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Lapalu N, Simon A, Lu A, Plaumann PL, Amselem J, Pigné S, Auger A, Koch C, Dallery JF, O'Connell RJ. Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome. Microb Genom 2024; 10:001283. [PMID: 39166978 PMCID: PMC11338638 DOI: 10.1099/mgen.0.001283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 07/22/2024] [Indexed: 08/23/2024] Open
Abstract
Colletotrichum destructivum (Cd) is a phytopathogenic fungus causing significant economic losses on forage legume crops (Medicago and Trifolium species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from Medicago sativa using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises ten core chromosomes and two accessory chromosomes, all of which were sequenced from telomere to telomere. A total of 15, 631 gene models were predicted, including genes encoding potentially pathogenicity-related proteins such as candidate-secreted effectors (484), secondary metabolism key enzymes (110) and carbohydrate-active enzymes (619). Synteny analysis revealed extensive structural rearrangements in the genome of Cd relative to the closely related Brassicaceae pathogen, Colletotrichum higginsianum. In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome of Cd that has all the characteristics of fungal accessory chromosomes (transposon-rich, gene-poor, distinct codon usage), providing evidence for exchange between these two genomic compartments. This region was also unique in having undergone extensive intra-chromosomal segmental duplications. Our findings provide insights into the evolution of accessory regions and possible mechanisms for generating genetic diversity in this asexual fungal pathogen.
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Affiliation(s)
- Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Adeline Simon
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Antoine Lu
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Peter-Louis Plaumann
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Joëlle Amselem
- Université Paris-Saclay, INRAE, URGI, 78000 Versailles, France
| | - Sandrine Pigné
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Annie Auger
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Christian Koch
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
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Ma W, Yang J, Ding J, Duan C, Zhao W, Peng YL, Bhadauria V. CRISPR/Cas9-mediated deletion of large chromosomal segments identifies a minichromosome modulating the Colletotrichum graminicola virulence on maize. Int J Biol Macromol 2023; 245:125462. [PMID: 37336378 DOI: 10.1016/j.ijbiomac.2023.125462] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
Colletotrichum graminicola causes anthracnose on maize, an economically significant disease worldwide. To decipher how the pathogen controls its virulence/pathogenicity on maize at the minichromosomal level, we sequenced the genome and transcriptome of the C. graminicola strain T1-3-3. The 61.91 Mb genome contains three transcriptionally repressed, full-length strain-specific minichromosomes (<1 Mb; Chr11 through Chr13). A CRISPR/Cas9-based system was developed to knock out large chromosomal segments; it involved the generation of multiple simultaneous DNA double-strand breaks across a targeted genomic region, followed by homology-directed replacement thereof with a donor DNA template carrying the selectable marker hygromycin phosphotransferase gene flanked by homologous sequence arms of the targeted region. Using this system, we obtained distinct mutants functionally nullisomic for individual minichromosomes. Only the ΔChr12 mutant lacking the 498.44 Kb genomic region carrying all of the 31 genes of Chr12 exhibited attenuated virulence on maize and was indistinguishable from T1-3-3 in fungal growth and conidiation, indicating that Chr12 is a conditionally dispensable minichromosome and imparts full virulence to C. graminicola on maize. The CRISPR/Cas9-mediated genome editing system developed in this study will enable the determination of the biological functions of minichromosomes or large chromosomal segments in fungal plant pathogens.
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Affiliation(s)
- Wendi Ma
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; Ministry of Agriculture and Rural Affairs-Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wensheng Zhao
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; Ministry of Agriculture and Rural Affairs-Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China
| | - You-Liang Peng
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; Ministry of Agriculture and Rural Affairs-Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China
| | - Vijai Bhadauria
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China; Ministry of Agriculture and Rural Affairs-Key Laboratory for Crop Pest Monitoring and Green Control, China Agricultural University, Beijing 100193, China.
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Rogério F, Van Oosterhout C, Ciampi-Guillardi M, Correr FH, Hosaka GK, Cros-Arteil S, Rodrigues Alves Margarido G, Massola Júnior NS, Gladieux P. Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen. Mol Ecol 2023; 32:2428-2442. [PMID: 35076152 DOI: 10.1111/mec.16366] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
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Affiliation(s)
- Flávia Rogério
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
- Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | | | - Maisa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | - Nelson S Massola Júnior
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | - Pierre Gladieux
- UMR PHIM, University of Montpellier, INRAE, CIRAD, Montpellier, France
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Kennedy AH, Schoch CL, Marrero G, Brover V, Robbertse B. Publicly Available and Validated DNA Reference Sequences Are Critical to Fungal Identification and Global Plant Protection Efforts: A Use-Case in Colletotrichum. PLANT DISEASE 2022; 106:1573-1596. [PMID: 35538602 PMCID: PMC9196201 DOI: 10.1094/pdis-09-21-2083-sr] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Publicly available and validated DNA reference sequences useful for phylogeny estimation and identification of fungal pathogens are an increasingly important resource in the efforts of plant protection organizations to facilitate safe international trade of agricultural commodities. Colletotrichum species are among the most frequently encountered and regulated plant pathogens at U.S. ports-of-entry. The RefSeq Targeted Loci (RTL) project at NCBI (BioProject no. PRJNA177353) contains a database of curated fungal internal transcribed spacer (ITS) sequences that interact extensively with NCBI Taxonomy, resulting in verified name-strain-sequence type associations for >12,000 species. We present a publicly available dataset of verified and curated name-type strain-sequence associations for all available Colletotrichum species. This includes an updated GenBank Taxonomy for 238 species associated with up to 11 protein coding loci and an updated RTL ITS dataset for 226 species. We demonstrate that several marker loci are well suited for phylogenetic inference and identification. We improve understanding of phylogenetic relationships among verified species, verify or improve phylogenetic circumscriptions of 14 species complexes, and reveal that determining relationships among these major clades will require additional data. We present detailed comparisons between phylogenetic and similarity-based approaches to species identification, revealing complex patterns among single marker loci that often lead to misidentification when based on single-locus similarity approaches. We also demonstrate that species-level identification is elusive for a subset of samples regardless of analytical approach, which may be explained by novel species diversity in our dataset and incomplete lineage sorting and lack of accumulated synapomorphies at these loci.
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Affiliation(s)
- Aaron H. Kennedy
- National Identification Services, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD 20705
| | - Conrad L. Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Glorimar Marrero
- National Identification Services, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Beltsville, MD 20705
| | - Vyacheslav Brover
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
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Boufleur TR, Massola Júnior NS, Tikami Í, Sukno SA, Thon MR, Baroncelli R. Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean. Pathogens 2021; 10:pathogens10111520. [PMID: 34832675 PMCID: PMC8625359 DOI: 10.3390/pathogens10111520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
Colletotrichum is one of the most important plant pathogenic genus of fungi due to its scientific and economic impact. A wide range of hosts can be infected by Colletotrichum spp., which causes losses in crops of major importance worldwide, such as soybean. Soybean anthracnose is mainly caused by C. truncatum, but other species have been identified at an increasing rate during the last decade, becoming one of the most important limiting factors to soybean production in several regions. To gain a better understanding of the evolutionary origin of soybean anthracnose, we compared the repertoire of effector candidates of four Colletotrichum species pathogenic to soybean and eight species not pathogenic. Our results show that the four species infecting soybean belong to two lineages and do not share any effector candidates. These results strongly suggest that two Colletotrichum lineages have acquired the capability to infect soybean independently. This study also provides, for each lineage, a set of candidate effectors encoding genes that may have important roles in pathogenicity towards soybean offering a new resource useful for further research on soybean anthracnose management.
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Affiliation(s)
- Thaís R. Boufleur
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
- Correspondence: (T.R.B.); (R.B.)
| | - Nelson S. Massola Júnior
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
| | - Ísis Tikami
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
| | - Serenella A. Sukno
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
| | - Michael R. Thon
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
| | - Riccardo Baroncelli
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 44, 40126 Bologna, Italy
- Correspondence: (T.R.B.); (R.B.)
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Colletotrichum species and complexes: geographic distribution, host range and conservation status. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00491-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Genetic diversity of Colletotrichum lupini and its virulence on white and Andean lupin. Sci Rep 2021; 11:13547. [PMID: 34188142 PMCID: PMC8242092 DOI: 10.1038/s41598-021-92953-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Lupin cultivation worldwide is threatened by anthracnose, a destructive disease caused by the seed- and air-borne fungal pathogen Colletotrichum lupini. In this study we explored the intraspecific diversity of 39 C. lupini isolates collected from different lupin cultivating regions around the world, and representative isolates were screened for their pathogenicity and virulence on white and Andean lupin. Multi-locus phylogeny and morphological characterizations showed intraspecific diversity to be greater than previously shown, distinguishing a total of six genetic groups and ten distinct morphotypes. Highest diversity was found across South America, indicating it as the center of origin of C. lupini. The isolates that correspond to the current pandemic belong to a genetic and morphological uniform group, were globally widespread, and showed high virulence on tested white and Andean lupin accessions. Isolates belonging to the other five genetic groups were mostly found locally and showed distinct virulence patterns. Two highly virulent strains were shown to overcome resistance of advanced white lupin breeding material. This stresses the need to be careful with international seed transports in order to prevent spread of currently confined but potentially highly virulent strains. This study improves our understanding of the diversity, phylogeography and pathogenicity of a member of one of the world's top 10 plant pathogen genera, providing valuable information for breeding programs and future disease management.
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Boufleur TR, Ciampi‐Guillardi M, Tikami Í, Rogério F, Thon MR, Sukno SA, Massola Júnior NS, Baroncelli R. Soybean anthracnose caused by Colletotrichum species: Current status and future prospects. MOLECULAR PLANT PATHOLOGY 2021; 22:393-409. [PMID: 33609073 PMCID: PMC7938629 DOI: 10.1111/mpp.13036] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 05/03/2023]
Abstract
Soybean (Glycine max) is one of the most important cultivated plants worldwide as a source of protein-rich foods and animal feeds. Anthracnose, caused by different lineages of the hemibiotrophic fungus Colletotrichum, is one of the main limiting factors to soybean production. Losses due to anthracnose have been neglected, but their impact may threaten up to 50% of the grain production. TAXONOMY While C. truncatum is considered the main species associated with soybean anthracnose, recently other species have been reported as pathogenic on this host. Until now, it has not been clear whether the association of new Colletotrichum species with the disease is related to emerging species or whether it is due to the undergoing changes in the taxonomy of the genus. DISEASE SYMPTOMS Typical anthracnose symptoms are pre- and postemergence damping-off; dark, depressed, and irregular spots on cotyledons, stems, petioles, and pods; and necrotic laminar veins on leaves that can result in premature defoliation. Symptoms may evolve to pod rot, immature opening of pods, and premature germination of grains. CHALLENGES As accurate species identification of the causal agent is decisive for disease control and prevention, in this work we review the taxonomic designation of Colletotrichum isolated from soybean to understand which lineages are pathogenic on this host. We also present a comprehensive literature review of soybean anthracnose, focusing on distribution, symptomatology, epidemiology, disease management, identification, and diagnosis. We consider the knowledge emerging from population studies and comparative genomics of Colletotrichum spp. associated with soybean providing future perspectives in the identification of molecular factors involved in the pathogenicity process. USEFUL WEBSITE Updates on Colletotrichum can be found at http://www.colletotrichum.org/. All available Colletotrichum genomes on GenBank can be viewed at http://www.colletotrichum.org/genomics/.
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Affiliation(s)
- Thais R. Boufleur
- Department of Plant Pathology and NematologyUniversity of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Piracicaba, São PauloBrazil
- Instituto Hispano‐Luso de Investigaciones Agrarias (CIALE)Universidad de SalamancaSalamancaSpain
| | - Maisa Ciampi‐Guillardi
- Department of Plant Pathology and NematologyUniversity of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Piracicaba, São PauloBrazil
| | - Ísis Tikami
- Department of Plant Pathology and NematologyUniversity of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Piracicaba, São PauloBrazil
| | - Flávia Rogério
- Department of Plant Pathology and NematologyUniversity of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Piracicaba, São PauloBrazil
| | - Michael R. Thon
- Instituto Hispano‐Luso de Investigaciones Agrarias (CIALE)Universidad de SalamancaSalamancaSpain
| | - Serenella A. Sukno
- Instituto Hispano‐Luso de Investigaciones Agrarias (CIALE)Universidad de SalamancaSalamancaSpain
| | - Nelson S. Massola Júnior
- Department of Plant Pathology and NematologyUniversity of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ)Piracicaba, São PauloBrazil
| | - Riccardo Baroncelli
- Instituto Hispano‐Luso de Investigaciones Agrarias (CIALE)Universidad de SalamancaSalamancaSpain
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Sagita R, Quax WJ, Haslinger K. Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts. Front Bioeng Biotechnol 2021; 9:649906. [PMID: 33791289 PMCID: PMC8005728 DOI: 10.3389/fbioe.2021.649906] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.
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Affiliation(s)
| | | | - Kristina Haslinger
- Groningen Institute of Pharmacy, Chemical and Pharmaceutical Biology, University of Groningen, Groningen, Netherlands
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