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Zhang S, Li R, Fan W, Chen X, Liu S, Zhu P, Gu X, Wang S, Zhao A. Effector Cs02526 from Ciboria shiraiana induces cell death and modulates plant immunity. PLANT PHYSIOLOGY 2024; 196:579-591. [PMID: 38753366 DOI: 10.1093/plphys/kiae286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 09/03/2024]
Abstract
Sclerotinia disease is one of the most devastating fungal diseases worldwide, as it reduces the yields of many economically important crops. Pathogen-secreted effectors play crucial roles in infection processes. However, key effectors of Ciboria shiraiana, the pathogen primarily responsible for sclerotinia disease in mulberry (Morus spp.), remain poorly understood. In this study, we identified and functionally characterized the effector Cs02526 in C. shiraiana and found that Cs02526 could induce cell death in a variety of plants. Moreover, Cs02526-induced cell death was mediated by the central immune regulator brassinosteroid insensitive 1-associated receptor kinase 1, dependent on a 67-amino acid fragment. Notably, Cs02526 homologs were widely distributed in hemibiotrophic and necrotrophic phytopathogenic fungi, but the homologs failed to induce cell death in plants. Pretreatment of plants with recombinant Cs02526 protein enhanced resistance against both C. shiraiana and Sclerotinia sclerotiorum. Furthermore, the pathogenicity of C. shiraiana was diminished upon spraying plants with synthetic dsRNA-Cs02526. In conclusion, our findings highlight the cell death-inducing effector Cs02526 as a potential target for future biological control strategies against plant diseases.
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Affiliation(s)
- Shuai Zhang
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Ruolan Li
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Wei Fan
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Xuefei Chen
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Shuman Liu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Panpan Zhu
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, China
| | - Xiaohui Gu
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
| | - Shuchang Wang
- Chinese Academy of Tropical Agricultural Sciences, Institute of Environment and Plant Protection, Haikou 570100, China
| | - Aichun Zhao
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China
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2
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He H, Xu T, Cao F, Xu Y, Dai T, Liu T. PcAvh87, a virulence essential RxLR effector of Phytophthora cinnamomi suppresses host defense and induces cell death in plant nucleus. Microbiol Res 2024; 286:127789. [PMID: 38870619 DOI: 10.1016/j.micres.2024.127789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
Plants have developed intricate immune mechanisms to impede Phytophthora colonization. In response, Phytophthora secretes RxLR effector proteins that disrupt plant defense and promote infection. The specific molecular interactions through which Phytophthora RxLR effectors undermine plant immunity, however, remain inadequately defined. In this study, we delineate the role of the nuclear-localized RxLR effector PcAvh87, which is pivotal for the full virulence of Phytophthora cinnamomi. Gene expression analysis indicates that PcAvh87 expression is significantly upregulated during the initial infection stages, interacting with the immune responses triggered by the elicitin protein INF1 and pro-apoptotic protein BAX. Utilizing PEG/CaCl2-mediated protoplast transformation and CRISPR/Cas9-mediated gene editing, we generated PcAvh87 knockout mutants, which demonstrated compromised hyphal growth, sporangium development, and zoospore release, along with a marked reduction in pathogenicity. This underscores PcAvh87's crucial role as a virulence determinant. Notably, PcAvh87, conserved across the Phytophthora genus, was found to modulate the activity of plant immune protein 113, thereby attenuating plant immune responses. This implies that the PcAvh87-mediated regulatory mechanism could be a common strategy in Phytophthora species to manipulate plant immunity. Our findings highlight the multifaceted roles of PcAvh87 in promoting P. cinnamomi infection, including its involvement in sporangia production, mycelial growth, and the targeting of plant immune proteins to enhance pathogen virulence.
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Affiliation(s)
- Haibin He
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingyan Xu
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Fuliang Cao
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yue Xu
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingting Dai
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China.
| | - Tingli Liu
- School of Food Science, Nanjing Xiaozhuang University, 3601 Hongjin Avenue, Nanjing 211171, China.
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3
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Netherway T, Bahram M. Melanized root-associated fungi: key players in plant-soil systems. Trends Microbiol 2024:S0966-842X(24)00169-0. [PMID: 38987052 DOI: 10.1016/j.tim.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024]
Abstract
Melanized root-associated fungi are a group of fungi that produce melanized structures and form root associations, including different mycorrhizal and endophytic symbioses with plants. They are pervasive across terrestrial ecosystems and play an important role in the prevailing soil carbon (C) and nutrient cycling syndromes through direct and indirect mechanisms, where they may strongly modulate plant-microbe interactions and structure root and soil microbiomes. Furthermore, melanized root-associated fungi can confer on plants an enhanced ability to tolerate abiotic and biotic stressors such as drought, extreme temperatures, heavy metals, and pathogen attacks. We propose that melanized root-associated fungi are a cohesive and ecologically relevant grouping that can be an indicator of plant-soil system functioning, and considering them will advance research on plant-soil interactions.
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Affiliation(s)
- Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden.
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden; Department of Agroecology, Aarhus University, Slagelse, Denmark; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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4
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Guan Y, Gajewska J, Floryszak‐Wieczorek J, Tanwar UK, Sobieszczuk‐Nowicka E, Arasimowicz‐Jelonek M. Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology. MOLECULAR PLANT PATHOLOGY 2024; 25:e13497. [PMID: 39034655 PMCID: PMC11261156 DOI: 10.1111/mpp.13497] [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: 10/04/2023] [Revised: 06/21/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024]
Abstract
Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant-damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome- and proteome-level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro-oxidative stress is also briefly discussed.
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Affiliation(s)
- Yufeng Guan
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Joanna Gajewska
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | | | - Umesh Kumar Tanwar
- Department of Plant Physiology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Ewa Sobieszczuk‐Nowicka
- Department of Plant Physiology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Magdalena Arasimowicz‐Jelonek
- Department of Plant Ecophysiology, Institute of Experimental Biology, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
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5
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Rodenburg SYA, de Ridder D, Govers F, Seidl MF. Oomycete Metabolism Is Highly Dynamic and Reflects Lifestyle Adaptations. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:571-582. [PMID: 38648121 DOI: 10.1094/mpmi-12-23-0200-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The selective pressure of pathogen-host symbiosis drives adaptations. How these interactions shape the metabolism of pathogens is largely unknown. Here, we use comparative genomics to systematically analyze the metabolic networks of oomycetes, a diverse group of eukaryotes that includes saprotrophs as well as animal and plant pathogens, with the latter causing devastating diseases with significant economic and/or ecological impacts. In our analyses of 44 oomycete species, we uncover considerable variation in metabolism that can be linked to lifestyle differences. Comparisons of metabolic gene content reveal that plant pathogenic oomycetes have a bipartite metabolism consisting of a conserved core and an accessory set. The accessory set can be associated with the degradation of defense compounds produced by plants when challenged by pathogens. Obligate biotrophic oomycetes have smaller metabolic networks, and taxonomically distantly related biotrophic lineages display convergent evolution by repeated gene losses in both the conserved as well as the accessory set of metabolisms. When investigating to what extent the metabolic networks in obligate biotrophs differ from those in hemibiotrophic plant pathogens, we observe that the losses of metabolic enzymes in obligate biotrophs are not random and that gene losses predominantly influence the terminal branches of the metabolic networks. Our analyses represent the first metabolism-focused comparison of oomycetes at this scale and will contribute to a better understanding of the evolution of oomycete metabolism in relation to lifestyle adaptation. Numerous oomycete species are devastating plant pathogens that cause major damage in crops and natural ecosystems. Their interactions with hosts are shaped by strong selection, but how selection affects adaptation of the primary metabolism to a pathogenic lifestyle is not yet well established. By pan-genome and metabolic network analyses of distantly related oomycete pathogens and their nonpathogenic relatives, we reveal considerable lifestyle- and lineage-specific adaptations. This study contributes to a better understanding of metabolic adaptations in pathogenic oomycetes in relation to lifestyle, host, and environment, and the findings will help in pinpointing potential targets for disease control. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Sander Y A Rodenburg
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Bioinformatics Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Wageningen, the Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
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6
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Lin L, Sun T, Guo J, Lin L, Chen M, Wang Z, Bao J, Norvienyeku J, Zhang D, Han Y, Lu G, Rensing C, Zheng H, Zhong Z, Wang Z. Transposable elements impact the population divergence of rice blast fungus Magnaporthe oryzae. mBio 2024; 15:e0008624. [PMID: 38534157 PMCID: PMC11077969 DOI: 10.1128/mbio.00086-24] [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: 01/13/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Dynamic transposition of transposable elements (TEs) in fungal pathogens has significant impact on genome stability, gene expression, and virulence to the host. In Magnaporthe oryzae, genome plasticity resulting from TE insertion is a major driving force leading to the rapid evolution and diversification of this fungus. Despite their importance in M. oryzae population evolution and divergence, our understanding of TEs in this context remains limited. Here, we conducted a genome-wide analysis of TE transposition dynamics in the 11 most abundant TE families in M. oryzae populations. Our results show that these TEs have specifically expanded in recently isolated M. oryzae rice populations, with the presence/absence polymorphism of TE insertions highly concordant with population divergence on Geng/Japonica and Xian/Indica rice cultivars. Notably, the genes targeted by clade-specific TEs showed clade-specific expression patterns and are involved in the pathogenic process, suggesting a transcriptional regulation of TEs on targeted genes. Our study provides a comprehensive analysis of TEs in M. oryzae populations and demonstrates a crucial role of recent TE bursts in adaptive evolution and diversification of the M. oryzae rice-infecting lineage. IMPORTANCE Magnaporthe oryzae is the causal agent of the destructive blast disease, which caused massive loss of yield annually worldwide. The fungus diverged into distinct clades during adaptation toward the two rice subspecies, Xian/Indica and Geng/Japonica. Although the role of TEs in the adaptive evolution was well established, mechanisms underlying how TEs promote the population divergence of M. oryzae remain largely unknown. In this study, we reported that TEs shape the population divergence of M. oryzae by differentially regulating gene expression between Xian/Indica-infecting and Geng/Japonica-infecting populations. Our results revealed a TE insertion-mediated gene expression adaption that led to the divergence of M. oryzae population infecting different rice subspecies.
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Affiliation(s)
- Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ting Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Meilian Chen
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Zhe Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiandong Bao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Justice Norvienyeku
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China
| | - Dongmei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yijuan Han
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huakun Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
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7
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Liang D, Jiang Y, Zhang Y, Mao C, Ma T, Zhang C. The Comparative Genomics of Botryosphaeriaceae Suggests Gene Families of Botryosphaeria dothidea Related to Pathogenicity on Chinese Hickory Tree. J Fungi (Basel) 2024; 10:299. [PMID: 38667970 PMCID: PMC11051394 DOI: 10.3390/jof10040299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Trunk canker poses a major threat to the production of Chinese hickory tree (Carya cathayensis Sarg.), which is primarily determined by Botryosphaeriaceae. In our previous work, we identified Botryosphaeria dothidea as the predominant pathogen of this disease. However, it is still unclear about corresponding gene families and mechanisms associated with B. dothidea's pathogenicity on Chinese hickory tree. Here, we present a comparative analysis of high-quality genome assemblies of Botryosphaeria dothidea and other isolated pathogens, showing highly syntenic relationships between B. dothidea and its closely related species and the conservative evolution of the Botryosphaeriaceae family. Higher GC contents were found in the genomes of B. dothidea and three other isolated pathogens (Botryshaeria cortices, Botryshaeria fabicerciana, and Botryshaeria qingyuanensis) compared to Macrophomina phaseolina, Neofusicoccum parvum, Diplodia corticola, and Lasiodiplodia theobromae. An investigation of genes specific to or expanded in B. dothidea revealed that one secreted glucanase, one orsellinic acid biosynthesis enzyme, and two MFS transporters positively regulated B. dothidea's pathogenicity. We also observed an overrepresentation of viral integrase like gene and heterokaryon incompatibility proteins in the B. dothidea's genome. In addition, we observed one LRR-domain-containing protein and two Sec-domain-containing proteins (Sec_1 and Sec_7) that underwent positive selection. This study will help to understand B. dothidea's pathogenicity and potential influence on the infection of Chinese hickory, which will help in the development of disease control and ensure the security of Chinese hickory production.
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Affiliation(s)
| | | | | | | | - Tianlin Ma
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
| | - Chuanqing Zhang
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
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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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9
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van Westerhoven AC, Aguilera-Galvez C, Nakasato-Tagami G, Shi-Kunne X, Martinez de la Parte E, Chavarro-Carrero E, Meijer HJG, Feurtey A, Maryani N, Ordóñez N, Schneiders H, Nijbroek K, Wittenberg AHJ, Hofstede R, García-Bastidas F, Sørensen A, Swennen R, Drenth A, Stukenbrock EH, Kema GHJ, Seidl MF. Segmental duplications drive the evolution of accessory regions in a major crop pathogen. THE NEW PHYTOLOGIST 2024; 242:610-625. [PMID: 38402521 DOI: 10.1111/nph.19604] [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: 08/05/2023] [Accepted: 02/01/2024] [Indexed: 02/26/2024]
Abstract
Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions (ARs) that carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such ARs, often spanning entire chromosomes. The presence of specific ARs influences the host range, and horizontal transfer of ARs can modify the pathogenicity of the receiving strain. However, how these ARs evolve in strains that infect the same host remains largely unknown. We defined the pan-genome of 69 diverse F. oxysporum strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and analyzed the diversity and evolution of the ARs. Accessory regions in F. oxysporum strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta-induced effectors. We demonstrate that segmental duplications drive the evolution of ARs. Furthermore, we show that recent segmental duplications specifically in accessory chromosomes cause the expansion of ARs in F. oxysporum. Taken together, we conclude that extensive recent duplications drive the evolution of ARs in F. oxysporum, which contribute to the evolution of virulence.
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Affiliation(s)
- Anouk C van Westerhoven
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Carolina Aguilera-Galvez
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Giuliana Nakasato-Tagami
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Einar Martinez de la Parte
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Edgar Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Department Biointeractions and Plant Health, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Alice Feurtey
- Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
- Plant Pathology, Eidgenössische Technische Hochschule Zürich, Rämistrasse 101, 8092, Zürich, Switzerland
| | - Nani Maryani
- Biology Education, Universitas Sultan Ageng Tirtayasa, Jalan Raya Palka No.Km 3, 42163, Banten, Indonesia
| | - Nadia Ordóñez
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Harrie Schneiders
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | - Koen Nijbroek
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | | | - Rene Hofstede
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | | | - Anker Sørensen
- KeyGene, Agro Business Park 90, 6708 PW, Wageningen, the Netherlands
| | - Ronny Swennen
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, Catholic University of Leuven, Oude Markt 13, 3000, Leuven, Belgium
- International Institute of Tropical Agriculture, Plot 15 Naguru E Rd, Kampala, PO Box 7878, Uganda
| | - Andre Drenth
- The University of Queensland, St Lucia, 4072, Brisbane, Queensland, Australia
| | - Eva H Stukenbrock
- Christian-Albrechts University of Kiel, Christian-Albrechts-Platz 4, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306, Plön, Germany
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Michael F Seidl
- Department of Biology, Theoretical Biology & Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
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10
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Ma Y, Su S, Fu Z, Zhou C, Qiao B, Wu Y, Yuan YJ. Convenient synthesis and delivery of a megabase-scale designer accessory chromosome empower biosynthetic capacity. Cell Res 2024; 34:309-322. [PMID: 38332200 PMCID: PMC10978979 DOI: 10.1038/s41422-024-00934-3] [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: 07/21/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Synthetic biology confers new functions to hosts by introducing exogenous genetic elements, yet rebuilding complex traits that are based on large-scale genetic information remains challenging. Here, we developed a CRISPR/Cas9-mediated haploidization method that bypasses the natural process of meiosis. Based on the programmed haploidization in yeast, we further developed an easy-to-use method designated HAnDy (Haploidization-based DNA Assembly and Delivery in yeast) that enables efficient assembly and delivery of large DNA, with no need for any fussy in vitro manipulations. Using HAnDy, a de novo designed 1.024 Mb synthetic accessory chromosome (synAC) encoding 542 exogenous genes was parallelly assembled and then directly transferred to six phylogenetically diverse yeasts. The synAC significantly promotes hosts' adaptations and increases the scope of the metabolic network, which allows the emergence of valuable compounds. Our approach should facilitate the assembly and delivery of large-scale DNA for expanding and deciphering complex biological functions.
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Affiliation(s)
- Yuan Ma
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Shuxin Su
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Zongheng Fu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Chu Zhou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China.
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11
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Amezrou R, Ducasse A, Compain J, Lapalu N, Pitarch A, Dupont L, Confais J, Goyeau H, Kema GHJ, Croll D, Amselem J, Sanchez-Vallet A, Marcel TC. Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing. Nat Commun 2024; 15:1933. [PMID: 38431601 PMCID: PMC10908820 DOI: 10.1038/s41467-024-46191-1] [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: 12/23/2022] [Accepted: 02/14/2024] [Indexed: 03/05/2024] Open
Abstract
Knowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the genetic architecture of fungal pathogenicity often focus on large-effect effector genes triggering strong, qualitative resistance. It is not clear how this translates to predominately quantitative interactions. Here, we use the Zymoseptoria tritici-wheat model to elucidate the genetic architecture of quantitative pathogenicity and mechanisms mediating host adaptation. With a multi-host genome-wide association study, we identify 19 high-confidence candidate genes associated with quantitative pathogenicity. Analysis of genetic diversity reveals that sequence polymorphism is the main evolutionary process mediating differences in quantitative pathogenicity, a process that is likely facilitated by genetic recombination and transposable element dynamics. Finally, we use functional approaches to confirm the role of an effector-like gene and a methyltransferase in phenotypic variation. This study highlights the complex genetic architecture of quantitative pathogenicity, extensive diversifying selection and plausible mechanisms facilitating pathogen adaptation.
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Affiliation(s)
- Reda Amezrou
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France.
| | - Aurélie Ducasse
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Jérôme Compain
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | - Anais Pitarch
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Laetitia Dupont
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Johann Confais
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | | | - Gert H J Kema
- Plant Research International B.V., Wageningen, The Netherlands
| | - Daniel Croll
- Department of Ecology and Evolution, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Joëlle Amselem
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
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12
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Torres DE, Kramer HM, Tracanna V, Fiorin GL, Cook DE, Seidl MF, Thomma BPHJ. Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen. Nat Commun 2024; 15:1701. [PMID: 38402218 PMCID: PMC10894299 DOI: 10.1038/s41467-024-45884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/05/2024] [Indexed: 02/26/2024] Open
Abstract
The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.
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Affiliation(s)
- David E Torres
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Vittorio Tracanna
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Manhattan, KS, USA
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany.
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13
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Treindl AD, Stapley J, Croll D, Leuchtmann A. Two-speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations. Mol Ecol 2024; 33:e17242. [PMID: 38084851 DOI: 10.1111/mec.17242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host-specific species that can sterilize their grass hosts. We performed selection scans using genome-wide SNP data from seven natural populations of two co-occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT-rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall-degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems.
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Affiliation(s)
- Artemis D Treindl
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jessica Stapley
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Adrian Leuchtmann
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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14
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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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15
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Oggenfuss U, Badet T, Croll D. A systematic screen for co-option of transposable elements across the fungal kingdom. Mob DNA 2024; 15:2. [PMID: 38245743 PMCID: PMC10799480 DOI: 10.1186/s13100-024-00312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or horizontal acquisition. Transposable elements (TEs) are increasingly recognized as a major source of novel domain-encoding sequences. However, the impact of TE coding sequences on the evolution of the proteome remains understudied. Here, we analyzed 1237 genomes spanning the phylogenetic breadth of the fungal kingdom. We scanned proteomes for evidence of co-occurrence of TE-derived domains along with other conventional protein functional domains. We detected more than 13,000 predicted proteins containing potentially TE-derived domain, of which 825 were identified in more than five genomes, indicating that many host-TE fusions may have persisted over long evolutionary time scales. We used the phylogenetic context to identify the origin and retention of individual TE-derived domains. The most common TE-derived domains are helicases derived from Academ, Kolobok or Helitron. We found putative TE co-options at a higher rate in genomes of the Saccharomycotina, providing an unexpected source of protein novelty in these generally TE depleted genomes. We investigated in detail a candidate host-TE fusion with a heterochromatic transcriptional silencing function that may play a role in TE and gene regulation in ascomycetes. The affected gene underwent multiple full or partial losses within the phylum. Overall, our work establishes a kingdom-wide view of putative host-TE fusions and facilitates systematic investigations of candidate fusion proteins.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Department of Microbiology and Immunology, University of Minnesota, Medical School, Minneapolis, Minnesota, United States of America
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
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16
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Westerberg I, Ament-Velásquez SL, Vogan AA, Johannesson H. Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations. Mob DNA 2024; 15:1. [PMID: 38218923 PMCID: PMC10787394 DOI: 10.1186/s13100-023-00311-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/22/2023] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND The genome of the filamentous ascomycete Podospora anserina shows a relatively high abundance of retrotransposons compared to other interspersed repeats. The LTR-retrotransposon family crapaud is particularly abundant in the genome, and consists of multiple diverged sequence variations specifically localized in the 5' half of both long terminal repeats (LTRs). P. anserina is part of a recently diverged species-complex, which makes the system ideal to classify the crapaud family based on the observed LTR variation and to study the evolutionary dynamics, such as the diversification and bursts of the elements over recent evolutionary time. RESULTS We developed a sequence similarity network approach to classify the crapaud repeats of seven genomes representing the P. anserina species complex into 14 subfamilies. This method does not utilize a consensus sequence, but instead it connects any copies that share enough sequence similarity over a set sequence coverage. Based on phylogenetic analyses, we found that the crapaud repeats likely diversified in the ancestor of the complex and have had activity at different time points for different subfamilies. Furthermore, while we hypothesized that the evolution into multiple subfamilies could have been a direct effect of escaping the genome defense system of repeat induced point mutations, we found this not to be the case. CONCLUSIONS Our study contributes to the development of methods to classify transposable elements in fungi, and also highlights the intricate patterns of retrotransposon evolution over short timescales and under high mutational load caused by nucleotide-altering genome defense.
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Affiliation(s)
- Ivar Westerberg
- Department of Ecology, environmental and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - S Lorena Ament-Velásquez
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden.
| | - Hanna Johannesson
- Department of Ecology, environmental and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- The Royal Swedish Academy of Sciences, Stockholm, 114 18, Sweden.
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17
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Dai M, Su Z, Zhu X, Li L, Ye Z, Tan X, Kong D, Liu X, Lin F. Genome-Wide Identification and Characterization of Effector Candidates with Conserved Motif in Falciphora oryzae. Int J Mol Sci 2024; 25:650. [PMID: 38203820 PMCID: PMC10779213 DOI: 10.3390/ijms25010650] [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: 11/17/2023] [Revised: 12/23/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Microbes employ effectors to disrupt immune responses and promote host colonization. Conserved motifs including RXLR, LFLAK-HVLVxxP (CRN), Y/F/WxC, CFEM, LysM, Chitin-bind, DPBB_1 (PNPi), and Cutinase have been discovered to play crucial roles in the functioning of effectors in filamentous fungi. Nevertheless, little is known about effectors with conserved motifs in endophytes. This research aims to discover the effector genes with conserved motifs in the genome of rice endophyte Falciphora oryzae. SignalP identified a total of 622 secreted proteins, out of which 227 were predicted as effector candidates by EffectorP. By utilizing HMM features, we discovered a total of 169 effector candidates with conserved motifs and three novel motifs. Effector candidates containing LysM, CFEM, DPBB_1, Cutinase, and Chitin_bind domains were conserved across species. In the transient expression assay, it was observed that one CFEM and one LysM activated cell death in tobacco leaves. Moreover, two CFEM and one Chitin_bind inhibited cell death induced by Bax protein. At various points during the infection, the genes' expression levels were increased. These results will help to identify functional effector proteins involving omics methods using new bioinformatics tools, thus providing a basis for the study of symbiosis mechanisms.
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Affiliation(s)
- Mengdi Dai
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.D.); (X.Z.); (L.L.)
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Z.Y.); (X.T.); (D.K.)
| | - Zhenzhu Su
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.S.); (X.L.)
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.D.); (X.Z.); (L.L.)
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.D.); (X.Z.); (L.L.)
| | - Ziran Ye
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Z.Y.); (X.T.); (D.K.)
| | - Xiangfeng Tan
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Z.Y.); (X.T.); (D.K.)
| | - Dedong Kong
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Z.Y.); (X.T.); (D.K.)
| | - Xiaohong Liu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Z.S.); (X.L.)
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (M.D.); (X.Z.); (L.L.)
- Xianghu Laboratory, Hangzhou 311231, China
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18
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Netherway T, Bengtsson J, Buegger F, Fritscher J, Oja J, Pritsch K, Hildebrand F, Krab EJ, Bahram M. Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe. Nat Commun 2024; 15:159. [PMID: 38167673 PMCID: PMC10761831 DOI: 10.1038/s41467-023-44172-4] [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: 06/21/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.
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Affiliation(s)
- Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden.
| | - Jan Bengtsson
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
| | - Franz Buegger
- Research Unit for Environmental Simulation (EUS), German Research Center for Environmental Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Joachim Fritscher
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Digital Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Jane Oja
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Karin Pritsch
- Research Unit for Environmental Simulation (EUS), German Research Center for Environmental Health, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Digital Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Eveline J Krab
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Lennart Hjelms väg 9, 750 07, Uppsala, Sweden
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
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19
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Suzuki M, Kitazawa Y, Iwabuchi N, Maejima K, Matsuyama J, Matsumoto O, Oshima K, Namba S, Yamaji Y. Target degradation specificity of phytoplasma effector phyllogen is regulated by the recruitment of host proteasome shuttle protein. MOLECULAR PLANT PATHOLOGY 2024; 25:e13410. [PMID: 38105442 PMCID: PMC10799209 DOI: 10.1111/mpp.13410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Phytoplasmas infect a wide variety of plants and can cause distinctive symptoms including the conversion of floral organs into leaf-like organs, known as phyllody. Phyllody is induced by an effector protein family called phyllogens, which interact with floral MADS-box transcription factors (MTFs) responsible for determining the identity of floral organs. The MTF/phyllogen complex then interacts with the proteasomal shuttle protein RADIATION SENSITIVE23 (RAD23), which facilitates delivery of the MTF/phyllogen complex to the host proteasome for MTF degradation. Previous studies have indicated that the MTF degradation specificity of phyllogens is determined by their ability to bind to MTFs. However, in the present study, we discovered a novel mechanism determining the degradation specificity through detailed functional analyses of a phyllogen homologue of rice yellow dwarf phytoplasma (PHYLRYD ). PHYLRYD degraded a narrower range of floral MTFs than other phyllody-inducing phyllogens, resulting in compromised phyllody phenotypes in plants. Interestingly, PHYLRYD was able to bind to some floral MTFs that PHYLRYD was unable to efficiently degrade. However, the complex of PHYLRYD and the non-degradable MTF could not interact with RAD23. These results indicate that the MTF degradation specificity of PHYLRYD is correlated with the ability to form the MTF/PHYLRYD /RAD23 ternary complex, rather than the ability to bind to MTF. This study elucidated that phyllogen target specificity is regulated by both the MTF-binding ability and RAD23 recruitment ability of the MTF/phyllogen complex.
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Affiliation(s)
- Masato Suzuki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Juri Matsuyama
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Oki Matsumoto
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Kenro Oshima
- Faculty of Bioscience, Hosei UniversityTokyoJapan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
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20
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Chavarro-Carrero EA, Snelders NC, Torres DE, Kraege A, López-Moral A, Petti GC, Punt W, Wieneke J, García-Velasco R, López-Herrera CJ, Seidl MF, Thomma BPHJ. The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization. PLoS Pathog 2024; 20:e1011866. [PMID: 38236788 PMCID: PMC10796067 DOI: 10.1371/journal.ppat.1011866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.
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Affiliation(s)
- Edgar A. Chavarro-Carrero
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Nick C. Snelders
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - David E. Torres
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Anton Kraege
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Ana López-Moral
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Gabriella C. Petti
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Wilko Punt
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Jan Wieneke
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Rómulo García-Velasco
- Laboratory of Phytopathology, Tenancingo University Center, Autonomous University of the State of Mexico, Tenancingo, State of Mexico, Mexico
| | - Carlos J. López-Herrera
- CSIC, Instituto de Agricultura Sostenible, Dept. Protección de Cultivos, C/Alameda del Obispo s/n, Córdoba, Spain
| | - Michael F. Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of Phytopathology, Wageningen University & Research, Wageningen, The Netherlands
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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21
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Zhang F, Chen S, Cui T, Zhang C, Dai T, Hao J, Liu X. Novel function of the PsDMAP1 protein in regulating the growth and pathogenicity of Phytophthora sojae. Int J Biol Macromol 2023; 253:127198. [PMID: 37802447 DOI: 10.1016/j.ijbiomac.2023.127198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 10/10/2023]
Abstract
The DNA methyltransferase 1-associated protein (DMAP1) was initially identified as an activator of DNA methyltransferase 1 (DNMT1), a conserved eukaryotic enzyme involved in diverse molecular processes, including histone acetylation and chromatin remodeling. However, the roles and regulatory mechanisms of DMAP1 in filamentous pathogens are still largely unknown. Here, employing bioinformatic analysis, we identified PsDMAP1 in P. sojae, which features a canonical histone tail-binding domain, as the ortholog of the human DMAP1. A phylogenetic analysis of DMAP1 protein sequences across diverse eukaryotic organisms revealed the remarkable conservation and distinctiveness of oomycete DMAP1 orthologs. Homozygous knockout of PsDMAP1 resulted in the mortality of P. sojae. Furthermore, silencing of PsDMAP1 caused a pronounced reduction in mycelial growth, production of sporangia and zoospore, cystospore germination, and virulence. PsDMAP1 also played a crucial role in the response of P. sojae to reactive oxygen species (ROS) and osmotic stresses. Moreover, PsDMAP1 interacted with DNA N6-methyladenine (6 mA) methyltransferase PsDAMT1, thereby enhancing its catalytic activity and effectively regulating 6 mA abundance in P. sojae. Our findings reveal the functional importance of PsDAMP1 in the development and infection of P. sojae, and this marks the initial exploration of the novel 6 mA regulator PsDMAP1 in plant pathogens.
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Affiliation(s)
- Fan Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shanshan Chen
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Tongshan Cui
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Can Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Tan Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jianjun Hao
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Xili Liu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China.
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22
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Collins G, Schneider C, Boštjančić LL, Burkhardt U, Christian A, Decker P, Ebersberger I, Hohberg K, Lecompte O, Merges D, Muelbaier H, Romahn J, Römbke J, Rutz C, Schmelz R, Schmidt A, Theissinger K, Veres R, Lehmitz R, Pfenninger M, Bálint M. The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution. Commun Biol 2023; 6:1241. [PMID: 38066075 PMCID: PMC10709333 DOI: 10.1038/s42003-023-05621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.
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Affiliation(s)
- Gemma Collins
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Clément Schneider
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ljudevit Luka Boštjančić
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | | | - Axel Christian
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Peter Decker
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Ingo Ebersberger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Karin Hohberg
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | - Dominik Merges
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hannah Muelbaier
- Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
| | - Juliane Romahn
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbH, Flörsheim, Germany
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Strasbourg, France
| | | | - Alexandra Schmidt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Kathrin Theissinger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Landau, Germany
| | - Robert Veres
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- Institute of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Ricarda Lehmitz
- Soil Zoology, Senckenberg Museum of Natural History, Görlitz, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany
- Johannes Gutenberg University, Mainz, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany.
- Department of Insect Biotechnology, Justus-Liebig University, Gießen, Germany.
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23
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Fan ZY, Peng J, Lou JQ, Chen Y, Wu XM, Tan R, Tan RX. Neuroprotective α-pyrones from Nigrospora oryzae, an endophytic fungus residing in Taxus chinensis var. mairei. PHYTOCHEMISTRY 2023; 216:113873. [PMID: 37769958 DOI: 10.1016/j.phytochem.2023.113873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Endophytes coevolve with plant hosts and thus are more probable to acquire the character (in favor) of producing undescribed bioactive metabolites. Consequently, the topic has been intensely investigated for over two decades, but endophytic metabolites with neuroprotective effect remain scarce. The study presents the discovery of eight undescribed (named solanapyrones U-Z and prosolanapyrones A and B) and six known pyrones (solanapyrones A-C and E-G) from the culture of Nigrospora oryzae, an endophytic fungus associated with Taxus chinensis var. mairei. The structures and absolute configurations of undescribed pyrones were elucidated by extensive spectroscopic analysis, modified Mosher's method, and induced circular dichroism (ICD) spectrum. Solanapyrones A and B and an undescribed pyrone (solanapyrone U) were demonstrated to be more neuroprotective than clenbuterol in inducing bone marrow mesenchymal stem cells (bMSCs) to secret nerve growth factor (NGF). The work updates the pyrone chemodiversity in nature and extends the biofunction repertoire of solanapyrone-related polyketides.
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Affiliation(s)
- Zi Yun Fan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jing Peng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Jun Qiao Lou
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yong Chen
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xue Ming Wu
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Rui Tan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China.
| | - Ren Xiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, Nanjing University, Nanjing 210023, China.
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24
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Li J, Zhang D, Du Y, Song J, Li R, Dai X, Chen J, Li G, Liu Z. Genome Sequence Resource of Cladosporium velox Strain C4 Causing Cotton Boll Disease in Xinjiang, China. PLANT DISEASE 2023; 107:4010-4015. [PMID: 37368501 DOI: 10.1094/pdis-11-22-2694-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Cladosporium spp., as one of the largest and most heterogeneous genera of hyphomycetes, are widely distributed worldwide. This genus is usually adaptable to a wide variety of extreme environments. However, only 11 genomes of Cladosporium genus have been publicly released. From 2017, we found for the first time that Cladosporium velox could cause cotton boll disease and lead to stiffness and cracking boll in Xinjiang, China. Herein, we provide a high-quality reference genome for the C. velox strain C4 isolated from cotton boll in Xinjiang, China. The genome size and encoding gene number of the C. velox strain C4 and C. cucumerinum strain CCNX2, which was recently released and caused the cucumber scab, showed minor differences. This resource will contribute to future research that aims to elucidate the genetic basis of C. velox pathogenicity and could expand our knowledge of Cladosporium spp. genomic characteristics that will be valuable for the development of Cladosporium disease control measures.
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Affiliation(s)
- Jingwen Li
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Dandan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Yejuan Du
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Jian Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Xiaofeng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jieyin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Guoying Li
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zheng Liu
- College of Agriculture/Key Laboratory of Oasis Agricultural Pest Management and Plant Protection Resources Utilization, Xinjiang Uygur Autonomous Region, Shihezi University, Shihezi, Xinjiang 832003, China
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25
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Nakamoto AA, Joubert PM, Krasileva KV. Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes. Genome Biol Evol 2023; 15:evad206. [PMID: 37975814 PMCID: PMC10691877 DOI: 10.1093/gbe/evad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.
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Affiliation(s)
- Anne A Nakamoto
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Pierre M Joubert
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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26
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Zhao F, Ding X, Liu Z, Yan X, Chen Y, Jiang Y, Chen S, Wang Y, Kang T, Xie C, He M, Zheng J. Application of CRISPR/Cas9-based genome editing in ecotoxicology. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122458. [PMID: 37633433 DOI: 10.1016/j.envpol.2023.122458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Chemicals are widely used and released into the environment, and their degradation, accumulation, migration, and transformation processes in the environment can pose a threat to the ecosystem. The advancement in analytical methods with high-throughput screening of biomolecules has revolutionized the way toxicologists used to explore the effects of chemicals on organisms. CRISPR/Cas is a newly developed tool, widely used in the exploration of basic science and biologically engineered products given its high efficiency and low cost. For example, it can edit target genes efficiently, and save loss of the crop yield caused by environmental pollution as well as gain a better understanding of the toxicity mechanisms from various chemicals. This review briefly introduces the development history of CRISPR/Cas and summarizes the current application of CRISPR/Cas in ecotoxicology, including its application on improving crop yield and drug resistance towards agricultural pollution, antibiotic pollution and other threats. The benefits by applying the CRISPR/Cas9 system in conventional toxicity mechanism studies are fully demonstrated here together with its foreseeable expansions in other area of ecotoxicology. Finally, the prospects and disadvantages of CRISPR/Cas system in the field of ecotoxicology are also discussed.
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Affiliation(s)
- Fang Zhao
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China; State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China; School of Public Health, Guizhou Medical University, Guizhou, China
| | - Xiaofan Ding
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Zimeng Liu
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xiao Yan
- State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China
| | - Yanzhen Chen
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Yaxin Jiang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Shunjie Chen
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yuanfang Wang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Tingting Kang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Chun Xie
- School of Public Health, Guizhou Medical University, Guizhou, China
| | - Mian He
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China.
| | - Jing Zheng
- State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China
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27
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Dionisio JF, Pezenti LF, de Souza RF, Sosa-Gómez DR, da Rosa R. Annotation of transposable elements in the transcriptome of the Neotropical brown stink bug Euschistus heros and its chromosomal distribution. Mol Genet Genomics 2023; 298:1377-1388. [PMID: 37646857 DOI: 10.1007/s00438-023-02063-9] [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: 01/30/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
Transposable elements (TEs) are DNA sequences capable of moving within the genome. Their distribution is very dynamic among organisms, and despite advances, there are still gaps in the understanding of the diversity and evolution of TEs in many insect species. In the case of Euschistus heros, considered the main stink bug in the soybean crop in Brazil, little is known about the participation of these elements. Therefore, the objective of the current work was to identify the different groups of transposable elements present in the E. heros transcriptome, evidencing their chromosomal distribution. Through RNA-Seq and de novo assembly, 60,009 transcripts were obtained, which were annotated locally via Blastn against specific databases. Of the 367 transcripts identified as TEs, 202 belong to Class II, with emphasis on the TIR order. Among Class I elements or retrotransposons, most were characterized as LINE. Phylogenetic analyses were performed with the protein domains, evidencing differences between Tc1-mariner sequences, which may be related to possible horizontal transfer events. The transposable elements that stood out in the transcriptome were selected for fluorescent in situ hybridization. DNA transposon probes hAT, Helitron, and Tc1-mariner showed mostly scattered signals, with the presence of some blocks. Retrotransposon probes Copia, Gypsy, Jockey, and RTE showed a more pulverized hybridization pattern, with the presence of small interstitial and/or terminal blocks. Studies like this one, integrating functional genomics and molecular cytogenetic tools, are essential to expanding knowledge about transcriptionally active mobile elements, and their behavior in the chromosomes.
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Affiliation(s)
- Jaqueline Fernanda Dionisio
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Larissa Forim Pezenti
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil
| | - Daniel Ricardo Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária/Centro Nacional de Pesquisa de Soja (Embrapa Soja), Caixa Postal: 4006, Londrina, PR, CEP: 86085-981, Brazil
| | - Renata da Rosa
- Laboratório de Citogenética e Entomologia Molecular, Departamento de Biologia Geral, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445 Km 350, Campus Universitário, Caixa Postal: 10.011, Londrina, PR, CEP:86.057-970, Brazil.
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Khayi S, Armitage AD, Gaboun F, Meftah-kadmiri I, Lahlali R, Fokar M, Mentag R. Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm. Front Microbiol 2023; 14:1268051. [PMID: 37886058 PMCID: PMC10599148 DOI: 10.3389/fmicb.2023.1268051] [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: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors. These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.
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Affiliation(s)
- Slimane Khayi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Andrew D. Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Greenwich, United Kingdom
| | - Fatima Gaboun
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
| | - Issam Meftah-kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Ben Guerir, Morocco
- Plant and Soil Microbiome Sub-Program, AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole Nationale D’Agriculture de Meknes, Meknès, Morocco
- Plant Pathology Laboratory, AgroBioSciences, College of Sustainable Agriculture and Environmental Sciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Rabat, Morocco
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Duhamel M, Hood ME, Rodríguez de la Vega RC, Giraud T. Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi. Nat Commun 2023; 14:5692. [PMID: 37709766 PMCID: PMC10502011 DOI: 10.1038/s41467-023-41413-4] [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: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
In the absence of recombination, the number of transposable elements (TEs) increases due to less efficient selection, but the dynamics of such TE accumulations are not well characterized. Leveraging a dataset of 21 independent events of recombination cessation of different ages in mating-type chromosomes of Microbotryum fungi, we show that TEs rapidly accumulated in regions lacking recombination, but that TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 million years following recombination suppression. The same TE superfamilies have expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements (Helitrons). Long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies also expanded, through transposition bursts (distinguished from gene conversion based on LTR divergence), with both non-recombining regions and autosomes affected, suggesting that non-recombining regions constitute TE reservoirs. This study improves our knowledge of genome evolution by showing that TEs can accumulate through bursts, following non-linear decelerating dynamics.
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Affiliation(s)
- Marine Duhamel
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France.
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
| | - Michael E Hood
- Department of Biology, Amherst College, 01002-5000, Amherst, MA, USA
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
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Narh Mensah DL, Wingfield BD, Coetzee MP. A practical approach to genome assembly and annotation of Basidiomycota using the example of Armillaria. Biotechniques 2023; 75:115-128. [PMID: 37681497 DOI: 10.2144/btn-2023-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
Abstract
Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to further our understanding of the biology of phytopathogens, including Armillaria species. Most Armillaria species are facultative necrotrophs that cause root- and stem-rot, usually on woody plants, significantly impacting agriculture and forestry worldwide. Genome sequencing, assembly and annotation in terms of samples used and methods applied in Armillaria genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future Armillaria genome projects were developed. Knowledge gained from genomic studies of Armillaria species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.
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Affiliation(s)
- Deborah L Narh Mensah
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
- Council for Scientific and Industrial Research - Food Research Institute (CSIR-FRI), PO Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Martin Pa Coetzee
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
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31
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Wang H, Huang R, Ren J, Tang L, Huang S, Chen X, Fan J, Li B, Wang Q, Hsiang T, Liu H, Li Q. The evolution of mini-chromosomes in the fungal genus Colletotrichum. mBio 2023; 14:e0062923. [PMID: 37283539 PMCID: PMC10470602 DOI: 10.1128/mbio.00629-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 06/08/2023] Open
Abstract
Anthracnose diseases caused by Colletotrichum species are among the most common fungal diseases. These symptoms typically manifest as dark, sunken lesions on leaves, stems, and fruit. In China, mango anthracnose seriously affects fruit yield and quality. Genome sequencing of several species shows the presence of mini-chromosomes. These are thought to contribute to virulence, but their formation and activity remain to be fully elucidated. Here, we assembled 17 Colletotrichum genomes (16 isolated from mango plus one from persimmon) through PacBio long-read sequencing. Half of the assembled scaffolds had telomeric repeats at both ends indicating full-length chromosomes. Based on comparative genomics analysis at interspecies and intraspecies levels, we identified extensive chromosomal rearrangements events. We analyzed mini-chromosomes of Colletotrichum spp. and found large variation among close relatives. In C. fructicola, homology between core chromosomes and mini-chromosomes suggested that some mini-chromosomes were generated by recombination of core chromosomes. In C. musae GZ23-3, we found 26 horizontally transferred genes arranged in clusters on mini-chromosomes. In C. asianum FJ11-1, several potential pathogenesis-related genes on mini-chromosomes were upregulated, especially in strains with highly pathogenic phenotypes. Mutants of these upregulated genes showed obvious defects in virulence. Our findings provide insights into the evolution and potential relationships to virulence associated with mini-chromosomes. IMPORTANCE Colletotrichum is a cosmopolitan fungal genus that seriously affects fruit yield and quality of many plant species. Mini-chromosomes have been found to be related to virulence in Colletotrichum. Further examination of mini-chromosomes can help us elucidate some pathogenic mechanisms of Colletotrichum. In this study, we generated novel assemblies of several Colletotrichum strains. Comparative genomic analyses within and between Colletotrichum species were conducted. We then identified mini-chromosomes in our sequenced strains systematically. The characteristics and generation of mini-chromosomes were investigated. Transcriptome analysis and gene knockout revealed pathogenesis-related genes located on mini-chromosomes of C. asianum FJ11-1. This study represents the most comprehensive investigation of chromosome evolution and potential pathogenicity of mini-chromosomes in the Colletotrichum genus.
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Affiliation(s)
- Haoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Rong Huang
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
| | - Jingyi Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Lihua Tang
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
| | - Suiping Huang
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
| | - Xiaolin Chen
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
| | - Jun Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Bintao Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qili Li
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs and Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, Guangxi, China
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32
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Zaccaron AZ, Neill T, Corcoran J, Mahaffee WF, Stergiopoulos I. A chromosome-scale genome assembly of the grape powdery mildew pathogen Erysiphe necator reveals its genomic architecture and previously unknown features of its biology. mBio 2023; 14:e0064523. [PMID: 37341476 PMCID: PMC10470754 DOI: 10.1128/mbio.00645-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/13/2023] [Indexed: 06/22/2023] Open
Abstract
Erysiphe necator is an obligate fungal pathogen that causes grape powdery mildew, globally the most important disease on grapevines. Previous attempts to obtain a quality genome assembly for this pathogen were hindered by its high repetitive DNA content. Here, chromatin conformation capture (Hi-C) with long-read PacBio sequencing was combined to obtain a chromosome-scale assembly and a high-quality annotation for E. necator isolate EnFRAME01. The resulting 81.1 Mb genome assembly is 98% complete and consists of 34 scaffolds, 11 of which represent complete chromosomes. All chromosomes contain large centromeric-like regions and lack synteny to the 11 chromosomes of the cereal PM pathogen Blumeria graminis. Further analysis of their composition showed that repeats and transposable elements (TEs) occupy 62.7% of their content. TEs were almost evenly interspersed outside centromeric and telomeric regions and massively overlapped with regions of annotated genes, suggesting that they could have a significant functional impact. Abundant gene duplicates were observed as well, particularly in genes encoding candidate secreted effector proteins. Moreover, younger in age gene duplicates exhibited more relaxed selection pressure and were more likely to be located physically close in the genome than older duplicates. A total of 122 genes with copy number variations among six isolates of E. necator were also identified and were enriched in genes that were duplicated in EnFRAME01, indicating they may reflect an adaptive variation. Taken together, our study illuminates higher-order genomic architectural features of E. necator and provides a valuable resource for studying genomic structural variations in this pathogen. IMPORTANCE Grape powdery mildew caused by the ascomycete fungus Erysiphe necator is economically the most important and recurrent disease in vineyards across the world. The obligate biotrophic nature of E. necator hinders the use of typical genetic methods to elucidate its pathogenicity and adaptation to adverse conditions, and thus comparative genomics has been a major method to study its genome biology. However, the current reference genome of E. necator isolate C-strain is highly fragmented with many non-coding regions left unassembled. This incompleteness prohibits in-depth comparative genomic analyses and the study of genomic structural variations (SVs) that are known to affect several aspects of microbial life, including fitness, virulence, and host adaptation. By obtaining a chromosome-scale genome assembly and a high-quality gene annotation for E. necator, we reveal the organization of its chromosomal content, unearth previously unknown features of its biology, and provide a reference for studying genomic SVs in this pathogen.
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Affiliation(s)
- Alex Z. Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | - Tara Neill
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, Oregon, USA
| | - Jacob Corcoran
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, Oregon, USA
| | - Walter F. Mahaffee
- USDA-ARS, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, Oregon, USA
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, California, USA
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33
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Derbyshire MC, Raffaele S. Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors. Nat Commun 2023; 14:5244. [PMID: 37640704 PMCID: PMC10462633 DOI: 10.1038/s41467-023-40949-9] [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: 01/10/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors are engaged in a molecular arms race with the host resulting in conflicting evolutionary constraints to manipulate host cells without triggering immune responses. The molecular mechanisms allowing effectors to be at the same time robust and evolvable remain largely enigmatic. Here, we show that 62 conserved structure-related families encompass the majority of fungal orphan effector candidates in the Pezizomycotina subphylum. These effectors diversified through changes in patterns of thermodynamic frustration at surface residues. The underlying mutations tended to increase the robustness of the overall effector protein structure while switching potential binding interfaces. This mechanism could explain how conserved effector families maintained biological activity over long evolutionary timespans in different host environments and provides a model for the emergence of sequence-unrelated effector families with conserved structures.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes Micro-organismes Environnement (LIPME), INRAE, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France.
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Kramer HM, Cook DE, Seidl MF, Thomma BP. Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathog 2023; 19:e1011525. [PMID: 37535497 PMCID: PMC10399791 DOI: 10.1371/journal.ppat.1011525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.
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Affiliation(s)
- H. Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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Zhang T, Feng J, He W, Rong X, Lv H, Li J, Li X, Wang H, Wang L, Zhang L, Yu L. Genomic and Transcriptomic Approaches Provide a Predictive Framework for Sesquiterpenes Biosynthesis in Desarmillaria tabescens CPCC 401429. J Fungi (Basel) 2023; 9:jof9040481. [PMID: 37108935 PMCID: PMC10146329 DOI: 10.3390/jof9040481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/08/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Terpenoids constitute a structurally diverse class of secondary metabolites with wide applications in the pharmaceutical, fragrance and flavor industries. Desarmillaria tabescens CPCC 401429 is a basidiomycetous mushroom that could produce anti-tumor melleolides. To date, no studies have been conducted to thoroughly investigate the sesquiterpenes biosynthetic potential in Desarmillaria or related genus. This study aims to unravel the phylogeny, terpenome, and functional characterization of unique sesquiterpene biosynthetic genes of the strain CPCC 401429. Herein, we report the genome of the fungus containing 15,145 protein-encoding genes. MLST-based phylogeny and comparative genomic analyses shed light on the precise reclassification of D. tabescens suggesting that it belongs to the genus Desarmillaria. Gene ontology enrichment and pathway analyses uncover the hidden capacity for producing polyketides and terpenoids. Genome mining directed predictive framework reveals a diverse network of sesquiterpene synthases (STSs). Among twelve putative STSs encoded in the genome, six ones are belonging to the novel minor group: diverse Clade IV. In addition, RNA-sequencing based transcriptomic profiling revealed differentially expressed genes (DEGs) of the fungus CPCC 401429 in three different fermentation conditions, that of which enable us to identify noteworthy genes exemplified as STSs coding genes. Among the ten sesquiterpene biosynthetic DEGs, two genes including DtSTS9 and DtSTS10 were selected for functional characterization. Yeast cells expressing DtSTS9 and DtSTS10 could produce diverse sesquiterpene compounds, reinforced that STSs in the group Clade IV might be highly promiscuous producers. This highlights the potential of Desarmillaria in generating novel terpenoids. To summarize, our analyses will facilitate our understanding of phylogeny, STSs diversity and functional significance of Desarmillaria species. These results will encourage the scientific community for further research on uncharacterized STSs of Basidiomycota phylum, biological functions, and potential application of this vast source of secondary metabolites.
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Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jianjv Feng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Wenni He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiaoting Rong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hui Lv
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jun Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xinxin Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Hao Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lu Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai 200237, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Oggenfuss U, Croll D. Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011130. [PMID: 36787337 PMCID: PMC9970103 DOI: 10.1371/journal.ppat.1011130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/27/2023] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a pathogen species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogen Zymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences, or as a consequence of insertion site preferences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that a Copia element burst was initiated from recent copies inserted substantially closer to genes compared to older copies. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation in pathogen genomes.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
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Snelders NC, Boshoven JC, Song Y, Schmitz N, Fiorin GL, Rovenich H, van den Berg GCM, Torres DE, Petti GC, Prockl Z, Faino L, Seidl MF, Thomma BPHJ. A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria. THE NEW PHYTOLOGIST 2023; 237:944-958. [PMID: 36300791 DOI: 10.1111/nph.18576] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Plant pathogens secrete effector proteins to support host colonization through a wide range of molecular mechanisms, while plant immune systems evolved receptors to recognize effectors or their activities to mount immune responses to halt pathogens. Importantly, plants do not act as single organisms, but rather as holobionts that actively shape their microbiota as a determinant of health. The soil-borne fungal pathogen Verticillium dahliae was recently demonstrated to exploit the VdAve1 effector to manipulate the host microbiota to promote vascular wilt disease in the absence of the corresponding immune receptor Ve1. We identify a multiallelic V. dahliae gene displaying c. 65% sequence similarity to VdAve1, named VdAve1-like (VdAve1L), which shows extreme sequence variation, including alleles that encode dysfunctional proteins, indicative of selection pressure to overcome host recognition. We show that the orphan cell surface receptor Ve2, encoded at the Ve locus, does not recognize VdAve1L. Additionally, we demonstrate that the full-length variant VdAve1L2 possesses antimicrobial activity, like VdAve1, yet with a divergent activity spectrum, that is exploited by V. dahliae to mediate tomato colonization through the direct suppression of antagonistic Actinobacteria in the host microbiota. Our findings open up strategies for more targeted biocontrol against microbial plant pathogens.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
| | - Jordi C Boshoven
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Yin Song
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Natalie Schmitz
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - David E Torres
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
| | - Gabriella C Petti
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Zoe Prockl
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
- Department of Ambiental Biology, Sapienza University of Rome, 00185, Rome, Italy
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, University of Utrecht, 3584CH, Utrecht, the Netherlands
| | - Bart P H J Thomma
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
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Disentangling the complex gene interaction networks between rice and the blast fungus identifies a new pathogen effector. PLoS Biol 2023; 21:e3001945. [PMID: 36656825 PMCID: PMC9851567 DOI: 10.1371/journal.pbio.3001945] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023] Open
Abstract
Studies focused solely on single organisms can fail to identify the networks underlying host-pathogen gene-for-gene interactions. Here, we integrate genetic analyses of rice (Oryza sativa, host) and rice blast fungus (Magnaporthe oryzae, pathogen) and uncover a new pathogen recognition specificity of the rice nucleotide-binding domain and leucine-rich repeat protein (NLR) immune receptor Pik, which mediates resistance to M. oryzae expressing the avirulence effector gene AVR-Pik. Rice Piks-1, encoded by an allele of Pik-1, recognizes a previously unidentified effector encoded by the M. oryzae avirulence gene AVR-Mgk1, which is found on a mini-chromosome. AVR-Mgk1 has no sequence similarity to known AVR-Pik effectors and is prone to deletion from the mini-chromosome mediated by repeated Inago2 retrotransposon sequences. AVR-Mgk1 is detected by Piks-1 and by other Pik-1 alleles known to recognize AVR-Pik effectors; recognition is mediated by AVR-Mgk1 binding to the integrated heavy metal-associated (HMA) domain of Piks-1 and other Pik-1 alleles. Our findings highlight how complex gene-for-gene interaction networks can be disentangled by applying forward genetics approaches simultaneously to the host and pathogen. We demonstrate dynamic coevolution between an NLR integrated domain and multiple families of effector proteins.
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Vuong UT, Iswanto ABB, Nguyen Q, Kang H, Lee J, Moon J, Kim SH. Engineering plant immune circuit: walking to the bright future with a novel toolbox. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:17-45. [PMID: 36036862 PMCID: PMC9829404 DOI: 10.1111/pbi.13916] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Plant pathogens destroy crops and cause severe yield losses, leading to an insufficient food supply to sustain the human population. Apart from relying on natural plant immune systems to combat biological agents or waiting for the appropriate evolutionary steps to occur over time, researchers are currently seeking new breakthrough methods to boost disease resistance in plants through genetic engineering. Here, we summarize the past two decades of research in disease resistance engineering against an assortment of pathogens through modifying the plant immune components (internal and external) with several biotechnological techniques. We also discuss potential strategies and provide perspectives on engineering plant immune systems for enhanced pathogen resistance and plant fitness.
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Affiliation(s)
- Uyen Thi Vuong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Arya Bagus Boedi Iswanto
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Quang‐Minh Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Hobin Kang
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Jihyun Lee
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Jiyun Moon
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Sang Hee Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
- Division of Life ScienceGyeongsang National UniversityJinjuRepublic of Korea
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Becerra S, Baroncelli R, Boufleur TR, Sukno SA, Thon MR. Chromosome-level analysis of the Colletotrichum graminicola genome reveals the unique characteristics of core and minichromosomes. Front Microbiol 2023; 14:1129319. [PMID: 37032845 PMCID: PMC10076810 DOI: 10.3389/fmicb.2023.1129319] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
The fungal pathogen Colletotrichum graminicola causes the anthracnose of maize (Zea mays) and is responsible for significant yield losses worldwide. The genome of C. graminicola was sequenced in 2012 using Sanger sequencing, 454 pyrosequencing, and an optical map to obtain an assembly of 13 pseudochromosomes. We re-sequenced the genome using a combination of short-read (Illumina) and long-read (PacBio) technologies to obtain a chromosome-level assembly. The new version of the genome sequence has 13 chromosomes with a total length of 57.43 Mb. We detected 66 (23.62 Mb) structural rearrangements in the new assembly with respect to the previous version, consisting of 61 (21.98 Mb) translocations, 1 (1.41 Mb) inversion, and 4 (221 Kb) duplications. We annotated the genome and obtained 15,118 predicted genes and 3,614 new gene models compared to the previous version of the assembly. We show that 25.88% of the new assembly is composed of repetitive DNA elements (13.68% more than the previous assembly version), which are mostly found in gene-sparse regions. We describe genomic compartmentalization consisting of repeat-rich and gene-poor regions vs. repeat-poor and gene-rich regions. A total of 1,140 secreted proteins were found mainly in repeat-rich regions. We also found that ~75% of the three smallest chromosomes (minichromosomes, between 730 and 551 Kb) are strongly affected by repeat-induced point mutation (RIP) compared with 28% of the larger chromosomes. The gene content of the minichromosomes (MCs) comprises 121 genes, of which 83.6% are hypothetical proteins with no predicted function, while the mean percentage of Chr1-Chr10 is 36.5%. No predicted secreted proteins are present in the MCs. Interestingly, only 2% of the genes in Chr11 have homologs in other strains of C. graminicola, while Chr12 and 13 have 58 and 57%, respectively, raising the question as to whether Chrs12 and 13 are dispensable. The core chromosomes (Chr1-Chr10) are very different with respect to the MCs (Chr11-Chr13) in terms of the content and sequence features. We hypothesize that the higher density of repetitive elements and RIPs in the MCs may be linked to the adaptation and/or host co-evolution of this pathogenic fungus.
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Affiliation(s)
- Sioly Becerra
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
| | - Riccardo Baroncelli
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Thaís R. Boufleur
- Department of Plant Pathology and Nematology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Serenella A. Sukno
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- *Correspondence: Serenella A. Sukno
| | - Michael R. Thon
- Department of Microbiology and Genetics, Institute for Agrobiotechnology Research (CIALE), University of Salamanca, Villamayor, Spain
- Michael R. Thon
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Blackman C, Subramaniam R. A Bioinformatic Guide to Identify Protein Effectors from Phytopathogens. Methods Mol Biol 2023; 2659:95-101. [PMID: 37249888 DOI: 10.1007/978-1-0716-3159-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Phytopathogenic fungi are a diverse and widespread group that has a significant detrimental impact on crops with an estimated annual average loss of 15% worldwide. Understanding the interaction between host plants and pathogenic fungi is critical to delineate underlying mechanisms of plant defense to mitigate agricultural losses. Fungal pathogens utilize suites of secreted molecules, called effectors, to modulate plant metabolism and immune response to overcome host defenses and promote colonization. Effectors come in many flavors including proteinaceous products, small RNAs, and metabolites such as mycotoxins. This review will focus on methods for identifying protein effectors from fungi. Excellent reviews have been published to identify secondary metabolites and small RNAs from fungi and therefore will not be part of this review.
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Affiliation(s)
- Christopher Blackman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
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42
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Cheng Z, Lv X, Duan C, Zhu H, Wang J, Xu Z, Yin H, Zhou X, Li M, Hao Z, Li F, Li X, Weng J. Pathogenicity Variation in Two Genomes of Cercospora Species Causing Gray Leaf Spot in Maize. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:14-25. [PMID: 36251001 DOI: 10.1094/mpmi-06-22-0138-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The gray leaf spots caused by Cercospora spp. severely affect the yield and quality of maize. However, the evolutionary relation and pathogenicity variation between species of the Cercospora genus is largely unknown. In this study, we constructed high-quality reference genomes by nanopore sequencing two Cercospora species, namely, C. zeae-maydis and C. zeina, with differing pathogenicity, collected from northeast (Liaoning [LN]) and southeast (Yunnan [YN]) China, respectively. The genome size of C. zeae-maydis-LN is 45.08 Mb, containing 10,839 annotated genes, whereas that of Cercospora zeina-YN is 42.18 Mb, containing 10,867 annotated genes, of which approximately 86.58% are common in the two species. The difference in their genome size is largely attributed to increased long terminal repeat retrotransposons of 3.8 Mb in total length in C. zeae-maydis-LN. There are 41 and 30 carbohydrate-binding gene subfamilies identified in C. zeae-maydis-LN and C. zeina-YN, respectively. A higher number of carbohydrate-binding families found in C. zeae-maydis-LN, and its unique CBM4, CBM37, and CBM66, in particular, may contribute to variation in pathogenicity between the two species, as the carbohydrate-binding genes are known to encode cell wall-degrading enzymes. Moreover, there are 114 and 107 effectors predicted, with 47 and 46 having unique potential pathogenicity in C. zeae-maydis-LN and C. zeina-YN, respectively. Of eight effectors randomly selected for pathogenic testing, five were found to inhibit cell apoptosis induced by Bcl-2-associated X. Taken together, our results provide genomic insights into variation in pathogenicity between C. zeae-maydis and C. zeina. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zixiang Cheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiangling Lv
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, 110161, China
| | - Canxing Duan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hanyong Zhu
- Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, 663000, China
| | - Jianjun Wang
- Corn Research Institute, Shanxi Agricultural University, Xinzhou, Shanxi, 030600, China
| | - Zhennan Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huifei Yin
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, 110161, China
| | - Xiaohang Zhou
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, 110161, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhuafang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, 110161, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Kronmiller BA, Feau N, Shen D, Tabima JF, Ali SS, Armitage AD, Arredondo F, Bailey BA, Bollmann SR, Dale A, Harrison RJ, Hrywkiw K, Kasuga T, McDougal R, Nellist CF, Panda P, Tripathy S, Williams NM, Ye W, Wang Y, Hamelin RC, Grünwald NJ. Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:26-46. [PMID: 36306437 DOI: 10.1094/mpmi-06-22-0133-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthora spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus Phytophthora. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Brent A Kronmiller
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Javier F Tabima
- Department of Biology, Clark University, Worcester, MA, U.S.A
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, Northeast Area, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD, U.S.A
| | - Andrew D Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, U.K
| | - Felipe Arredondo
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, Northeast Area, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD, U.S.A
| | - Stephanie R Bollmann
- Department of Integrative Biology, Oregon State University, Corvallis, OR, U.S.A
| | - Angela Dale
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
- SC-New Construction Materials, FPInnovations, Vancouver, V6T 1Z4, Canada
| | | | - Kelly Hrywkiw
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Davis, CA, U.S.A
| | - Rebecca McDougal
- Scion (Zealand Forest Research Institute), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua, New Zealand
| | | | - Preeti Panda
- The New Zealand Institute for Plant and Food Research Ltd, 74 Gerald Street, Lincoln, 7608, New Zealand
| | | | - Nari M Williams
- Scion (Zealand Forest Research Institute), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua, New Zealand
- Department of Pathogen Ecology and Control, Plant and Food Research, Private Bag 1401, Havelock North, New Zealand
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Département des sciences du bois et de la forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, Canada
| | - Niklaus J Grünwald
- Horticultural Crop Research Unit, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, U.S.A
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Xia C, Huang L, Huang J, Zhang H, Huang Y, Benhamed M, Wang M, Chen X, Zhang M, Liu T, Chen W. Folding Features and Dynamics of 3D Genome Architecture in Plant Fungal Pathogens. Microbiol Spectr 2022; 10:e0260822. [PMID: 36250889 PMCID: PMC9769607 DOI: 10.1128/spectrum.02608-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/18/2022] [Indexed: 01/07/2023] Open
Abstract
The folding and dynamics of three-dimensional (3D) genome organization are fundamental for eukaryotes executing genome functions but have been largely unexplored in nonmodel fungi. Using high-throughput sequencing coupled with chromosome conformation capture (Hi-C) data, we generated two chromosome-level assemblies for Puccinia striiformis f. sp. tritici, a fungus causing stripe rust disease on wheat, for studying 3D genome architectures of plant pathogenic fungi. The chromatin organization of the fungus followed a combination of the fractal globule model and the equilibrium globule model. Surprisingly, chromosome compartmentalization was not detected. Dynamics of 3D genome organization during two developmental stages of P. striiformis f. sp. tritici indicated that regulation of gene activities might be independent of the changes of genome organization. In addition, chromatin conformation conservation was found to be independent of genome sequence synteny conservation among different fungi. These results highlighted the distinct folding principles of fungal 3D genomes. Our findings should be an important step toward a holistic understanding of the principles and functions of genome architecture across different eukaryotic kingdoms. IMPORTANCE Previously, our understanding of 3D genome architecture has mainly come from model mammals, insects, and plants. However, the organization and regulatory functions of 3D genomes in fungi are largely unknown. In this study, we comprehensively investigated P. striiformis f. sp. tritici, a plant fungal pathogen, and revealed distinct features of the 3D genome, comparing it with the universal folding feature of 3D genomes in higher eukaryotic organisms. We further suggested that there might be distinct regulatory mechanisms of gene expression that are independent of chromatin organization changes during the developmental stages of this rust fungus. Moreover, we showed that the evolutionary pattern of 3D genomes in this fungus is also different from the cases in mammalian genomes. In addition, the genome assembly pipeline and the generated two chromosome-level genomes will be valuable resources. These results highlighted the unexplored distinct features of 3D genome organization in fungi. Therefore, our study provided complementary knowledge to holistically understand the organization and functions of 3D genomes across different eukaryotes.
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Affiliation(s)
- Chongjing Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Liang Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
| | - Jie Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Huang
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Paris, France
| | - Moussa Benhamed
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Paris, France
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, Washington, USA
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, Washington, USA
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu, China
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Todd JNA, Carreón-Anguiano KG, Islas-Flores I, Canto-Canché B. Fungal Effectoromics: A World in Constant Evolution. Int J Mol Sci 2022; 23:13433. [PMID: 36362218 PMCID: PMC9656242 DOI: 10.3390/ijms232113433] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 10/28/2023] Open
Abstract
Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present review, the different characteristics that underly effector classifications are discussed, contrasting past and present knowledge regarding these molecules to foster a more comprehensive understanding of effectors for the reader. Research gaps in effector identification and perspectives for effector application in plant disease management are also presented, with a focus on fungal effectors in the plant-microbe interaction and interactions beyond the plant host. In summary, the review provides an amenable yet thorough introduction to fungal effector biology, presenting noteworthy examples of effectors and effector studies that have shaped our present understanding of the field.
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Affiliation(s)
- Jewel Nicole Anna Todd
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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Macquet J, Mounichetty S, Raffaele S. Genetic co-option into plant-filamentous pathogen interactions. TRENDS IN PLANT SCIENCE 2022; 27:1144-1158. [PMID: 35909010 DOI: 10.1016/j.tplants.2022.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant-pathogen interactions, such as molecular decoys, trans-kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant-pathogen interactions emerges generally from (i) cis-regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant-pathogen interactions.
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Affiliation(s)
- Joris Macquet
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Shantala Mounichetty
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France.
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Depotter JRL, Ökmen B, Ebert MK, Beckers J, Kruse J, Thines M, Doehlemann G. High Nucleotide Substitution Rates Associated with Retrotransposon Proliferation Drive Dynamic Secretome Evolution in Smut Pathogens. Microbiol Spectr 2022; 10:e0034922. [PMID: 35972267 PMCID: PMC9603552 DOI: 10.1128/spectrum.00349-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/22/2022] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated with the mating-type locus sizes, which is up to ~560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these occur in specific genome regions of smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more accessory nature results in substitutions that often lead to amino acid alterations. IMPORTANCE Genomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. They also impact genome evolution as their repetitive nature facilitates nonhomologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, Ustilago hordei. This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. We hypothesize that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.
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Affiliation(s)
- J. R. L. Depotter
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - B. Ökmen
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - M. K. Ebert
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Beckers
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - J. Kruse
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt a. M., Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt a. M., Germany
| | - G. Doehlemann
- CEPLAS, Institute for Plant Sciences, University of Cologne, Cologne, Germany
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Guo Y, Betzen B, Salcedo A, He F, Bowden RL, Fellers JP, Jordan KW, Akhunova A, Rouse MN, Szabo LJ, Akhunov E. Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races. Nat Commun 2022; 13:6287. [PMID: 36271077 PMCID: PMC9587050 DOI: 10.1038/s41467-022-34050-w] [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: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for studying the evolution of Pgt virulence and preventing future epidemic outbreaks.
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Affiliation(s)
- Yuanwen Guo
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Bliss Betzen
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Present Address: USDA-APHIS-PPQ Field Operations, Kansas State University, Manhattan, KS USA
| | - Andres Salcedo
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.40803.3f0000 0001 2173 6074Present Address: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Fei He
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.9227.e0000000119573309Present Address: State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Robert L. Bowden
- grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - John P. Fellers
- grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - Katherine W. Jordan
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - Alina Akhunova
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Integrated Genomics Facility, Kansas State University, Manhattan, KS USA
| | - Mathew N. Rouse
- grid.512864.c0000 0000 8881 3436Department of Plant Pathology, University of Minnesota & USDA-ARS, Cereal Disease Lab, St. Paul, MN USA
| | - Les J. Szabo
- grid.512864.c0000 0000 8881 3436Department of Plant Pathology, University of Minnesota & USDA-ARS, Cereal Disease Lab, St. Paul, MN USA
| | - Eduard Akhunov
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Wheat Genetics Resource Center, Kansas State University, Manhattan, KS USA
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Yang LN, Ouyang H, Nkurikiyimfura O, Fang H, Waheed A, Li W, Wang YP, Zhan J. Genetic variation along an altitudinal gradient in the Phytophthora infestans effector gene Pi02860. Front Microbiol 2022; 13:972928. [PMID: 36160230 PMCID: PMC9492930 DOI: 10.3389/fmicb.2022.972928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Effector genes, together with climatic and other environmental factors, play multifaceted roles in the development of plant diseases. Understanding the role of environmental factors, particularly climate conditions affecting the evolution of effector genes, is important for predicting the long-term value of the genes in controlling agricultural diseases. Here, we collected Phytophthora infestans populations from five locations along a mountainous hill in China and sequenced the effector gene Pi02860 from >300 isolates. To minimize the influence of other ecological factors, isolates were sampled from the same potato cultivar on the same day. We also expressed the gene to visualise its cellular location, assayed its pathogenicity and evaluated its response to experimental temperatures. We found that Pi02860 exhibited moderate genetic variation at the nucleotide level which was mainly generated by point mutation. The mutations did not change the cellular location of the effector gene but significantly modified the fitness of P. infestans. Genetic variation and pathogenicity of the effector gene were positively associated with the altitude of sample sites, possibly due to increased mutation rate induced by the vertical distribution of environmental factors such as UV radiation and temperature. We further found that Pi02860 expression was regulated by experimental temperature with reduced expression as experimental temperature increased. Together, these results indicate that UV radiation and temperature are important environmental factors regulating the evolution of effector genes and provide us with considerable insight as to their future sustainable action under climate and other environmental change.
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Affiliation(s)
- Li-Na Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
- *Correspondence: Li-Na Yang,
| | - Haibing Ouyang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Oswald Nkurikiyimfura
- Institute of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hanmei Fang
- Institute of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Abdul Waheed
- Institute of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenyang Li
- Institute of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Jiasui Zhan,
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50
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Xia C, Qiu A, Wang M, Liu T, Chen W, Chen X. Current Status and Future Perspectives of Genomics Research in the Rust Fungi. Int J Mol Sci 2022; 23:9629. [PMID: 36077025 PMCID: PMC9456177 DOI: 10.3390/ijms23179629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.
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Affiliation(s)
- Chongjing Xia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Age Qiu
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430, USA
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