Nanopore Data-Driven T2T Genome Assemblies of Colletotrichum lini Strains DOI Creative Commons
Elizaveta A. Sigova, Ekaterina M. Dvorianinova, Alexander A. Arkhipov

et al.

Journal of Fungi, Journal Year: 2024, Volume and Issue: 10(12), P. 874 - 874

Published: Dec. 16, 2024

Colletotrichum lini is a pathogenic fungus that infects flax and causes significant yield losses. In this study, we assembled the genomes of four highly virulent C. strains using Oxford Nanopore Technologies (ONT, R10.4.1 flow cells) Illumina platforms. The performance two tools developed for telomere-to-telomere (T2T) genome assembly was compared: Verkko Hifiasm. Prior to assembly, ONT reads were corrected HERRO algorithm. generated assemblies high completeness but low contiguity, while Hifiasm allowed generation T2T assemblies. Despite significantly different coverage with data (25–100×), equal contiguity obtained: 53.6–54.7 Mb, ten core chromosomes, or three accessory chromosomes. A comparative analysis polishing showed at certain (≥35×), additional did not improve its accuracy, even data. An structures revealed similarity between Thus, our approach enabled assembling only from obtained cells may be promising other fungal genera. These will allow accurate identification strain-specific differences chromosome level aid in development effective strategies protect anthracnose.

Language: Английский

Genome evolution and transcriptome plasticity is associated with adaptation to monocot and dicot plants in Colletotrichum fungi DOI Creative Commons
Riccardo Baroncelli, José F. Cobo‐Díaz, Tiziano Benocci

et al.

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

Citations

8
Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex DOI Creative Commons

Ziying Ma,

Fang Liu, Clement K. M. Tsui

et al.

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

Citations

0
Comparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini DOI Creative Commons
Joris Alkemade, Pierre Hohmann, Monika Messmer

et al.

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

Citations

2
Complete Annotated Genome Assembly of Flax Pathogen Colletotrichum lini DOI Creative Commons
Elizaveta A. Sigova, Ekaterina M. Dvorianinova, Tatiana A. Rozhmina

et al.

Journal of Fungi, Journal Year: 2024, Volume and Issue: 10(9), P. 605 - 605

Published: Aug. 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

Language: Английский

Citations

1
Nanopore Data-Driven T2T Genome Assemblies of Colletotrichum lini Strains DOI Creative Commons
Elizaveta A. Sigova, Ekaterina M. Dvorianinova, Alexander A. Arkhipov

et al.

Journal of Fungi, Journal Year: 2024, Volume and Issue: 10(12), P. 874 - 874

Published: Dec. 16, 2024

Colletotrichum lini is a pathogenic fungus that infects flax and causes significant yield losses. In this study, we assembled the genomes of four highly virulent C. strains using Oxford Nanopore Technologies (ONT, R10.4.1 flow cells) Illumina platforms. The performance two tools developed for telomere-to-telomere (T2T) genome assembly was compared: Verkko Hifiasm. Prior to assembly, ONT reads were corrected HERRO algorithm. generated assemblies high completeness but low contiguity, while Hifiasm allowed generation T2T assemblies. Despite significantly different coverage with data (25–100×), equal contiguity obtained: 53.6–54.7 Mb, ten core chromosomes, or three accessory chromosomes. A comparative analysis polishing showed at certain (≥35×), additional did not improve its accuracy, even data. An structures revealed similarity between Thus, our approach enabled assembling only from obtained cells may be promising other fungal genera. These will allow accurate identification strain-specific differences chromosome level aid in development effective strategies protect anthracnose.

Language: Английский

Citations

0