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Wang H, Yao G, Chen W, Ayhan DH, Wang X, Sun J, Yi S, Meng T, Chen S, Geng X, Meng D, Zhang L, Guo L. A gap-free genome assembly of Fusarium oxysporum f. sp. conglutinans, a vascular wilt pathogen. Sci Data 2024; 11:925. [PMID: 39191793 PMCID: PMC11349993 DOI: 10.1038/s41597-024-03763-6] [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: 07/24/2023] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Fusarium oxysporum is an asexual filamentous fungus that causes vascular wilt in hundreds of crop plants and poses a threat to public health through Fusariosis. F. oxysporum f. sp. conglutinans strain Fo5176, originally isolated from Brassica oleracea, is pathogenic to Arabidopsis, making it a model pathosystem for dissecting the molecular mechanisms underlying host-pathogen interactions. Assembling the F. oxysporum genome is notoriously challenging due to the presence of repeat-rich accessory chromosomes. Here, we report a gap-free genome assembly of Fo5176 using PacBio HiFi and Hi-C data. The 69.56 Mb assembly contained 18 complete chromosomes, including all centromeres and most telomeres (20/36), representing the first gap-free genome sequence of a pathogenic F. oxysporum strain. In total, 21,460 protein-coding genes were annotated, a 26.3% increase compared to the most recent assembly. This high-quality reference genome for F. oxysporum f. sp. conglutinans Fo5176 provides a valuable resource for further research into fungal pathobiology and evolution.
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Affiliation(s)
- Huan Wang
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Gang Yao
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
- Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Weikai Chen
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Dilay Hazal Ayhan
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xiangfeng Wang
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Jie Sun
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Shu Yi
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Tan Meng
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Shaoying Chen
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Xin Geng
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Dian Meng
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Lili Zhang
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
- Weifang Institute of Technology, College of Modern Agriculture and Environment, Weifang, Shandong, 262500, China.
| | - Li Guo
- Shandong Provincial Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
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Yang M, Smit S, de Ridder D, Feng J, Liu T, Xu J, van der Lee TAJ, Zhang H, Chen W. Adaptation of Fusarium Head Blight Pathogens to Changes in Agricultural Practices and Human Migration. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401899. [PMID: 39099330 DOI: 10.1002/advs.202401899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/28/2024] [Indexed: 08/06/2024]
Abstract
Fusarium head blight (FHB) is one of the most destructive wheat diseases worldwide. To understand the impact of human migration and changes in agricultural practices on crop pathogens, here population genomic analysis with 245 representative strains from a collection of 4,427 field isolates of Fusarium asiaticum, the causal agent of FHB in Southern China is conducted. Three populations with distinct evolution trajectories are identifies over the last 10,000 years that can be correlated with historically documented changes in agricultural practices due to human migration caused by the Southern Expeditions during the Jin Dynasty. The gradual decrease of 3ADON-producing isolates from north to south along with the population structure and spore dispersal patterns shows the long-distance (>250 km) dispersal of F. asiaticum. These insights into population dynamics and evolutionary history of FHB pathogens are corroborated by a genome-wide analysis with strains originating from Japan, South America, and the USA, confirming the adaptation of FHB pathogens to cropping systems and human migration.
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Affiliation(s)
- Meixin Yang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB, 6708, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB, 6708, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, PB, 6708, The Netherlands
| | - Jie Feng
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Tianshui, 741200, P. R. China
| | - Jinrong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Droevendaalsesteeg 1, Wageningen, PB, 6708, The Netherlands
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Tianshui, 741200, P. R. China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
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Logachev A, Kanapin A, Rozhmina T, Stanin V, Bankin M, Samsonova A, Orlova E, Samsonova M. Pangenomics of flax fungal parasite Fusarium oxysporum f. sp. lini. FRONTIERS IN PLANT SCIENCE 2024; 15:1383914. [PMID: 38872883 PMCID: PMC11169931 DOI: 10.3389/fpls.2024.1383914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.
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Affiliation(s)
- Anton Logachev
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Alexander Kanapin
- Center for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Rozhmina
- Flax Institute, Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Vladislav Stanin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Mikhail Bankin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Anastasia Samsonova
- Center for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Ekaterina Orlova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
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Garcia JF, Morales-Cruz A, Cochetel N, Minio A, Figueroa-Balderas R, Rolshausen PE, Baumgartner K, Cantu D. Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors Among Grapevine Trunk Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:127-142. [PMID: 37934016 DOI: 10.1094/mpmi-09-23-0129-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: 11/08/2023]
Abstract
The permanent organs of grapevines (Vitis vinifera L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in E. lata and P. minimum, glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence. [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)
- Jadran F Garcia
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, U.S.A
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, U.S.A
| | - Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Davis, CA, U.S.A
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, U.S.A
- Genome Center, University of California, Davis, Davis, CA, U.S.A
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De Vos L, van der Nest MA, Santana QC, van Wyk S, Leeuwendaal KS, Wingfield BD, Steenkamp ET. Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum. Pathogens 2024; 13:70. [PMID: 38251377 PMCID: PMC10819268 DOI: 10.3390/pathogens13010070] [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: 12/03/2023] [Revised: 12/26/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome's distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.
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Affiliation(s)
- Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Magriet A. van der Nest
- Hans Merensky Chair in Avocado Research, Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute FABI, University of Pretoria, Pretoria 0002, South Africa;
| | - Quentin C. Santana
- Biotechnology Platform, Agricultural Research Council, 100 Old Soutpan Road, Onderstepoort, Pretoria 0010, South Africa;
| | - Stephanie van Wyk
- Collaborating Centre for Optimising Antimalarial Therapy (CCOAT), Mitigating Antimalarial Resistance Consortium in South-East Africa (MARC SEA), Department of Medicine, Division of Clinical Pharmacology, University of Cape Town, Cape Town 7925, South Africa;
| | - Kyle S. Leeuwendaal
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
| | - Emma T. Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria (UP), Pretoria 0002, South Africa; (L.D.V.); (K.S.L.); (B.D.W.)
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He T, Li X, Iacovelli R, Hackl T, Haslinger K. Genomic and Metabolomic Analysis of the Endophytic Fungus Fusarium sp. VM-40 Isolated from the Medicinal Plant Vinca minor. J Fungi (Basel) 2023; 9:704. [PMID: 37504693 PMCID: PMC10381429 DOI: 10.3390/jof9070704] [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: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
The genus Fusarium is well-known to comprise many pathogenic fungi that affect cereal crops worldwide, causing severe damage to agriculture and the economy. In this study, an endophytic fungus designated Fusarium sp. VM-40 was isolated from a healthy specimen of the traditional European medicinal plant Vinca minor. Our morphological characterization and phylogenetic analysis reveal that Fusarium sp. VM-40 is closely related to Fusarium paeoniae, belonging to the F. tricinctum species complex (FTSC), the genomic architecture and secondary metabolite profile of which have not been investigated. Thus, we sequenced the whole genome of Fusarium sp. VM-40 with the new Oxford Nanopore R10.4 flowcells. The assembled genome is 40 Mb in size with a GC content of 47.72%, 15 contigs (≥50,000 bp; N 50~4.3 Mb), and 13,546 protein-coding genes, 691 of which are carbohydrate-active enzyme (CAZyme)-encoding genes. We furthermore predicted a total of 56 biosynthetic gene clusters (BGCs) with antiSMASH, 25 of which showed similarity with known BGCs. In addition, we explored the potential of this fungus to produce secondary metabolites through untargeted metabolomics. Our analyses reveal that this fungus produces structurally diverse secondary metabolites of potential pharmacological relevance (alkaloids, peptides, amides, terpenoids, and quinones). We also employed an epigenetic manipulation method to activate cryptic BGCs, which led to an increased abundance of several known compounds and the identification of several putative new compounds. Taken together, this study provides systematic research on the whole genome sequence, biosynthetic potential, and metabolome of the endophytic fungus Fusarium sp. VM-40.
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Affiliation(s)
- Ting He
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Xiao Li
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Riccardo Iacovelli
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Thomas Hackl
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Kristina Haslinger
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Yu H, Yang H, Haridas S, Hayes RD, Lynch H, Andersen S, Newman M, Li G, Martínez-Soto D, Milo-Cochavi S, Hazal Ayhan D, Zhang Y, Grigoriev IV, Ma LJ. Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex. J Fungi (Basel) 2023; 9:359. [PMID: 36983527 PMCID: PMC10056406 DOI: 10.3390/jof9030359] [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: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The Fusarium oxysporum species complex (FOSC) includes both plant and human pathogens that cause devastating plant vascular wilt diseases and threaten public health. Each F. oxysporum genome comprises core chromosomes (CCs) for housekeeping functions and accessory chromosomes (ACs) that contribute to host-specific adaptation. This study inspects global transcription factor profiles (TFomes) and their potential roles in coordinating CC and AC functions to accomplish host-specific interactions. Remarkably, we found a clear positive correlation between the sizes of TFomes and the proteomes of an organism. With the acquisition of ACs, the FOSC TFomes were larger than the other fungal genomes included in this study. Among a total of 48 classified TF families, 14 families involved in transcription/translation regulations and cell cycle controls were highly conserved. Among the 30 FOSC expanded families, Zn2-C6 and Znf_C2H2 were most significantly expanded to 671 and 167 genes per family including well-characterized homologs of Ftf1 (Zn2-C6) and PacC (Znf_C2H2) that are involved in host-specific interactions. Manual curation of characterized TFs increased the TFome repertoires by 3% including a disordered protein Ren1. RNA-Seq revealed a steady pattern of expression for conserved TF families and specific activation for AC TFs. Functional characterization of these TFs could enhance our understanding of transcriptional regulation involved in FOSC cross-kingdom interactions, disentangle species-specific adaptation, and identify targets to combat diverse diseases caused by this group of fungal pathogens.
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Affiliation(s)
- Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - He Yang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sajeet Haridas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Richard D. Hayes
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
| | - Hunter Lynch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Sawyer Andersen
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Madison Newman
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Gengtan Li
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Domingo Martínez-Soto
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Shira Milo-Cochavi
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Dilay Hazal Ayhan
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Yong Zhang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94598, USA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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8
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Li J, He K, Zhang Q, Wu X, Li Z, Pan X, Wang Y, Li C, Zhang M. Draft Genome and Biological Characteristics of Fusarium solani and Fusarium oxysporum Causing Black Rot in Gastrodia elata. Int J Mol Sci 2023; 24:ijms24054545. [PMID: 36901977 PMCID: PMC10003674 DOI: 10.3390/ijms24054545] [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: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Gastrodia elata is a valuable traditional Chinese medicinal plant. However, G. elata crops are affected by major diseases, such as brown rot. Previous studies have shown that brown rot is caused by Fusarium oxysporum and F. solani. To further understand the disease, we studied the biological and genome characteristics of these pathogenic fungi. Here, we found that the optimum growth temperature and pH of F. oxysporum (strain QK8) and F. solani (strain SX13) were 28 °C and pH 7, and 30 °C and pH 9, respectively. An indoor virulence test showed that oxime tebuconazole, tebuconazole, and tetramycin had significant bacteriostatic effects on the two Fusarium species. The genomes of QK8 and SX13 were assembled, and it was found that there was a certain gap in the size of the two fungi. The size of strain QK8 was 51,204,719 bp and that of strain SX13 was 55,171,989 bp. Afterwards, through phylogenetic analysis, it was found that strain QK8 was closely related to F. oxysporum, while strain SX13 was closely related to F. solani. Compared with the published whole-genome data for these two Fusarium strains, the genome information obtained here is more complete; the assembly and splicing reach the chromosome level. The biological characteristics and genomic information we provide here lay the foundation for further research on G. elata brown rot.
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Affiliation(s)
- Jinshao Li
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Ke He
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Qian Zhang
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xiaoyi Wu
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Zhong Li
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Xuejun Pan
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Yong Wang
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Cheng Li
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
- Correspondence: (C.L.); (M.Z.)
| | - Manman Zhang
- Key Laboratory of Agricultural Microbiology of Guizhou Province, College of Agriculture, Guizhou University, Guiyang 550025, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (C.L.); (M.Z.)
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Martínez-Soto D, Yu H, Allen KS, Ma LJ. Differential Colonization of the Plant Vasculature Between Endophytic Versus Pathogenic Fusarium oxysporum Strains. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:4-13. [PMID: 36279112 PMCID: PMC10052776 DOI: 10.1094/mpmi-08-22-0166-sc] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Plant xylem colonization is the hallmark of vascular wilt diseases caused by phytopathogens within the Fusarium oxysporum species complex. Recently, xylem colonization has also been reported among endophytic F. oxysporum strains, resulting in some uncertainty. This study compares xylem colonization processes by pathogenic versus endophytic strains in Arabidopsis thaliana and Solanum lycopersicum, using Arabidopsis pathogen Fo5176, tomato pathogen Fol4287, and the endophyte Fo47, which can colonize both plant hosts. We observed that all strains were able to advance from epidermis to endodermis within 3 days postinoculation (dpi) and reached the root xylem at 4 dpi. However, this shared progression was restricted to lateral roots and the elongation zone of the primary root. Only pathogens reached the xylem above the primary-root maturation zone (PMZ). Related to the distinct colonization patterns, we also observed stronger induction of callose at the PMZ and lignin deposition at primary-lateral root junctions by the endophyte in both plants. This observation was further supported by stronger induction of Arabidopsis genes involved in callose and lignin biosynthesis during the endophytic colonization (Fo47) compared with the pathogenic interaction (Fo5176). Moreover, both pathogens encode more plant cell wall-degrading enzymes than the endophyte Fo47. Therefore, observed differences in callose and lignin deposition could be the combination of host production and the subsequent fungal degradation. In summary, this study demonstrates spatial differences between endophytic and pathogenic colonization, strongly suggesting that further investigations of molecular arm-races are needed to understand how plants differentiate friend from foe. [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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10
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Wang L, Calabria J, Chen HW, Somssich M. The Arabidopsis thaliana-Fusarium oxysporum strain 5176 pathosystem: an overview. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6052-6067. [PMID: 35709954 PMCID: PMC9578349 DOI: 10.1093/jxb/erac263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Fusarium oxysporum is a soil-borne fungal pathogen of several major food crops. Research on understanding the molecular details of fungal infection and the plant's defense mechanisms against this pathogen has long focused mainly on the tomato-infecting F. oxysporum strains and their specific host plant. However, in recent years, the Arabidopsis thaliana-Fusarium oxysporum strain 5176 (Fo5176) pathosystem has additionally been established to study this plant-pathogen interaction with all the molecular biology, genetic, and genomic tools available for the A. thaliana model system. Work on this system has since produced several new insights, especially with regards to the role of phytohormones involved in the plant's defense response, and the receptor proteins and peptide ligands involved in pathogen detection. Furthermore, work with the pathogenic strain Fo5176 and the related endophytic strain Fo47 has demonstrated the suitability of this system for comparative studies of the plant's specific responses to general microbe- or pathogen-associated molecular patterns. In this review, we highlight the advantages of this specific pathosystem, summarize the advances made in studying the molecular details of this plant-fungus interaction, and point out open questions that remain to be answered.
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Affiliation(s)
- Liu Wang
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jacob Calabria
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hsiang-Wen Chen
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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11
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Insights on KP4 Killer Toxin-like Proteins of Fusarium Species in Interspecific Interactions. J Fungi (Basel) 2022; 8:jof8090968. [PMID: 36135693 PMCID: PMC9506348 DOI: 10.3390/jof8090968] [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: 08/09/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
KP4 killer toxins are secreted proteins that inhibit cell growth and induce cell death in target organisms. In Fusarium graminearum, KP4-like (KP4L) proteins contribute to fungal virulence in wheat seedling rot and are expressed during Fusarium head blight development. However, fungal KP4L proteins are also hypothesized to support fungal antagonism by permeabilizing cell walls of competing fungi to enable penetration of toxic compounds. Here, we report the differential expression patterns of F. graminearum KP4L genes (Fgkp4l-1, -2, -3 and -4) in a competitive interaction, using Trichoderma gamsii as the antagonist. The results from dual cultures indicate that Fgkp4l-3 and Fgkp4l-4 could participate in the recognition at the distance of the antagonist, while all Fgkp4l genes were highly activated in the pathogen during the physical interaction of both fungi. Only Fgkp4l-4 was up-regulated during the interaction with T. gamsii in wheat spikes. This suggests the KP4L proteins could participate in supporting F. graminearum interspecific interactions, even in living plant tissues. The distribution of KP4L orthologous within the genus Fusarium revealed they are more represented in species with broad host-plant range than in host-specific species. Phylogeny inferred provides evidence that KP4L genes evolved through gene duplications, gene loss and sequence diversification in the genus Fusarium.
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12
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Kuang W, Zhang L, Ye L, Ma J, Shi X, Lin Y, Sun X, Cui R. Genome and Transcriptome Sequencing Analysis of Fusarium commune Provides Insights into the Pathogenic Mechanisms of the Lotus Rhizome Rot. Microbiol Spectr 2022; 10:e0017522. [PMID: 35867414 PMCID: PMC9431280 DOI: 10.1128/spectrum.00175-22] [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: 01/17/2022] [Accepted: 06/04/2022] [Indexed: 11/20/2022] Open
Abstract
Fusarium wilt, a vascular wilt caused by F. commune, has been a serious problem for the lotus. Although some F. commune isolate genomes have been sequenced, little is known about the genomic information of the strain that causes Fusarium wilt of aquatic plants. In this study, the genome of F. commune FCN23 isolated from lotuses in China was sequenced using Illumina and PacBio sequencing platforms. The FCN23 genome consisted of 53 scaffolds with a combined size of 46,211,149 bp. According to the reference genome, F. oxysporum f. sp. lycopersici 4287 isolated from tomato, it was finally assembled into 14 putative chromosomes, including 10 core and 4 lineage-specific chromosomes. The genome contains about 3.45% repeats and encodes 14,698 putative protein-coding genes. Among these, 1,038 and 296 proteins were potentially secreted proteins and candidate effector proteins, respectively. Comparative genomic analysis showed that the CAZyme-coding genes and secondary metabolite biosynthesis genes of FCN23 were similar to those of other Ascomycetes. Additionally, the transcriptome of FCN23 during infection of lotus was analyzed and 7,013 differentially expressed genes were identified. Eight putative effectors that were upregulated in the infection stage were cloned. Among them, F23a002499 exhibited strong hypersensitive response after transiently expressed in Nicotiana benthamiana leaves. Our results provide a valuable genetic basis for understanding the molecular mechanism of the interaction between F. commune and aquatic plants. IMPORTANCE Fusarium commune is an important soilborne pathogen with a wide range of hosts and can cause Fusarium wilt of land plants. However, there are few studies on Fusarium wilt of aquatic plants. Lotus rhizome rot mainly caused by F. commune is a devastating disease that causes extensive yield and quality losses in China. Here, we obtained high-quality genomic information of the FCN23 using Illumina NovaSeq and the third-generation sequencing technology PacBio Sequel II. Compared to the reference genome F. oxysporum f. sp. lycopersici strain 4287, it contains 11 core and 3 lineage-specific chromosomes. Many differentially expressed genes associated with pathogenicity were identified by RNA sequencing. The genome and transcriptome sequences of FCN23 will provide important genomic information and insights into the infection mechanisms of F. commune on aquatic plants.
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Affiliation(s)
- Weigang Kuang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lianhu Zhang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lifang Ye
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jian Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xugen Shi
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yachun Lin
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xiaotang Sun
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ruqiang Cui
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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13
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Fulton JC, Yu PL, Smith KE, Huguet-Tapia JC, Hudson O, Meeks A, Quesada T, McKeever K, Brawner JT. Comparative Genomics of Fusarium circinatum Isolates Used to Screen Southern Pines for Pitch Canker Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:477-487. [PMID: 35266808 DOI: 10.1094/mpmi-10-21-0247-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Pitch canker, caused by the fungal pathogen Fusarium circinatum, is a global disease affecting many Pinus spp. Often fatal, this disease causes significant mortality in both commercially grown and natural pine forests and is an issue of current and growing concern. F. circinatum isolates collected from three locations in the U.S. state of Florida were shown to be virulent on both slash and loblolly pine, with two of the isolates causing equivalent and significantly larger lesions than those caused by the third isolate during pathogenicity trials. In addition, significant genetic variation in lesion length in the pedigreed slash pine population was evident and rankings of parents for lesion length were similar across isolates. Experimental data demonstrate that both host and pathogen genetics contribute to disease severity. High-quality genomic assemblies of all three isolates were created and compared for structural differences and gene content. No major structural differences were observed among the isolates; however, missing or altered genes do contribute to genomic variation in the pathogen population. This work evaluates in planta virulence among three isolates of F. circinatum, provides genomic resources to facilitate study of this organism, and details comparative genomic methods that may be used to explore the pathogen's contribution to disease development.[Formula: see text] Copyright © 2022 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)
- James C Fulton
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Pei-Ling Yu
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Katherine E Smith
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL, U.S.A
- United States Department of Agriculture Forest Service, Southern Institute of Forest Genetics, Saucier, MS, U.S.A
| | - Jose C Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Owen Hudson
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | | | - Tania Quesada
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL, U.S.A
| | - Kathleen McKeever
- United States Department of Agriculture Forest Service, Resistance Screening Center, Asheville, NC, U.S.A
| | - Jeremy T Brawner
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
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14
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Redkar A, Gimenez Ibanez S, Sabale M, Zechmann B, Solano R, Di Pietro A. Marchantia polymorpha model reveals conserved infection mechanisms in the vascular wilt fungal pathogen Fusarium oxysporum. THE NEW PHYTOLOGIST 2022; 234:227-241. [PMID: 34877655 DOI: 10.1111/nph.17909] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Root-infecting vascular fungi cause wilt diseases and provoke devastating losses in hundreds of crops. It is currently unknown how these pathogens evolved and whether they can also infect nonvascular plants, which diverged from vascular plants over 450 million years ago. We established a pathosystem between the nonvascular plant Marchantia polymorpha (Mp) and the root-infecting vascular wilt fungus Fusarium oxysporum (Fo). On angiosperms, Fo exhibits exquisite adaptation to the plant xylem niche as well as host-specific pathogenicity, both of which are conferred by effectors encoded on lineage-specific chromosomes. Fo isolates displaying contrasting lifestyles on angiosperms - pathogenic vs endophytic - are able to infect Mp and cause tissue maceration and host cell killing. Using isogenic fungal mutants we define a set of conserved fungal pathogenicity factors, including mitogen activated protein kinases, transcriptional regulators and cell wall remodelling enzymes, that are required for infection of both vascular and nonvascular plants. Markedly, two host-specific effectors and a morphogenetic regulator, which contribute to vascular colonisation and virulence on tomato plants are dispensable on Mp. Collectively, these findings suggest that vascular wilt fungi employ conserved infection strategies on nonvascular and vascular plant lineages but also have specific mechanisms to access the vascular niche of angiosperms.
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Affiliation(s)
- Amey Redkar
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
| | - Selena Gimenez Ibanez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
| | - Mugdha Sabale
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
| | - Bernd Zechmann
- Center for Microscopy and Imaging, Baylor University, Waco, TX, 76798, USA
| | - Roberto Solano
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
| | - Antonio Di Pietro
- Departamento de Genética, Universidad de Córdoba, Córdoba, 14071, Spain
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15
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Mirghasempour SA, Studholme DJ, Chen W, Cui D, Mao B. Identification and Characterization of Fusarium nirenbergiae Associated with Saffron Corm Rot Disease. PLANT DISEASE 2022; 106:486-495. [PMID: 35113681 DOI: 10.1094/pdis-04-21-0871-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Saffron (Crocus sativus L.) is the most expensive spice plant and is distributed widely around the world. However, its production is limited by corm rot, a disastrous disease, attributed to Fusarium oxysporum in many regions of the world. In 2020, extensive surveys were carried out in Zhejiang, Shanghai, Anhui, and Guizhou provinces as saffron growing areas of China. Fourteen single-spore isolates were obtained from rotted corms and identified as F. nirenbergiae according to morphological appearance and multilocus phylogenetic analysis with translation elongation factor 1-α (tef1), DNA-directed RNA polymerase II largest subunit (rpb2), and β-tubulin (tub2). Results of the pathogenicity assay supported the conclusion that F. nirenbergiae is the pathogen responsible for corm rot. In this study, we obtained the whole genome sequence of two highly virulent F. nirenbergiae strains via the Illumina HiSeq platform. Genome sequence assemblies of approximately 52.7 and 52.2 Mb were generated for isolates WY5 and SH1, respectively. To the best of our knowledge, this is the first report of F. nirenbergiae causing C. sativus corm rot in China and indeed worldwide. Results from this research contribute to our understanding of genetic diversity, genomic information, and host determination, which will enable researchers to design appropriate management measures for this hazardous disease.
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Affiliation(s)
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, Devon, EX4 4QD, United Kingdom
| | - Weiliang Chen
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Dongzhu Cui
- Agricultural Technology Extension Service Center of Jiande City, Jiande, 311600, China
| | - Bizeng Mao
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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16
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McTaggart AR, James TY, Shivas RG, Drenth A, Wingfield BD, Summerell BA, Duong TA. Population genomics reveals historical and ongoing recombination in the Fusarium oxysporum species complex. Stud Mycol 2022; 99:100132. [PMID: 35027981 PMCID: PMC8693468 DOI: 10.1016/j.simyco.2021.100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Fusarium oxysporum species complex (FOSC) is a group of closely related plant pathogens long-considered strictly clonal, as sexual stages have never been recorded. Several studies have questioned whether recombination occurs in FOSC, and if it occurs its nature and frequency are unknown. We analysed 410 assembled genomes to answer whether FOSC diversified by occasional sexual reproduction interspersed with numerous cycles of asexual reproduction akin to a model of predominant clonal evolution (PCE). We tested the hypothesis that sexual reproduction occurred in the evolutionary history of FOSC by examining the distribution of idiomorphs at the mating locus, phylogenetic conflict and independent measures of recombination from genome-wide SNPs and genes. A phylogenomic dataset of 40 single copy orthologs was used to define structure a priori within FOSC based on genealogical concordance. Recombination within FOSC was tested using the pairwise homoplasy index and divergence ages were estimated by molecular dating. We called SNPs from assembled genomes using a k-mer approach and tested for significant linkage disequilibrium as an indication of PCE. We clone-corrected and tested whether SNPs were randomly associated as an indication of recombination. Our analyses provide evidence for sexual or parasexual reproduction within, but not between, clades of FOSC that diversified from a most recent common ancestor about 500 000 years ago. There was no evidence of substructure based on geography or host that might indicate how clades diversified. Competing evolutionary hypotheses for FOSC are discussed in the context of our results.
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Affiliation(s)
- A R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, 4102, Queensland, Australia
| | - T Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - R G Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, 4350, Australia
| | - A Drenth
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, 4102, Queensland, Australia
| | - B D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
| | - B A Summerell
- Australian Institute of Botanical Science, Royal Botanic Gardens & Domain Trust, Sydney, Australia
| | - T A Duong
- Department of Biochemistry, Genetics and Microbiology, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa
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17
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Shishupala S. Biocontrol Potential of Fungi for Pest and Pathogen Management. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Brizuela AM, Lalak-Kańczugowska J, Koczyk G, Stępień Ł, Kawaliło M, Palmero D. Geographical Origin Does Not Modulate Pathogenicity or Response to Climatic Variables of Fusarium oxysporum Associated with Vascular Wilt on Asparagus. J Fungi (Basel) 2021; 7:jof7121056. [PMID: 34947038 PMCID: PMC8703408 DOI: 10.3390/jof7121056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Asparagus crop is distributed worldwide, covering very different climatic regions. Among the different diseases that affect asparagus, vascular Fusarium wilt, caused by Fusarium oxysporum f. sp. aparagi (Foa), stands out. It is not only the cause of large economic losses due to a decrease in yield and shortened longevity of the plantation, but also prevents replanting. This work aimed to determine if F. oxysporum isolates associated with vascular wilt on asparagus have adapted differentially to the different agro-environmental conditions. The potential correlation between origin and mycelial growth under different temperatures and humidity conditions was analysed for isolates from asparagus fields cultivated in northern and southern Europe. The genetic and pathogenic variability were also analysed. While a clear effect of water activity on mycelial growth was observed, all isolates responded in a similar way to changes in water activity in the medium, regardless of their geographical origin. The results revealed a low genetic variability of F. oxysporum isolates associated with vascular wilt on asparagus without signs of differentiation correlated to geographical origin. The southernmost isolates of the two cultivated varieties inoculated did not express more pathogenicity than those isolated from the colder region.
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Affiliation(s)
- Alexandri María Brizuela
- Department of Agricultural Production, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain;
| | - Justyna Lalak-Kańczugowska
- Plant-Pathogen Interaction Team, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; (J.L.-K.); (Ł.S.)
| | - Grzegorz Koczyk
- Biometry and Bioinformatics Team, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; (G.K.); (M.K.)
| | - Łukasz Stępień
- Plant-Pathogen Interaction Team, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; (J.L.-K.); (Ł.S.)
| | - Michał Kawaliło
- Biometry and Bioinformatics Team, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland; (G.K.); (M.K.)
| | - Daniel Palmero
- Department of Agricultural Production, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain;
- Correspondence: ; Tel.: +34-91-067-1075
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19
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Guo L, Yu H, Wang B, Vescio K, Delulio GA, Yang H, Berg A, Zhang L, Edel-Hermann V, Steinberg C, Kistler HC, Ma LJ. Metatranscriptomic Comparison of Endophytic and Pathogenic Fusarium-Arabidopsis Interactions Reveals Plant Transcriptional Plasticity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1071-1083. [PMID: 33856230 PMCID: PMC9048145 DOI: 10.1094/mpmi-03-21-0063-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two F. oxysporum strains share a core genome of about 46 Mb, in addition to 1,229 and 5,415 unique accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (about 80%) in responding to both fungal inoculums at all timepoints from 12 to 96 h postinoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses functions related to plant growth and development, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest timepoint sampled, and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.[Formula: see text] Copyright © 2021 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)
- Li Guo
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049 China
| | - Houlin Yu
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
| | - Bo Wang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049 China
| | - Kathryn Vescio
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
| | - Gregory A. Delulio
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
| | - He Yang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
| | - Andrew Berg
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
| | - Lili Zhang
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
| | - Véronique Edel-Hermann
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Christian Steinberg
- Agroécologie, AgroSup Dijon, INRA, University of Bourgogne Franche-Comté, F-21000 Dijon, France
| | - H. Corby Kistler
- USDA ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003, U.S.A
- Corresponding author: L.-J. Ma;
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20
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Dvorianinova EM, Pushkova EN, Novakovskiy RO, Povkhova LV, Bolsheva NL, Kudryavtseva LP, Rozhmina TA, Melnikova NV, Dmitriev AA. Nanopore and Illumina Genome Sequencing of Fusarium oxysporum f. sp. lini Strains of Different Virulence. Front Genet 2021; 12:662928. [PMID: 34220940 PMCID: PMC8248858 DOI: 10.3389/fgene.2021.662928] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/06/2021] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ekaterina M Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Elena N Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Roman O Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Liubov V Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Nadezhda L Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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21
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Xingxing P, Khan RAA, Yan L, Yuhong Y, Bingyan X, Zhenchuan M, Jian L. Draft Genome Resource of Fusarium oxysporum f. sp. capsici, the Infectious Agent of Pepper Fusarium Wilt. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:715-717. [PMID: 33512247 DOI: 10.1094/mpmi-12-20-0355-a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fusarium oxysporum f. sp. capsici is the specific pathogen of pepper Fusarium wilt and causes a significant reduction in pepper yield. Its narrow host specificity has led to the concept of formae speciales. This interesting phenomenon has great potential and needs to be analyzed at the molecular level. In this study, we obtained the draft genome sequence of F. oxysporum f. sp. capsici, using the Oxford Nanopore sequencing technology. The long read-based assembly consisted of 34 contigs, with a total length of 54,516,562 bp. The contig N50 was 4,962,668 bp and the GC content was 47.6%. Our genome assembly of F. oxysporum f. sp. capsici provides a valuable resource for the study of pepper Fusarium wilt, and the comparative genomic study of F. oxysporum.[Formula: see text] Copyright © 2021 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)
- Ping Xingxing
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Raja Asad Ali Khan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Department of Plant Pathology, The University of Agriculture Peshawar, 25000, Pakistan
| | - Li Yan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Yuhong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xie Bingyan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mao Zhenchuan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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22
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Cui Y, Wu B, Peng A, Song X, Chen X. The Genome of Banana Leaf Blight Pathogen Fusarium sacchari str. FS66 Harbors Widespread Gene Transfer From Fusarium oxysporum. FRONTIERS IN PLANT SCIENCE 2021; 12:629859. [PMID: 33613610 PMCID: PMC7889605 DOI: 10.3389/fpls.2021.629859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Fusarium species have been identified as pathogens causing many different plant diseases, and here we report an emerging banana leaf blight (BLB) caused by F. sacchari (Fs) discovered in Guangdong, China. From the symptomatic tissues collected in the field, a fungal isolate was obtained, which induced similar symptoms on healthy banana seedlings after inoculation. Koch's postulates were fulfilled after the re-isolation of the pathogen. Phylogenetic analysis on two gene segments and the whole genome sequence identified the pathogen belonging to Fs and named as Fs str. FS66. A 45.74 Mb genome of FS66 was acquired through de novo assembly using long-read sequencing data, and its contig N50 (1.97 Mb) is more than 10-fold larger than the previously available genome in the species. Based on transcriptome sequencing and ab initio gene annotation, a total of 14,486 protein-encoding genes and 418 non-coding RNAs were predicted. A total of 48 metabolite biosynthetic gene clusters including the fusaric acid biosynthesis gene cluster were predicted in silico in the FS66 genome. Comparison between FS66 and other 11 Fusarium genomes identified tens to hundreds of genes specifically gained and lost in FS66, including some previously correlated with Fusarium pathogenicity. The FS66 genome also harbors widespread gene transfer on the core chromosomes putatively from F. oxysporum species complex (FOSC), including 30 involved in Fusarium pathogenicity/virulence. This study not only reports the BLB caused by Fs, but also provides important information and clues for further understanding of the genome evolution among pathogenic Fusarium species.
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Affiliation(s)
- Yiping Cui
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Bo Wu
- School of Computing, Clemson University, Clemson, SC, United States
| | - Aitian Peng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaobing Song
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xia Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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23
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Reinhardt D, Roux C, Corradi N, Di Pietro A. Lineage-Specific Genes and Cryptic Sex: Parallels and Differences between Arbuscular Mycorrhizal Fungi and Fungal Pathogens. TRENDS IN PLANT SCIENCE 2021; 26:111-123. [PMID: 33011084 DOI: 10.1016/j.tplants.2020.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/29/2020] [Accepted: 09/08/2020] [Indexed: 05/25/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) live as obligate root symbionts on almost all land plants. They have long been regarded as ancient asexuals that have propagated clonally for millions of years. However, genomic studies in Rhizophagus irregularis and other AMF revealed many features indicative of sex. Surprisingly, comparative genomics of conspecific isolates of R. irregularis revealed an unexpected interstrain diversity, suggesting that AMF carry a high number of lineage-specific (LS) genes. Intriguingly, cryptic sex and LS genomic regions have previously been reported in a number of fungal pathogens of plants and humans. Here, we discuss these genomic similarities and highlight their potential relevance for AMF adaptation to the environment and for symbiotic functioning.
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Affiliation(s)
- Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, UPS, CNRS, Université de Toulouse, Castanet-Tolosan 31326, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Antonio Di Pietro
- Departamento de Genética, Universidad de Cordoba, 14071 Cordoba, Spain
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