Molecular Dialogue During Host Manipulation by the Vascular Wilt Fungus Fusarium oxysporum

Annual Review of Phytopathology, Год журнала: 2024, Номер 62(1), С. 97 - 126

Опубликована: Июнь 17, 2024

Vascular wilt fungi are a group of hemibiotrophic phytopathogens that infect diverse crop plants. These pathogens have adapted to thrive in the nutrient-deprived niche plant xylem. Identification and functional characterization effectors their role establishment compatibility across multiple hosts, suppression defense, host reprogramming, interaction with surrounding microbes been studied mainly model vascular Fusarium oxysporum Verticillium dahliae. Comparative analysis genomes from fungal isolates has accelerated our understanding genome compartmentalization its effector evolution. Also, advances recent years shed light on cross talk root-infecting scales cellular ecosystem level, covering microbiome as well interkingdom signaling. This review elaborates current between plant, which eventually leads specialized lifestyle We particularly focus findings F. oxysporum, including multihost associations, how they contributed biology adaptation In addition, we discuss emerging research areas highlight open questions future challenges.

Язык: Английский

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

GigaScience, Год журнала: 2024, Номер 13

Опубликована: Янв. 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.

Язык: Английский

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Horizontal transfer of accessory chromosomes in fungi – a regulated process for exchange of genetic material?

Heredity, Год журнала: 2025, Номер unknown

Опубликована: Фев. 10, 2025

Abstract Horizontal transfer of entire chromosomes has been reported in several fungal pathogens, often significantly impacting the fitness recipient fungus. All documented instances horizontal chromosome transfers (HCTs) showed a marked propensity for accessory chromosomes, consistently involving an while other were seldom, if ever, co-transferred. The mechanisms underlying HCTs, as well factors regulating specificity HCTs remain unclear. In this perspective, we provide overview observed cases transfers. We hypothesize existence signal that distinguishes mobile, i.e., horizontally transferred, from rest donor genome. Recent findings Metarhizium robertsii and Magnaporthe oryzae , suggest mobile may contain putative histones and/or histone modifiers, which could generate such signal. Based on this, propose encode machinery required their own transmission, implying HCT be regulated process. Finally, present evidence substantial differences codon usage bias between core 14 out 19 analysed species strains. Such indicate past these chromosomes. Interestingly, was previously unknown many species, suggesting more widespread than thought, therefore important factor genome evolution.

Язык: Английский

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Genomic insights and comparative analysis of Colletotrichum species associated with anthracnose fruit rot and crown rot of strawberry in North Carolina

Frontiers in Microbiology, Год журнала: 2025, Номер 16

Опубликована: Фев. 10, 2025

Colletotrichum is a large genus of fungal phytopathogens responsible for significant economic losses in numerous crops globally. These pathogens exhibit varying host specificities; some have broad range, while others are more limited. To explore the genetic composition and underlying factors virulence pathogenicity, we sequenced genomes seven isolates spp.: three from C. acutatum four gloeosporioides . were sourced anthracnose fruit rot crown strawberry North Carolina. Phylogenetic phylogenomic analyses classified within as nymphaeae , those identified siamense The genome sizes ranged 50.3 Mb to 50.7 Mb, with 14,235 14,260 predicted protein-coding gene models. In contrast, 55.7 58.6 models ranging 17,420 17,729. GC content across all spanned 51.9 53.7%. included effectors (339 480), secondary metabolic clusters (67 90), carbohydrate-active enzymes (800 1,060), exhibiting highest numbers these categories. genomic resources this study will aid resolving taxonomic challenges associated spp., elucidate their evolutionary history, enhance understanding biology ecology, which crucial developing effective disease management strategies.

Язык: Английский

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Long-distance gene flow and recombination shape the evolutionary history of a maize pathogen

IMA Fungus, Год журнала: 2025, Номер 16

Опубликована: Фев. 21, 2025

The evolutionary history of crop pathogens is shaped by a complex interaction natural and anthropogenic factors. fungus Colletotrichumgraminicola causes maize anthracnose which results in significant yield losses worldwide. We conducted comprehensive investigation into the genomics C.graminicola using collection 212 isolates from 17 countries across five continents. Genomic analyses supported existence three geographically isolated genetic lineages, with pattern isolation distance. identified two distinct gene flow patterns, driven short- long-distance dispersal, likely resulting spread pathogen exchange contaminated seeds. present evidence introgression between suggesting long recombination. recombination events coalescing at points time, North American lineage displaying most ancient Demographic modelling has indicated that America an intermediate Brazil, Europe ancestral, unsampled source population, hypothesised to be Mesoamerican. Our revealed global genomic structure geographic differentiation migration introgression. show historical relationships amongst these identifying potential route for fungal spread, population emerging ancestrally, followed sequentially Brazilian European populations. research indicates more virulent, implications emergence new outbreaks Europe.

Язык: Английский

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Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex

Communications Biology, Год журнала: 2025, Номер 8(1)

Опубликована: Апрель 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.

Язык: Английский

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A practical assembly guideline for genomes with various levels of heterozygosity

Briefings in Bioinformatics, Год журнала: 2023, Номер 24(6)

Опубликована: Сен. 9, 2023

Abstract Although current long-read sequencing technologies have a length that facilitates assembly for genome reconstruction, they high sequence errors. While various assemblers with different perspectives been developed, no systematic evaluation of long reads diploid genomes varying heterozygosity has performed. Here, we evaluated series processes, including the estimation characteristics such as size and heterozygosity, de novo assembly, polishing, removal allelic contigs, using six levels. We five long-read-only (Canu, Flye, miniasm, NextDenovo Redbean) hybrid combine short (HASLR, MaSuRCA, Platanus-allee, SPAdes WENGAN) proposed concrete guideline construction haplotype representation according to degree followed by polishing purging haplotigs, stable high-performance assemblers: Redbean, Flye MaSuRCA.

Язык: Английский

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

Molecular Plant Pathology, Год журнала: 2024, Номер 25(12)

Опубликована: Дек. 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.

Язык: Английский

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Comparative Genomic Analysis of <em>Colletotrichum lini </em>Strains with Different Virulence on Flax

Опубликована: Дек. 13, 2023

Colletotrichum lini is a flax fungal pathogen, comprising differently virulent strains. In this work, we sequenced the genomes of three C. strains different virulence: high #390-1, medium #757, and low #771. We obtained more than 100× genome coverage with Oxford Nanopore Technologies reads 50× Illumina data. To construct high-quality genomes, several assembly strategies were tested. The final assemblies using Canu – Racon ×2 Medaka Polca scheme 54.0-55.3 Mb in length, contained 26-32 contigs, had an N50 &gt; 5 BUSCO completeness 96%. Comparative analysis constructed showed similarity between mitochondrial nuclear genomes. However, rearrangement event loss 0.9 contig revealed. candidate effectors predicted sets proteins received after annotation. sequences extend knowledge on genetic diversity species are basis for establishing molecular mechanisms pathogenicity pathogen effective control anthracnose.

Язык: Английский

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Complete Annotated Genome Assembly of Flax Pathogen Colletotrichum lini

Journal of Fungi, Год журнала: 2024, Номер 10(9), С. 605 - 605

Опубликована: Авг. 26, 2024

is a fungal pathogen of flax that can cause significant yield and quality losses. In this work, we obtained the first complete annotated genome assembly highly virulent

Язык: Английский

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