Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Abstract Background Colletotrichum fungi infect a wide diversity of monocot and dicot hosts, causing diseases on almost all economically important plants worldwide. is also suitable model for studying gene family evolution fine scale to uncover events in the genome associated with biological changes. Results Here we present sequences 30 species covering within genus. Evolutionary analyses revealed that ancestor diverged late Cretaceous parallel diversification flowering plants. We provide evidence independent host jumps from dicots monocots during Colletotrichum, coinciding progressive shrinking plant cell wall degradative arsenal expansions lineage-specific families. Comparative transcriptomics 4 adapted different hosts similarity content but high modulation their transcription profiles substrates. Combining genomics transcriptomics, identified set core genes such as specific factors, putatively involved degradation. Conclusions These results indicate ancestral were certain branches progressively reshaping its regulation.

Language: Английский

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Evolutionary history of the cytochrome P450s from Colletotrichum species and prediction of their putative functional roles during host-pathogen interactions

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Jan. 12, 2024

The genomes of species belonging to the genus Colletotrichum harbor a substantial number cytochrome P450 monooxygenases (CYPs) encoded by broad diversity gene families. However, biological role their CYP complement (CYPome) has not been elucidated. Here, we investigated putative evolutionary scenarios that occurred during evolution CYPome Graminicola complex (s.c.) and implications. study revealed most families s.c. experienced contractions. reductive resulted in restricted CYPs are predominant each members from s.c., whereas only 18 absolutely conserved among these species. displayed notably different phylogenetic relationship at tertiary structure level, suggesting convergent scenario. Most enzymes share redundant functions secondary metabolite biosynthesis xenobiotic metabolism. Hence, this current work suggests presence plays critical optimization colonization capability virulence.

Language: Английский

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Uncovering the Host Range–Lifestyle Relationship in the Endophytic and Anthracnose Pathogenic Genus Colletotrichum

Microorganisms, Journal Year: 2025, Volume and Issue: 13(2), P. 428 - 428

Published: Feb. 16, 2025

Colletotrichum includes agriculturally and scientifically important pathogens that infect numerous plants. They can also adopt an endophytic lifestyle, refraining from causing disease and/or even promoting plant growth when inoculated on a non-susceptible host. In this manner, the host range of fungus shift, depending whether it exhibits or pathogenic lifestyles. Some fungi, such as tofieldiae, shift between pathogenicity endophytism within same environmental conditions. Here, we aim to disentangle relationship lifestyle in Colletotrichum. Specifically, demonstrate is dependent colonized many fungi. We discuss ways which species may act endophytically alternative hosts, how comparative genomics has uncovered candidate molecules (namely effectors, CAZymes, secondary metabolites) underlying fungal merits using fungi alongside research, facilitates use reverse genetics uncover molecular determinants lifestyle. particular, reference Arabidopsis thaliana-Colletotrichum tofieldiae study system model for elucidating dual roles plant-fungus interactions, both pathogenic, through integrative omics approaches genetics. This because C. contains closely related endophytes, making ideal identifying approach could identify key targets effective pathogen management agriculture. Lastly, propose occupies different than will enhance our understanding globally significant genus lay groundwork future research examining plant-associated

Language: Английский

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Can whole genome sequencing resolve taxonomic ambiguities in fungi? The case study of Colletotrichum associated with ferns

Frontiers in Fungal Biology, Journal Year: 2025, Volume and Issue: 6

Published: Feb. 28, 2025

Introduction The genus Colletotrichum comprises numerous fungal species with diverse ecological roles, including plant pathogenic, endophytic, and saprophytic lifestyles. Accurate identification is crucial for understanding host-pathogen interactions, disease epidemiology, ecology. However, taxonomic classification within remains challenging due to genetic complexity phenotypic plasticity. Conventional approaches such as single-gene analyses multilocus sequence typing (MLST) frequently fail resolve closely related taxa, leading misidentifications that hinder delimitation comparative evolutionary studies. Whole-genome sequencing (WGS) offers a promising alternative by providing genome-wide resolution phylogenetic analysis. This study investigates isolates associated the fern Rumohra adiantiformis evaluates effectiveness of WGS in addressing uncertainties. Methods A total 18 isolates, fern-associated strains, were analyzed. Genomic DNA was extracted sequenced using Illumina NovaSeq platform. High-quality genome assemblies generated, gene prediction conducted AUGUSTUS. Orthogroup assignment phylogenomic analysis performed based on single-copy orthologs, trees constructed MLST WGS-based approaches. Comparative carried out assess provided relation traditional methods. Results Genome-wide revealed distinct lineages among failed resolve, highlighting host geographic differentiation. obtained, 98.3% genes assigned orthogroups, indicating strong genomic conservation. Phylogenetic confirmed close relationship between -associated filicis , reinforcing identification. Discussion These findings demonstrate superiority over resolving boundaries reconstructing relationships. enhanced data enables more accurate classification, reducing improving our biodiversity. By refining taxonomy, facilitates pathogenic studies, offering robust framework future research systematics pathology. As technologies continue advance, expected become standard tool delineation

Language: Английский

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Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: April 9, 2025

The Colletotrichum gloeosporioides species complex (CGSC) is one of the most devastating fungal phytopathogens, and composed three main clades: Kahawae, Musae, Theobromicola. Despite diversity CGSC, there limited understanding on their evolutionary mechanisms. By analysing 49 newly assembled genomes, we found that expansion transposable elements, especially long terminal repeat retrotransposons, facilitates genome size genetic variation. In-depth analyses suggested an intra-chromosomal inversion may have been driving force behind divergence Kahawae clade from its ancestor. Within clade, narrow-hosted quarantine C. kahawae has undergone extensive chromosomal rearrangements mediated by repetitive sequences, generating highly dynamic lineage-specific genomic regions compared to closely related broad-hosted cigarro. findings this study highlight role in promoting diversification host adaptation, provide new perspectives for evolution phytopathogenic fungi.

Language: Английский

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Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

Molecular Plant Pathology, Journal Year: 2023, Volume and Issue: 24(6), P. 616 - 627

Published: April 20, 2023

Abstract Colletotrichum lupini , the causative agent of lupin anthracnose, affects cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective this study was employ genetics investigate diversity, dynamics, molecular basis interaction notorious pathogen with host. A collection globally representative C. isolates genotyped through triple digest restriction site‐associated DNA sequencing, resulting in a data set unparalleled resolution. Phylogenetic structural analysis could distinguish four independent lineages (I–IV). strong high overall standardized index association ( r̅ d ) indicates that reproduces clonally. Different morphologies virulence patterns on white Lupinus albus Andean mutabilis were observed between within clonal lineages. Isolates belonging lineage II shown have minichromosome also partly present III IV, but not I isolates. Variation presence imply role host–pathogen interaction. All South American Andes region, which suggested be centre origin species. Only members been found outside America since 1990s, indicating it as current pandemic population. As seedborne pathogen, has mainly spread infected symptomless seeds, stressing importance phytosanitary measures prevent future outbreaks strains are yet confined America.

Language: Английский

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Comparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini

Molecular Plant Pathology, Journal Year: 2024, Volume and Issue: 25(12)

Published: Dec. 1, 2024

ABSTRACT Fungal plant pathogens cause major crop losses worldwide, with many featuring compartmentalised genomes that include both core and accessory regions, which are believed to drive adaptation. The highly host‐specific fungus Colletotrichum lupini greatly impacts lupin ( Lupinus spp.) cultivation. This pathogen is part of clade 1 the C. acutatum species complex comprises four genetically uniform, presumably clonal, lineages (I–IV). Despite this, variation in virulence morphology has been observed within these lineages. To investigate potential sources genetic variability this asexual fungus, we compared 16 strains 17 related species. Phylogenomics confirmed presence distinct lineages, but further examination based on genome size, gene content, transposable elements (TEs), deletions revealed lineage II could be split into two groups, II‐A II‐B. TE content varied between correlated strongly size variation, supporting a role for TEs expansion Pangenome analysis variable genome, including minichromosome present II, III, IV, absent I. Accessory genes effectors appeared cluster proximity TEs. Presence/absence putative was lineage‐specific, suggesting play crucial determining host range. Notably, no were found TE‐rich minichromosome. Our findings shed light mechanisms generating diversity fungal aid future disease management.

Language: Английский

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Genomic streamlining of seagrass-associatedColletotrichumsp. may be related to its adaptation to a marine monocot host

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

Abstract Colletotrichum spp. have a complicated history of association with land plants. Perhaps most well-known as plant pathogens for the devastating effect they can on agricultural crops, some been reported beneficial endophytes. However, there only handful reports isolated from aquatic hosts and their ecological role in marine ecosystem is underexplored. To address this, we present draft genome annotation sp. CLE4, previously rhizome tissue seagrass Zostera marina . This (48.03 Mbp length) highly complete (BUSCO ascomycota: 98.8%) encodes 12,015 genes, which 5.7% are carbohydrate-active enzymes (CAZymes) 12.6% predicted secreted proteins. Phylogenetic placement puts CLE4 within C. acutatum complex, closely related to godetiae We found 8.69% smaller size, 21.90% gene count, absence 591 conserved families relative other members suggesting streamlined possibly linked its specialized niche ecosystem. Machine learning analyses using CATAStrophy CAZyme domains predict this isolate be hemibiotroph, such that it has biotrophic phase where kept alive during optimal environmental conditions followed by necrotrophic fungi actively serves pathogen. While future work still needed definitively tease apart lifestyle strategy study provides foundational insight high-quality genomic resource starting understand evolutionary trajectory adaptations marine-plant associated fungi.

Language: Английский

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