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Zaccaron AZ, Stergiopoulos I. The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance. J Genet Genomics 2025; 52:628-640. [PMID: 39522682 DOI: 10.1016/j.jgg.2024.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 10/15/2024] [Accepted: 10/21/2024] [Indexed: 11/16/2024]
Abstract
Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions. In this review, we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance. We examine key features and the heterogeneity of genomes across different fungal species, including but not limited to their chromosome content, DNA composition, distribution and arrangement of their content across chromosomes, and other major traits. We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions. Fungal genomes exhibit large variations in size, gene content, and structural features, such as the abundance of transposable elements (TEs), compartmentalization into gene-rich and TE-rich regions, and the presence or absence of dispensable chromosomes. Genomic structural variations are equally diverse in fungi, ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds, to targeted deletion of effector encoding genes that may promote virulence. Finally, the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides. Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.
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Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis (UCD), Davis, CA, USA; Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA 95616, USA
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis (UCD), Davis, CA, USA.
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D’Angelo D, Sorrentino R, Nkomo T, Zhou X, Vaghefi N, Sonnekus B, Bose T, Cerrato D, Cozzolino L, Creux N, D’Agostino N, Fourie G, Fusco G, Hammerbacher A, Idnurm A, Kiss L, Hu Y, Hu H, Lahoz E, Risteski J, Steenkamp ET, Viscardi M, van der Nest MA, Wu Y, Yu H, Zhou J, Karandeni Dewage CS, Kotta-Loizou LI, Stotz HU, Fitt BDL, Huang Y, Wingfield BD. IMA GENOME - F20 A draft genome assembly of Agroatheliarolfsii, Ceratobasidiumpapillatum, Pyrenopezizabrassicae, Neopestalotiopsismacadamiae, Sphaerellopsisfilum and genomic resources for Colletotrichumspaethianum and Colletotrichumfructicola. IMA Fungus 2025; 16:e141732. [PMID: 40052082 PMCID: PMC11882029 DOI: 10.3897/imafungus.16.141732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Accepted: 11/13/2024] [Indexed: 03/09/2025] Open
Abstract
This is a genome announacment there is no abstract
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Affiliation(s)
- Davide D’Angelo
- Department of Agricultural Sciences, University of Naples Federico II, piazza Carlo di Borbone 1, 80055, Portici, Naples, Italy
| | - Roberto Sorrentino
- Research Centre for Cereal and Industrial Crops (CREA-CI), via Torrino 3, 81100, Caserta, Italy
| | - Tiphany Nkomo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Xianzhi Zhou
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Wusi Road 247, Fuzhou 350003, China
| | - Niloofar Vaghefi
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Byron Sonnekus
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Tanay Bose
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Domenico Cerrato
- Department of Zoology and Entomology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Loredana Cozzolino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055, Portici, Naples, Italy
| | - Nicky Creux
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, piazza Carlo di Borbone 1, 80055, Portici, Naples, Italy
| | - Gerda Fourie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Giovanna Fusco
- Department of Plant and Soil Science, Forestry and Agricultural Biotechnology (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - Almuth Hammerbacher
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Alexander Idnurm
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Levente Kiss
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Australia
- Eszterházy Károly Catholic University, Eger, Hungary
| | - Yanping Hu
- Plant Protection Institute, Centre for Agricultural Research, HUN-REN, Budapest, Hungary
| | - Hongli Hu
- Plant Protection Institute, Centre for Agricultural Research, HUN-REN, Budapest, Hungary
| | - Ernesto Lahoz
- Research Centre for Cereal and Industrial Crops (CREA-CI), via Torrino 3, 81100, Caserta, Italy
| | - Jason Risteski
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Emma T. Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Maurizio Viscardi
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055, Portici, Naples, Italy
| | - Magriet A. van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Yuan Wu
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hao Yu
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - Jianjin Zhou
- Technology Center, Xiamen Customs, Xiamen 361026, China
| | - Chinthani S. Karandeni Dewage
- Sanming Academy of Agricultural Sciences/Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming, Fujian 365051, China
| | - Loly I. Kotta-Loizou
- Sanming Academy of Agricultural Sciences/Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming, Fujian 365051, China
| | - Henrik U. Stotz
- Sanming Academy of Agricultural Sciences/Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming, Fujian 365051, China
| | - Bruce D. L. Fitt
- Sanming Academy of Agricultural Sciences/Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming, Fujian 365051, China
| | - Yongju Huang
- Sanming Academy of Agricultural Sciences/Fujian Key Laboratory of Crop Genetic Improvement and Innovative Utilization for Mountain Area, Sanming, Fujian 365051, China
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
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Bundhun D, Jones EBG, Jayawardena RS, Camporesi E, Wanasinghe DN, Senanayake IC, Thiyagaraja V, Hyde KD. Taxonomic novelty in Pleomonodictydaceae and new reports for Ampelomycesquisqualis (Phaeosphaeriaceae), Melomastiamaolanensis and M.oleae (Pleurotremataceae). MycoKeys 2024; 111:147-180. [PMID: 39723167 PMCID: PMC11669012 DOI: 10.3897/mycokeys.111.135456] [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: 08/24/2024] [Accepted: 10/26/2024] [Indexed: 12/28/2024] Open
Abstract
This study introduces a novel genus Robiniigena, with its type R.hyalinospora. The specimen was collected on dead aerial branches of Robiniapseudoacacia in Italy. Based on the examination of morphology and the results of phylogenetic analyses involving nuclear 18S rDNA (SSU), nuclear 28S rDNA (LSU), nuclear rDNA ITS1-5.8S-ITS2 (ITS), translation elongation factor 1-alpha (tef1-α) and RNA polymerase II second largest subunit (rpb2) sequences, Robiniigena is referred to the family Pleomonodictydaceae (Pleosporales). It is characterized by immersed to erumpent, ostiolate ascomata, filiform, septate and cellular pseudoparaphyses, bitunicate, clavate to cylindric-clavate asci and fusiform, hyaline ascospores surrounded by a mucilaginous sheath. This research also establishes the taxonomic placement of the previously unclassified Inflatispora (Pleosporales genus incertae sedis) within the Pleomonodictydaceae. The sexual morph of Ampelomycesquisqualis (Phaeosphaeriaceae) is described for the first time and it is characterized by immersed, perithecial ascomata, a peridium comprising two layers, branched, septate and filiform pseudoparaphyses, short-pedicellate, bitunicate asci with an ocular chamber and sub-hyaline, fusiform, septate ascospores. This species, previously known only in its asexual morph, has been found as a saprobe on Sonchus sp. in Italy. Our identification of the sexual morph was based on LSU rDNA and ITS rDNA sequence data. Melomastiamaolanensis (Pleurotremataceae) is reported for the first time in Thailand, collected from Chromolaenaodorata, while M.oleae is documented as a new record from Durantaerecta in Thailand.
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Affiliation(s)
- Digvijayini Bundhun
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - E. B. Gareth Jones
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | | | - Erio Camporesi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Gruppo Micologico Forlivese “Antonio Cicognani”, Via Roma 18, Forli, Italy
| | - Dhanushka N. Wanasinghe
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- A.M.B, Circolo Micologico “Giovanni carini”, C.P. 314, Brescia, Italy
| | - Indunil C. Senanayake
- Center for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe County 654400, China
| | - Vinodhini Thiyagaraja
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Kevin D. Hyde
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
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Liu L, Yang C, Liang F, Li C, Zeng Q, Han S, Li S, Liu Y. Genome-wide survey of the bipartite structure and pathogenesis-related genes of Neostagonosporella sichuanensis, a causal agent of Fishscale bamboo rhombic-spot disease. Front Microbiol 2024; 15:1456993. [PMID: 39360322 PMCID: PMC11444983 DOI: 10.3389/fmicb.2024.1456993] [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: 06/29/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024] Open
Abstract
Bamboo resources have garnered significant global attention due to their excellent capacity for regeneration and high yield. Rhombic-spot disease, a substantial threat to fishscale bamboo (Phyllostachys heteroclada), is primarily caused by Neostagonosporella sichuanensis. This study first reported the genome assemblies and characteristics of two N. sichuanensis isolates using PacBio and Illumina sequencing platforms. The genomes of N. sichuanensis strain SICAUCC 16-0001 and strain SICAUCC 23-0140, with sizes of 48.0 Mb and 48.4 Mb, respectively, revealed 10,289 and 10,313 protein-coding genes. Additionally, they contained 34.99 and 34.46% repetitive sequences within AT-rich regions, with notable repeat-induced point mutation activity. Comparative genome analysis identified 1,049 contracted and 45 expanded gene families in the genome of N. sichuanensis, including several related to pathogenicity. Several gene families involved in mycotoxin metabolism, secondary metabolism, sterol biosynthesis and transport, and cell wall degradation were contracted. Compared to most analyzed necrotrophic, hemibiotrophic, and phaeosphaeriacous pathogens, the genomes of two N. sichuanensis isolates exhibited fewer secondary metabolite enzymes, carbohydrate-active enzymes, plant cell wall degrading enzymes, secreted proteins, and effectors. Comparative genomics analysis suggested that N. sichuanensis shares more similar characteristics with hemibiotrophic pathogens. Based on single carbon source tests, N. sichuanensis strains demonstrated a higher potential for xylan decomposition than pectin and cellulose. The proportion of cell wall-degrading enzyme effectors occupied a high proportion of the total effectors of the N. sichuanensis genomes. These findings provide valuable insights into uncovering the pathogenesis of N. sichuanensis toward the efficient management of rhombic-spot disease of fishscale bamboo.
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Affiliation(s)
- Lijuan Liu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Chunlin Yang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Fang Liang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Chengsong Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Qian Zeng
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yinggao Liu
- College of Forestry, Sichuan Agricultural University, Chengdu, China
- National Forestry and Grassland Administration, Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River and Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, China
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Bermúdez-Cova MA, Cruz-Laufer AJ, Piepenbring M. Hyperparasitic Fungi on Black Mildews (Meliolales, Ascomycota): Hidden Fungal Diversity in the Tropics. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:885279. [PMID: 37746226 PMCID: PMC10512288 DOI: 10.3389/ffunb.2022.885279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 09/26/2023]
Abstract
Hyperparasitism on plant-parasitic fungi is a widespread but rarely studied phenomenon. Here, for the first time, we compile in a checklist information provided by peer-reviewed literature for fungi growing on colonies of black mildews (Meliolales, Ascomycota), a species-rich group of tropical and subtropical plant-parasitic microfungi. The checklist contains information on 189 species of contact-biotrophic microfungi in 82 genera. They belong to seven morphological groups: dematiaceous hyphomycetes, moniliaceous hyphomycetes, pycnidioid, perithecioid, catathecioid, and apothecioid fungi. By the fact that species accumulation curves do not reach saturation for any tropical country, it is evident that the knowledge of the diversity of hyperparasitic fungi on Meliolales is incomplete. A network analysis of records of hyperparasitic fungi, their host fungi and host plants shows that genera of hyperparasitic fungi are generalists concerning genera of Meliolales. However, most species of hyperparasitic fungi are restricted to meliolalean hosts. In addition to hyperparasitic fungi, diverse further microorganisms use meliolalean colonies as ecological niche. Systematic positions of most species are unknown because DNA sequence data are lacking for species of fungi hyperparasitic on Meliolales. We discuss the specific challenges of obtaining DNA sequence data from hyperparasitic fungi. In order to better understand the diversity, evolution and biology of hyperparasitic fungi, it is necessary to increase sampling efforts and to undertake further morphological, molecular, and ecological studies.
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Affiliation(s)
- Miguel A. Bermúdez-Cova
- Mycology Research Group, Faculty of Biological Sciences, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Departamento de Biología de Organismos, División de Ciencias Biológicas, Universidad Simón Bolívar, Caracas, Venezuela
| | - Armando J. Cruz-Laufer
- Centre for Environmental Sciences, Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
| | - Meike Piepenbring
- Mycology Research Group, Faculty of Biological Sciences, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
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