Zhang KQ. Expansion of Adhesion Genes Drives Pathogenic Adaptation of Nematode-Trapping Fungi. iScience 2020; 23:101057. [PMID: 32339992 PMCID: PMC7186526 DOI: 10.1016/j.isci.2020.101057] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/12/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2022] Open
Abstract
Understanding how fungi interact with other organisms has significant medical, environmental, and agricultural implications. Nematode-trapping fungi (NTF) can switch to pathogens by producing various trapping devices to capture nematodes. Here we perform comparative genomic analysis of the NTF with four representative trapping devices. Phylogenomic reconstruction of these NTF suggested an evolutionary trend of trapping device simplification in morphology. Interestingly, trapping device simplification was accompanied by expansion of gene families encoding adhesion proteins and their increasing adhesiveness on trap surfaces. Gene expression analysis revealed a consistent up-regulation of the adhesion genes during their lifestyle transition from saprophytic to nematophagous stages. Our results suggest that the expansion of adhesion genes in NTF genomes and consequential increase in trap surface adhesiveness are likely the key drivers of fungal adaptation in trapping nematodes, providing new insights into understanding mechanisms underlying infection and adaptation of pathogenic fungi. Expansion of subtilisin, adhesion protein, and polygalacturonase gene families Trap simplification during evolution of nematode-trapping fungi Connection between trap simplification and expansion of adhesion genes
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Affiliation(s)
- Xinglai Ji
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; Smart Health Big Data Analysis and Location Services Engineering Lab of Jiangsu Province, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Zefen Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Jinkui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China; Department of Biology, McMaster University, 1280 Main St. West, Hamilton, ON L8S 4K1, Canada
| | - Ying Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Shuqun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Chenggang Zou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Lianming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China.
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24
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Moolhuijzen PM, Muria-Gonzalez MJ, Syme R, Rawlinson C, See PT, Moffat CS, Ellwood SR. Expansion and Conservation of Biosynthetic Gene Clusters in Pathogenic Pyrenophora spp. Toxins (Basel) 2020; 12:toxins12040242. [PMID: 32283749 PMCID: PMC7232245 DOI: 10.3390/toxins12040242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 12/28/2022] Open
Abstract
Pyrenophora is a fungal genus responsible for a number of major cereal diseases. Although fungi produce many specialised or secondary metabolites for defence and interacting with the surrounding environment, the repertoire of specialised metabolites (SM) within Pyrenophora pathogenic species remains mostly uncharted. In this study, an in-depth comparative analysis of the P. teres f. teres, P teres f. maculata and P. tritici-repentis potential to produce SMs, based on in silico predicted biosynthetic gene clusters (BGCs), was conducted using genome assemblies from PacBio DNA reads. Conservation of BGCs between the Pyrenophora species included type I polyketide synthases, terpene synthases and the first reporting of a type III polyketide synthase in P teres f. maculata. P. teres isolates exhibited substantial expansion of non-ribosomal peptide synthases relative to P. tritici-repentis, hallmarked by the presence of tailoring cis-acting nitrogen methyltransferase domains. P. teres isolates also possessed unique non-ribosomal peptide synthase (NRPS)-indole and indole BGCs, while a P. tritici-repentis phytotoxin BGC for triticone production was absent in P. teres. These differences highlight diversification between the pathogens that reflects their different evolutionary histories, host adaption and lifestyles.
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Affiliation(s)
- Paula M. Moolhuijzen
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
- Correspondence:
| | - Mariano Jordi Muria-Gonzalez
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Robert Syme
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Catherine Rawlinson
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Caroline S. Moffat
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
| | - Simon R. Ellwood
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, WA 6102, Australia
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25
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Lee RC, Farfan-Caceres LM, Debler JW, Syme RA. Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean ( Vicia faba L.). Front Microbiol 2020; 11:217. [PMID: 32132988 PMCID: PMC7040437 DOI: 10.3389/fmicb.2020.00217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/30/2020] [Indexed: 11/13/2022] Open
Abstract
Chocolate spot is a major fungal disease of faba bean caused by the ascomycete fungus, Botrytis fabae. B. fabae is also implicated in botrytis gray mold disease in lentils, along with B. cinerea. Here we have isolated and characterized two B. fabae isolates from chocolate spot lesions on faba bean leaves. In plant disease assays on faba bean and lentil, B. fabae was more aggressive than B. cinerea and we observed variation in susceptibility among a small set of cultivars for both plant hosts. Using light microscopy, we observed a spreading, generalized necrosis response in faba bean toward B. fabae. In contrast, the plant response to B. cinerea was localized to epidermal cells underlying germinated spores and appressoria. In addition to the species characterization of B. fabae, we produced genome assemblies for both B. fabae isolates using Illumina sequencing. Genome sequencing coverage and assembly size for B. fabae isolates, were 27x and 45x, and 43.2 and 44.5 Mb, respectively. Following genome assembly and annotation, carbohydrate-active enzyme (CAZymes) and effector genes were predicted. There were no major differences in the numbers of each of the major classes of CAZymes. We predicted 29 effector genes for B. fabae, and using the same selection criteria for B. cinerea, we predicted 34 putative effector genes. For five of the predicted effector genes, the pairwise dN/dS ratio between orthologs from B. fabae and B. cinerea was greater than 1.0, suggesting positive selection and the potential evolution of molecular mechanisms for host specificity in B. fabae. Furthermore, a homology search of secondary metabolite clusters revealed the absence of the B. cinerea phytotoxin botrydial and several other uncharacterized secondary metabolite biosynthesis genes from B. fabae. Although there were no obvious differences in the number or proportional representation of different transposable element classes, the overall proportion of AT-rich DNA sequence in B. fabae was double that of B. cinerea.
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Affiliation(s)
- Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Lina M Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Johannes W Debler
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Robert A Syme
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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26
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Fouché S, Badet T, Oggenfuss U, Plissonneau C, Francisco CS, Croll D. Stress-Driven Transposable Element De-repression Dynamics and Virulence Evolution in a Fungal Pathogen. Mol Biol Evol 2020; 37:221-239. [PMID: 31553475 DOI: 10.1093/molbev/msz216] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are drivers of genome evolution and affect the expression landscape of the host genome. Stress is a major factor inducing TE activity; however, the regulatory mechanisms underlying de-repression are poorly understood. Plant pathogens are excellent models to dissect the impact of stress on TEs. The process of plant infection induces stress for the pathogen, and virulence factors (i.e., effectors) located in TE-rich regions become expressed. To dissect TE de-repression dynamics and contributions to virulence, we analyzed the TE expression landscape of four strains of the major wheat pathogen Zymoseptoria tritici. We experimentally exposed strains to nutrient starvation and host infection stress. Contrary to expectations, we show that the two distinct conditions induce the expression of different sets of TEs. In particular, the most highly expressed TEs, including miniature inverted-repeat transposable element and long terminal repeat-Gypsy element, show highly distinct de-repression across stress conditions. Both the genomic context of TEs and the genetic background stress (i.e., different strains harboring the same TEs) were major predictors of de-repression under stress. Gene expression profiles under stress varied significantly depending on the proximity to the closest TEs and genomic defenses against TEs were largely ineffective to prevent de-repression. Next, we analyzed the locus encoding the Avr3D1 effector. We show that the insertion and subsequent silencing of TEs in close proximity likely contributed to reduced expression and virulence on a specific wheat cultivar. The complexity of TE responsiveness to stress across genetic backgrounds and genomic locations demonstrates substantial intraspecific genetic variation to control TEs with consequences for virulence.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Badet
- 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
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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27
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Min B, Yoon H, Park J, Oh YL, Kong WS, Kim JG, Choi IG. Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by insertions of transposable elements. PLoS One 2020; 15:e0227923. [PMID: 31978083 PMCID: PMC6980582 DOI: 10.1371/journal.pone.0227923] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/02/2020] [Indexed: 12/15/2022] Open
Abstract
Genome sequencing of Tricholoma matsutake revealed its unusually large size as 189.0 Mbp, which is a consequence of extraordinarily high transposable element (TE) content. We identified that 702 genes were surrounded by TEs, and 83.2% of these genes were not transcribed at any developmental stage. This observation indicated that the insertion of TEs alters the transcription of the genes neighboring these TEs. Repeat-induced point mutation, such as C to T hypermutation with a bias over "CpG" dinucleotides, was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both the primordia and fruiting body stages, which indicates that many regulatory processes are shared during the developmental stages. Small secreted protein genes (<300 aa) were dominantly transcribed in the hyphae, where symbiotic interactions occur with the hosts. Comparative analysis with 37 Agaricomycetes genomes revealed that IstB-like domains (PF01695) were conserved across taxonomically diverse mycorrhizal genomes, where the T. matsutake genome contained four copies of this domain. Three of the IstB-like genes were overexpressed in the hyphae. Similar to other ectomycorrhizal genomes, the CAZyme gene set was reduced in T. matsutake, including losses in the glycoside hydrolase genes. The T. matsutake genome sequence provides insight into the causes and consequences of genome size inflation.
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Affiliation(s)
- Byoungnam Min
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Hyeokjun Yoon
- School of Life Sciences and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu, Korea
| | - Julius Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
| | - Youn-Lee Oh
- Mushroom Research Division, National Institute of Horticulture and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, Korea
| | - Won-Sik Kong
- Mushroom Research Division, National Institute of Horticulture and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, Korea
- * E-mail: (IC); (WK); (JK)
| | - Jong-Guk Kim
- School of Life Sciences and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu, Korea
- * E-mail: (IC); (WK); (JK)
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Korea
- * E-mail: (IC); (WK); (JK)
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28
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da Silva LL, Moreno HLA, Correia HLN, Santana MF, de Queiroz MV. Colletotrichum: species complexes, lifestyle, and peculiarities of some sources of genetic variability. Appl Microbiol Biotechnol 2020; 104:1891-1904. [PMID: 31932894 DOI: 10.1007/s00253-020-10363-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/30/2019] [Accepted: 01/09/2020] [Indexed: 11/25/2022]
Abstract
The genus Colletotrichum comprises species with different lifestyles but is mainly known for phytopathogenic species that infect crops of agronomic relevance causing considerable losses. The fungi of the genus Colletotrichum are distributed in species complexes and within each complex some species have particularities regarding their lifestyle. The most commonly found and described lifestyles in Colletotrichum are endophytic and hemibiotrophic phytopathogenic. Several of these phytopathogenic species show wide genetic variability, which makes long-term maintenance of resistance in plants difficult. Different mechanisms may play an important role in the emergence of genetic variants but are not yet fully understood in this genus. These mechanisms include heterokaryosis, a parasexual cycle, sexual cycle, transposable element activity, and repeat-induced point mutations. This review provides an overview of the genus Colletotrichum, the species complexes described so far and the most common lifestyles in the genus, with a special emphasis on the mechanisms that may be responsible, at least in part, for the emergence of new genotypes under field conditions.
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Affiliation(s)
- Leandro Lopes da Silva
- Laboratório de Genética Molecular de Fungos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Hanna Lorena Alvarado Moreno
- Laboratório de Genética Molecular de Fungos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Hilberty Lucas Nunes Correia
- Laboratório de Genética Molecular de Fungos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Mateus Ferreira Santana
- Laboratório de Genética Molecular de Fungos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marisa Vieira de Queiroz
- Laboratório de Genética Molecular de Fungos, Departamento de Microbiologia/Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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29
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Venice F, Ghignone S, Salvioli di Fossalunga A, Amselem J, Novero M, Xianan X, Sędzielewska Toro K, Morin E, Lipzen A, Grigoriev IV, Henrissat B, Martin FM, Bonfante P. At the nexus of three kingdoms: the genome of the mycorrhizal fungus Gigaspora margarita provides insights into plant, endobacterial and fungal interactions. Environ Microbiol 2019; 22:122-141. [PMID: 31621176 DOI: 10.1111/1462-2920.14827] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/16/2019] [Accepted: 09/20/2019] [Indexed: 01/04/2023]
Abstract
As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize plant roots. AMF also possess their own microbiota, hosting some uncultivable endobacteria. Ongoing research has revealed the genetics underlying plant responses to colonization by AMF, but the fungal side of the relationship remains in the dark. Here, we sequenced the genome of Gigaspora margarita, a member of the Gigasporaceae in an early diverging group of the Glomeromycotina. In contrast to other AMF, G. margarita may host distinct endobacterial populations and possesses the largest fungal genome so far annotated (773.104 Mbp), with more than 64% transposable elements. Other unique traits of the G. margarita genome include the expansion of genes for inorganic phosphate metabolism, the presence of genes for production of secondary metabolites and a considerable number of potential horizontal gene transfer events. The sequencing of G. margarita genome reveals the importance of its immune system, shedding light on the evolutionary pathways that allowed early diverging fungi to interact with both plants and bacteria.
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Affiliation(s)
- Francesco Venice
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection-CNR, Turin Unit, Turin, Italy
| | | | | | - Mara Novero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Xie Xianan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Key Laboratory of Innovation and Utilization of Forest Plant Germplasm in Guangdong Province, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Kinga Sędzielewska Toro
- Genetics, Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR, 1136, Champenoux, France
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France.,Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Francis M Martin
- Institut National de la Recherche Agronomique (INRA), Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR, 1136, Champenoux, France
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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30
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The Parauncinula polyspora Draft Genome Provides Insights into Patterns of Gene Erosion and Genome Expansion in Powdery Mildew Fungi. mBio 2019; 10:mBio.01692-19. [PMID: 31551331 PMCID: PMC6759760 DOI: 10.1128/mbio.01692-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Powdery mildew fungi are widespread and agronomically relevant phytopathogens causing major yield losses. Their genomes have disproportionately large numbers of mobile genetic elements, and they have experienced a significant loss of highly conserved fungal genes. In order to learn more about the evolutionary history of this fungal group, we explored the genome of an Asian oak tree pathogen, Parauncinula polyspora, a species that diverged early during evolution from the remaining powdery mildew fungi. We found that the P. polyspora draft genome is comparatively compact, has a low number of protein-coding genes, and, despite the absence of a dedicated genome defense system, lacks the massive proliferation of repetitive sequences. Based on these findings, we infer an evolutionary trajectory that shaped the genomes of powdery mildew fungi. Due to their comparatively small genome size and short generation time, fungi are exquisite model systems to study eukaryotic genome evolution. Powdery mildew fungi present an exceptional case because of their strict host dependency (termed obligate biotrophy) and the atypical size of their genomes (>100 Mb). This size expansion is largely due to the pervasiveness of transposable elements on 70% of the genome and is associated with the loss of multiple conserved ascomycete genes required for a free-living lifestyle. To date, little is known about the mechanisms that drove these changes, and information on ancestral powdery mildew genomes is lacking. We report genome analysis of the early-diverged and exclusively sexually reproducing powdery mildew fungus Parauncinula polyspora, which we performed on the basis of a natural leaf epiphytic metapopulation sample. In contrast to other sequenced species of this taxonomic group, the assembled P. polyspora draft genome is surprisingly small (<30 Mb), has a higher content of conserved ascomycete genes, and is sparsely equipped with transposons (<10%), despite the conserved absence of a common defense mechanism involved in constraining repetitive elements. We speculate that transposable element spread might have been limited by this pathogen’s unique reproduction strategy and host features and further hypothesize that the loss of conserved ascomycete genes may promote the evolutionary isolation and host niche specialization of powdery mildew fungi. Limitations associated with this evolutionary trajectory might have been in part counteracted by the evolution of plastic, transposon-rich genomes and/or the expansion of gene families encoding secreted virulence proteins.
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31
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Transposon-Mediated Horizontal Transfer of the Host-Specific Virulence Protein ToxA between Three Fungal Wheat Pathogens. mBio 2019; 10:mBio.01515-19. [PMID: 31506307 PMCID: PMC6737239 DOI: 10.1128/mbio.01515-19] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This work dissects the tripartite horizontal transfer of ToxA, a gene that has a direct negative impact on global wheat yields. Defining the extent of horizontally transferred DNA is important because it can provide clues to the mechanisms that facilitate HGT. Our analysis of ToxA and its surrounding 14 kb suggests that this gene was horizontally transferred in two independent events, with one event likely facilitated by a type II DNA transposon. These horizontal transfer events are now in various processes of decay in each species due to the repeated insertion of new transposons and subsequent rounds of targeted mutation by a fungal genome defense mechanism known as repeat induced point mutation. This work highlights the role that HGT plays in the evolution of host adaptation in eukaryotic pathogens. It also increases the growing body of evidence indicating that transposons facilitate adaptive HGT events between fungi present in similar environments and hosts. Most known examples of horizontal gene transfer (HGT) between eukaryotes are ancient. These events are identified primarily using phylogenetic methods on coding regions alone. Only rarely are there examples of HGT where noncoding DNA is also reported. The gene encoding the wheat virulence protein ToxA and the surrounding 14 kb is one of these rare examples. ToxA has been horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis, and Bipolaris sorokiniana) as part of a conserved ∼14 kb element which contains coding and noncoding regions. Here we used long-read sequencing to define the extent of HGT between these three fungal species. Construction of near-chromosomal-level assemblies enabled identification of terminal inverted repeats on either end of the 14 kb region, typical of a type II DNA transposon. This is the first description of ToxA with complete transposon features, which we call ToxhAT. In all three species, ToxhAT resides in a large (140-to-250 kb) transposon-rich genomic island which is absent in isolates that do not carry the gene (annotated here as toxa−). We demonstrate that the horizontal transfer of ToxhAT between P. tritici-repentis and P. nodorum occurred as part of a large (∼80 kb) HGT which is now undergoing extensive decay. In B. sorokiniana, in contrast, ToxhAT and its resident genomic island are mobile within the genome. Together, these data provide insight into the noncoding regions that facilitate HGT between eukaryotes and into the genomic processes which mask the extent of HGT between these species.
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32
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Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, Tang H, Farman M, Cook D, White FF, Valent B, Liu S. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genet 2019; 15:e1008272. [PMID: 31513573 PMCID: PMC6741851 DOI: 10.1371/journal.pgen.1008272] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 11/28/2022] Open
Abstract
Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome.
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Affiliation(s)
- Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, China
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
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Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, Tang H, Farman M, Cook D, White FF, Valent B, Liu S. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genet 2019; 15:e1008272. [PMID: 31513573 DOI: 10.1101/359455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 05/26/2023] Open
Abstract
Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome.
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Affiliation(s)
- Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, China
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
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Dhillon B, Kema GHJ, Hamelin RC, Bluhm BH, Goodwin SB. Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene. Mob DNA 2019; 10:37. [PMID: 31462936 PMCID: PMC6710886 DOI: 10.1186/s13100-019-0177-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/05/2019] [Indexed: 11/24/2022] Open
Abstract
Background Transposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. For example, a DNA methyltransferase gene in the wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) was amplified to tens of copies, all of which were inactivated by Repeat-Induced Point mutation (RIP) including the original, resulting in loss of cytosine methylation. In another wheat pathogen, Pyrenophora tritici-repentis, a histone H3 gene was amplified to tens of copies with little evidence of RIP, leading to many potentially active copies. To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, Pseudocercospora fijiensis, was analyzed in greater detail. Results These analyses identified a housekeeping gene, histone H3, which was captured and amplified to hundreds of copies by a hAT DNA transposon, all of which were inactivated by RIP, except for the original. In P. fijiensis the original H3 gene probably was not protected from RIP, but most likely was maintained intact due to strong purifying selection. Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal genera Cercospora, Pseudocercospora and Sphaerulina. Conclusions These results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution. Electronic supplementary material The online version of this article (10.1186/s13100-019-0177-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Braham Dhillon
- 1Department of Plant Pathology, Division of Agriculture, University of Arkansas, Fayetteville, AR USA
| | - Gert H J Kema
- 2Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands.,3Plant Research International B.V, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Richard C Hamelin
- 4Faculty of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC Canada
| | - Burt H Bluhm
- 1Department of Plant Pathology, Division of Agriculture, University of Arkansas, Fayetteville, AR USA
| | - Stephen B Goodwin
- 5U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Crop Production and Pest Control Research Unit, Purdue University, West Lafayette, IN USA
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van Wyk S, Harrison CH, Wingfield BD, De Vos L, van der Merwe NA, Steenkamp ET. The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations. PeerJ 2019; 7:e7447. [PMID: 31523495 PMCID: PMC6714961 DOI: 10.7717/peerj.7447] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022] Open
Abstract
Background The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes. Results We demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses. Conclusion This software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses.
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Affiliation(s)
- Stephanie van Wyk
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa
| | - Christopher H Harrison
- Department of product and software development, Amplo PTY, Pretoria, Gauteng, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa
| | - Nicolaas A van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, Gauteng, South Africa
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van de Vossenberg BTLH, Warris S, Nguyen HDT, van Gent-Pelzer MPE, Joly DL, van de Geest HC, Bonants PJM, Smith DS, Lévesque CA, van der Lee TAJ. Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. Sci Rep 2019; 9:8672. [PMID: 31209237 PMCID: PMC6572847 DOI: 10.1038/s41598-019-45128-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/31/2019] [Indexed: 01/09/2023] Open
Abstract
Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.
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Affiliation(s)
- Bart T L H van de Vossenberg
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands.
- Dutch National Plant Protection Organization, National Reference Centre, Geertjesweg 15, 6706EA, Wageningen, The Netherlands.
| | - Sven Warris
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Hai D T Nguyen
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Marga P E van Gent-Pelzer
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - David L Joly
- Université de Moncton, 18 avenue Antonine-Maillet, Moncton, Canada
| | - Henri C van de Geest
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Peter J M Bonants
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
| | - Donna S Smith
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, Canada
| | - C André Lévesque
- Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Canada
| | - Theo A J van der Lee
- Wageningen University & Research, Droevendaalsesteeg 1, Plant Science Group, 6708PB, Wageningen, The Netherlands
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Lelwala RV, Korhonen PK, Young ND, Scott JB, Ades PK, Gasser RB, Taylor PWJ. Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti. PLoS One 2019; 14:e0212248. [PMID: 31150449 PMCID: PMC6544218 DOI: 10.1371/journal.pone.0212248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/02/2019] [Indexed: 01/30/2023] Open
Abstract
Colletotrichum tanaceti is an emerging foliar fungal pathogen of commercially grown pyrethrum (Tanacetum cinerariifolium). Despite being reported consistently from field surveys in Australia, the molecular basis of pathogenicity of C. tanaceti on pyrethrum is unknown. Herein, the genome of C. tanaceti (isolate BRIP57314) was assembled de novo and annotated using transcriptomic evidence. The inferred putative pathogenicity gene suite of C. tanaceti comprised a large array of genes encoding secreted effectors, proteases, CAZymes and secondary metabolites. Comparative analysis of its putative pathogenicity gene profiles with those of closely related species suggested that C. tanaceti likely has additional hosts to pyrethrum. The genome of C. tanaceti had a high repeat content and repetitive elements were located significantly closer to genes inferred to influence pathogenicity than other genes. These repeats are likely to have accelerated mutational and transposition rates in the genome, resulting in a rapid evolution of certain CAZyme families in this species. The C. tanaceti genome showed strong signals of Repeat Induced Point (RIP) mutation which likely caused its bipartite nature consisting of distinct gene-sparse, repeat and A-T rich regions. Pathogenicity genes within these RIP affected regions were likely to have a higher evolutionary rate than the rest of the genome. This "two-speed" genome phenomenon in certain Colletotrichum spp. was hypothesized to have caused the clustering of species based on the pathogenicity genes, to deviate from taxonomic relationships. The large repertoire of pathogenicity factors that potentially evolve rapidly due to the plasticity of the genome, indicated that C. tanaceti has a high evolutionary potential. Therefore, C. tanaceti poses a high-risk to the pyrethrum industry. Knowledge of the evolution and diversity of the putative pathogenicity genes will facilitate future research in disease management of C. tanaceti and other Colletotrichum spp.
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Affiliation(s)
- Ruvini V. Lelwala
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jason B. Scott
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania, Australia
| | - Peter K. Ades
- Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul W. J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Mousavi-Derazmahalleh M, Chang S, Thomas G, Derbyshire M, Bayer PE, Edwards D, Nelson MN, Erskine W, Lopez-Ruiz FJ, Clements J, Hane JK. Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics. BMC Genomics 2019; 20:385. [PMID: 31101009 PMCID: PMC6525431 DOI: 10.1186/s12864-019-5774-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 05/03/2019] [Indexed: 01/13/2023] Open
Abstract
Background Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea – both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts. Results Genomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum, which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents. Conclusions Detection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens. Electronic supplementary material The online version of this article (10.1186/s12864-019-5774-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Steven Chang
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Geoff Thomas
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Mark Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Phillip E Bayer
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Matthew N Nelson
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex, RH17 6TN, UK.,Current address: Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Wembley, WA, 6913, Australia
| | - William Erskine
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Jon Clements
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - James K Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia. .,Curtin Institute for Computation, Curtin University, Bentley, WA, 6102, Australia.
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Valero-Jiménez CA, Veloso J, Staats M, van Kan JAL. Comparative genomics of plant pathogenic Botrytis species with distinct host specificity. BMC Genomics 2019; 20:203. [PMID: 30866801 PMCID: PMC6417074 DOI: 10.1186/s12864-019-5580-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/03/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae. RESULTS Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed. CONCLUSIONS Comparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.
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Affiliation(s)
| | - Javier Veloso
- Laboratory of Phytopathology, Wageningen University, 6708PB Wageningen, the Netherlands
- Department of Biology, Faculty of Sciences, University of A Coruña, A Coruña, Spain
| | - Martijn Staats
- Biosystematics Group, Wageningen University, 6708PB Wageningen, the Netherlands
- Present address: RIKILT Wageningen University and Research, 6708WB Wageningen, the Netherlands
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, 6708PB Wageningen, the Netherlands
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40
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Botcinic acid biosynthesis in Botrytis cinerea relies on a subtelomeric gene cluster surrounded by relics of transposons and is regulated by the Zn2Cys6 transcription factor BcBoa13. Curr Genet 2019; 65:965-980. [DOI: 10.1007/s00294-019-00952-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 01/11/2023]
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41
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Van de Wouw AP, Elliott CE, Popa KM, Idnurm A. Analysis of Repeat Induced Point (RIP) Mutations in Leptosphaeria maculans Indicates Variability in the RIP Process Between Fungal Species. Genetics 2019; 211:89-104. [PMID: 30389803 PMCID: PMC6325690 DOI: 10.1534/genetics.118.301712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/24/2018] [Indexed: 01/01/2023] Open
Abstract
Gene duplication contributes to evolutionary potential, yet many duplications in a genome arise from the activity of "selfish" genetic elements such as transposable elements. Fungi have a number of mechanisms by which they limit the expansion of transposons, including Repeat Induced Point mutation (RIP). RIP has been best characterized in the Sordariomycete Neurospora crassa, wherein duplicated DNA regions are recognized after cell fusion, but before nuclear fusion during the sexual cycle, and then mutated. While "signatures" of RIP appear in the genome sequences of many fungi, the species most distant from N. crassa in which the process has been experimentally demonstrated to occur is the Dothideomycete Leptosphaeria maculans In the current study, we show that similar to N. crassa, nonlinked duplications can trigger RIP; however, the frequency of the generated RIP mutations is extremely low in L maculans (< 0.1%) and requires a large duplication to initiate RIP, and that multiple premeiotic mitoses are involved in the RIP process. However, a single sexual cycle leads to the generation of progeny with unique haplotypes, despite progeny pairs being generated from mitosis. We hypothesize that these different haplotypes may be the result of the deamination process occurring post karyogamy, leading to unique mutations within each of the progeny pairs. These findings indicate that the RIP process, while common to many fungi, differs between fungi and that this impacts on the fate of duplicated DNA.
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Affiliation(s)
- Angela P Van de Wouw
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Candace E Elliott
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kerryn M Popa
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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Rao S, Sharda S, Oddi V, Nandineni MR. The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum. Front Microbiol 2018; 9:2367. [PMID: 30337918 PMCID: PMC6180176 DOI: 10.3389/fmicb.2018.02367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022] Open
Abstract
The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and "two-speed" genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.
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Affiliation(s)
- Soumya Rao
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Saphy Sharda
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vineesha Oddi
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Syme RA, Tan KC, Rybak K, Friesen TL, McDonald BA, Oliver RP, Hane JK. Pan-Parastagonospora Comparative Genome Analysis-Effector Prediction and Genome Evolution. Genome Biol Evol 2018; 10:2443-2457. [PMID: 30184068 PMCID: PMC6152946 DOI: 10.1093/gbe/evy192] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2018] [Indexed: 01/01/2023] Open
Abstract
We report a fungal pan-genome study involving Parastagonospora spp., including 21 isolates of the wheat (Triticum aestivum) pathogen Parastagonospora nodorum, 10 of the grass-infecting Parastagonospora avenae, and 2 of a closely related undefined sister species. We observed substantial variation in the distribution of polymorphisms across the pan-genome, including repeat-induced point mutations, diversifying selection and gene gains and losses. We also discovered chromosome-scale inter and intraspecific presence/absence variation of some sequences, suggesting the occurrence of one or more accessory chromosomes or regions that may play a role in host-pathogen interactions. The presence of known pathogenicity effector loci SnToxA, SnTox1, and SnTox3 varied substantially among isolates. Three P. nodorum isolates lacked functional versions for all three loci, whereas three P. avenae isolates carried one or both of the SnTox1 and SnTox3 genes, indicating previously unrecognized potential for discovering additional effectors in the P. nodorum-wheat pathosystem. We utilized the pan-genomic comparative analysis to improve the prediction of pathogenicity effector candidates, recovering the three confirmed effectors among our top-ranked candidates. We propose applying this pan-genomic approach to identify the effector repertoire involved in other host-microbe interactions involving necrotrophic pathogens in the Pezizomycotina.
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Affiliation(s)
- Robert A Syme
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Kasia Rybak
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Timothy L Friesen
- Cereal Crops Research Unit, USDA-ARS Red River Valley Agricultural Research Center, Fargo, North Dakota
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Richard P Oliver
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - James K Hane
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Curtin Institute for Computation, Curtin University, Bentley, Western Australia, Australia
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Rivera Y, Salgado-Salazar C, Veltri D, Malapi-Wight M, Crouch JA. Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola. PeerJ 2018; 6:e5401. [PMID: 30155349 PMCID: PMC6110257 DOI: 10.7717/peerj.5401] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/18/2018] [Indexed: 01/15/2023] Open
Abstract
Boxwood (Buxus spp.) are broad-leaved, evergreen landscape plants valued for their longevity and ornamental qualities. Volutella leaf and stem blight, caused by the ascomycete fungi Pseudonectria foliicola and P. buxi, is one of the major diseases affecting the health and ornamental qualities of boxwood. Although this disease is less severe than boxwood blight caused by Calonectria pseudonaviculata and C. henricotiae, its widespread occurrence and disfiguring symptoms have caused substantial economic losses to the ornamental industry. In this study, we sequenced the genome of P. foliicola isolate ATCC13545 using Illumina technology and compared it to other publicly available fungal pathogen genomes to better understand the biology of this organism. A de novo assembly estimated the genome size of P. foliicola at 28.7 Mb (425 contigs; N50 = 184,987 bp; avg. coverage 188×), with just 9,272 protein-coding genes. To our knowledge, P. foliicola has the smallest known genome within the Nectriaceae. Consistent with the small size of the genome, the secretome, CAzyme and secondary metabolite profiles of this fungus are reduced relative to two other surveyed Nectriaceae fungal genomes: Dactylonectria macrodidyma JAC15-245 and Fusarium graminearum Ph-1. Interestingly, a large cohort of genes associated with reduced virulence and loss of pathogenicity was identified from the P. foliicola dataset. These data are consistent with the latest observations by plant pathologists that P. buxi and most likely P. foliicola, are opportunistic, latent pathogens that prey upon weak and stressed boxwood plants.
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Affiliation(s)
- Yazmín Rivera
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
- Current affiliation: Center for Plant Health, Science and Technology, USDA, Animal and Plant Health Inspection Service, Beltsville, MD, United States of America
| | - Catalina Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
- Department of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States of America
- ARS Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Daniel Veltri
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
- ARS Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
- Current affiliation: Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, United States of America
| | - Martha Malapi-Wight
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
- Current affiliation: Plant Germplasm Quarantine Program, USDA, Animal and Plant Health Inspection Service, Beltsville, MD, United States of America
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, US Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States of America
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Wang B, Liang X, Gleason ML, Zhang R, Sun G. Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation. IMA Fungus 2018; 9:243-257. [PMID: 30622881 PMCID: PMC6317582 DOI: 10.5598/imafungus.2018.09.02.02] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 08/10/2018] [Indexed: 12/25/2022] Open
Abstract
Ring rot, one of the most destructive diseases of apple worldwide, is caused primarily by Botryosphaeria dothidea and B. kuwatsukai. Here, we sequenced the genomes of B. dothidea strain PG45 (44.3 Mb with 5.12 % repeat rate) and B. kuwatsukai epitype strain PG2 (48.0 Mb with 13.02 % repeat rate), and conducted a comparative analysis of these two genomes, as well as other sequenced fungal genomes, in order to understand speciation and distinctive patterns of evolution of pathogenicity-related genes. Pair-wise genome alignments revealed that the two species are highly syntenic (96.74 % average sequence identity). Both species encode a significant number of pathogenicity-related genes, e.g. carbohydrate active enzymes (CAZYs), plant cell wall degrading enzymes (PCWDEs), secondary metabolites (SMs) biosynthetic enzymes, cytochrome P450 enzymes (CYPs), and secreted peptidases, in comparison to all additional sequenced fungal species involved in various life-styles. The number of pathogenicity-related genes in B. dothidea and B. kuwatsukai is higher than other genomes of Botryosphaeriaceae pathogens (Macrophomina phaseolina and Neofusicoccum parvum), suggesting a secondary round of Botryosphaeria-lineage expansion in the family. There were, however, also significant differences in the genomes of the two Botryosphaeria species. Botryosphaeria kuwatsukai, which infects only apple and pear, apparently lost a set of SMs genes, CAZYs and PCWDEs, possibly as a result of host specialization. Botryosphaeria kuwatsukai contained significantly more transposable elements and higher value of repeat induced point (RIP) index than B. dothidea. Our results will be instrumental in understanding how both phytopathogens interact with their plant hosts and in designing efficient strategies for disease control and molecular breeding to help ensure global apple production and food security.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100, China
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Moolhuijzen P, See PT, Hane JK, Shi G, Liu Z, Oliver RP, Moffat CS. Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity. BMC Genomics 2018; 19:279. [PMID: 29685100 PMCID: PMC5913888 DOI: 10.1186/s12864-018-4680-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/16/2018] [Indexed: 02/08/2023] Open
Abstract
Background Pyrenophora tritici-repentis (Ptr) is a necrotrophic fungal pathogen that causes the major wheat disease, tan spot. We set out to provide essential genomics-based resources in order to better understand the pathogenicity mechanisms of this important pathogen. Results Here, we present eight new Ptr isolate genomes, assembled and annotated; representing races 1, 2 and 5, and a new race. We report a high quality Ptr reference genome, sequenced by PacBio technology with Illumina paired-end data support and optical mapping. An estimated 98% of the genome coverage was mapped to 10 chromosomal groups, using a two-enzyme hybrid approach. The final reference genome was 40.9 Mb and contained a total of 13,797 annotated genes, supported by transcriptomic and proteogenomics data sets. Conclusions Whole genome comparative analysis revealed major chromosomal segmental rearrangements and fusions, highlighting intraspecific genome plasticity in this species. Furthermore, the Ptr race classification was not supported at the whole genome level, as phylogenetic analysis did not cluster the ToxA producing isolates. This expansion of available Ptr genomics resources will directly facilitate research aimed at controlling tan spot disease. Electronic supplementary material The online version of this article (10.1186/s12864-018-4680-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paula Moolhuijzen
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia.
| | - Pao Theen See
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - James K Hane
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Richard P Oliver
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | - Caroline S Moffat
- Centre for Crop Disease and Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
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Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi. Sci Rep 2018; 8:5862. [PMID: 29651164 PMCID: PMC5897359 DOI: 10.1038/s41598-018-24301-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/29/2018] [Indexed: 11/08/2022] Open
Abstract
The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.
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McDonald MC, Ahren D, Simpfendorfer S, Milgate A, Solomon PS. The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana. MOLECULAR PLANT PATHOLOGY 2018; 19:432-439. [PMID: 28093843 PMCID: PMC6638140 DOI: 10.1111/mpp.12535] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 05/18/2023]
Abstract
Bipolaris sorokiniana is the causal agent of multiple diseases on wheat and barley and is the primary constraint to cereal production throughout South Asia. Despite its significance, the molecular basis of disease is poorly understood. To address this, the genomes of three Australian isolates of B. sorokiniana were sequenced and screened for known pathogenicity genes. Sequence analysis revealed that the isolate BRIP10943 harboured the ToxA gene, which has been associated previously with disease in the wheat pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis. Analysis of the regions flanking ToxA within B. sorokiniana revealed that it was embedded within a 12-kb genomic element nearly identical to the corresponding regions in P. nodorum and P. tritici-repentis. A screen of 35 Australian B. sorokiniana isolates confirmed that ToxA was present in 12 isolates. Sequencing of the ToxA genes within these isolates revealed two haplotypes, which differed by a single non-synonymous nucleotide substitution. Pathogenicity assays showed that a B. sorokiniana isolate harbouring ToxA was more virulent on wheat lines that contained the sensitivity gene when compared with a non-ToxA isolate. This work demonstrates that proteins that confer host-specific virulence can be horizontally acquired across multiple species. This acquisition can dramatically increase the virulence of pathogenic strains on susceptible cultivars, which, in an agricultural setting, can have devastating economic and social impacts.
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Affiliation(s)
- Megan C. McDonald
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityCanberra2601Australia
| | - Dag Ahren
- Department of BiologyLund UniversityLund22101Sweden
| | - Steven Simpfendorfer
- SW Department of Primary IndustriesTamworth Agricultural InstituteTamworthNSW2340Australia
| | - Andrew Milgate
- NSW Department of Primary IndustriesWagga Wagga Agricultural InstituteWagga WaggaNSW2650Australia
| | - Peter S. Solomon
- Plant Sciences Division, Research School of BiologyThe Australian National UniversityCanberra2601Australia
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Molano EPL, Cabrera OG, Jose J, do Nascimento LC, Carazzolle MF, Teixeira PJPL, Alvarez JC, Tiburcio RA, Tokimatu Filho PM, de Lima GMA, Guido RVC, Corrêa TLR, Leme AFP, Mieczkowski P, Pereira GAG. Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC). BMC Genomics 2018; 19:58. [PMID: 29343217 PMCID: PMC5773145 DOI: 10.1186/s12864-018-4440-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. RESULTS We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. CONCLUSION Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity.
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Affiliation(s)
- Eddy Patricia Lopez Molano
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Odalys García Cabrera
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Juliana Jose
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | | | - Marcelo Falsarella Carazzolle
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.,Centro Nacional de Processamento de Alto Desempenho, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo José Pereira Lima Teixeira
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.,Present Address: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Javier Correa Alvarez
- Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Medellın, Colombia
| | - Ricardo Augusto Tiburcio
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Paulo Massanari Tokimatu Filho
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Gustavo Machado Alvares de Lima
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael Victório Carvalho Guido
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | | | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Gonçalo Amarante Guimarães Pereira
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.
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Li WC, Chen CL, Wang TF. Repeat-induced point (RIP) mutation in the industrial workhorse fungus Trichoderma reesei. Appl Microbiol Biotechnol 2018; 102:1567-1574. [DOI: 10.1007/s00253-017-8731-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 02/01/2023]
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