The Many Questions about Mini Chromosomes in Colletotrichum spp.

Plaumann, Peter-Louis; Koch, Christian A.

doi:10.3390/plants9050641

Cited by 11 publications

(7 citation statements)

References 96 publications

(135 reference statements)

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“…Coll-524 and C. higginsianum IMI 349063 have similar genome sizes but C. higginsianum IMI 349063 carries nearly three times the number of transposable element genes to Coll-524 (Supplementary Table 13). Moreover, compared with C. higginsianum IMI 349063, Coll-524 was found to be unlikely to have sequence structures like mini chromosomes which harbor high density transposable elements with over 40% sequences encoding transposable elements (Plaumann and Koch, 2020).…”

Section: Discussionmentioning

confidence: 95%

Comparative Genomics of Three Colletotrichum scovillei Strains and Genetic Analysis Revealed Genes Involved in Fungal Growth and Virulence on Chili Pepper

et al. 2022

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Colletotrichum scovillei causes anthracnose of chili pepper in many countries. Three strains of this pathogen, Coll-524, Coll-153, and Coll-365, show varied virulence on chili pepper. Among the three strains, Coll-365 showed significant defects in growth and virulence. To decipher the genetic variations among these strains and identify genes contributing to growth and virulence, comparative genomic analysis and gene transformation to show gene function were applied in this study. Compared to Coll-524, Coll-153, and Coll-365 had numerous gene losses including 32 candidate effector genes that are mainly exist in acutatum species complex. A cluster of 14 genes in a 34-kb genomic fragment was lost in Coll-365. Through gene transformation, three genes in the 34-kb fragment were identified to have functions in growth and/or virulence of C. scovillei. CsPLAA encoding a phospholipase A2-activating protein enhanced the growth of Coll-365. A combination of CsPLAA with one transcription factor CsBZTF and one C6 zinc finger domain-containing protein CsCZCP was found to enhance the pathogenicity of Coll-365. Introduction of CsGIP, which encodes a hypothetical protein, into Coll-365 caused a reduction in the germination rate of Coll-365. In conclusion, the highest virulent strain Coll-524 had more genes and encoded more pathogenicity related proteins and transposable elements than the other two strains, which may contribute to the high virulence of Coll-524. In addition, the absence of the 34-kb fragment plays a critical role in the defects of growth and virulence of strain Coll-365.

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Section: Discussionmentioning

confidence: 95%

Comparative Genomics of Three Colletotrichum scovillei Strains and Genetic Analysis Revealed Genes Involved in Fungal Growth and Virulence on Chili Pepper

et al. 2022

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“…Colletotrichum minichromosomes have been reported to contribute to virulence and host speciation (Plaumann & Koch, 2020), with a minichromosome (11) found in Colletotrichum lentis (Bhadauria et al, 2019) and Colletotrichum higginsianum (Plaumann et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…lycopersici led to virulence of a previously nonpathogenic Fusarium strain (Ma et al, 2010 ). Colletotrichum minichromosomes have been reported to contribute to virulence and host speciation (Plaumann & Koch, 2020 ), with a minichromosome (11) found in Colletotrichum lentis (Bhadauria et al, 2019 ) and Colletotrichum higginsianum (Plaumann et al, 2018 ). In C. lupini , the minichromosome could play a role in virulence and host adaptation but does not seem to be required for pathogenicity on lupins for its lack in lineage I.…”

Section: Discussionmentioning

confidence: 99%

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

Alkemade

Baroncelli

Messmer

et al. 2023

Molecular Plant Pathology

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

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“…The availability of complete genome sequences is crucial not only for the analysis of large gene clusters, such as secondary metabolism biosynthetic gene clusters, but also for understanding fungal genome evolution. Complete or near-complete genome sequences have enabled the structure and dynamics of accessory mini-chromosomes to be analyzed in several Colletotrichum species [9, 13, 14]. The importance of mini-chromosomes for virulence on plant hosts has been demonstrated in several fungal pathogens including Fusarium oxysporum f.sp.…”

Section: Introductionmentioning

confidence: 99%

Complete genome of the Medicago anthracnose fungus,Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome

Lapalu,

Simon,

et al. 2023

Preprint

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Colletotrichum destructivum(Cd) is a phytopathogenic fungus causing significant economic losses on forage legume crops (MedicagoandTrifoliumspecies) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate fromM. sativausing long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises 10 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 ofCdrelative to the closely-related Brassicaceae pathogen,C. higginsianum. In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome ofCdthat 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.Data summaryAll RNA-seq data were submitted to the NCBI GEO portal under the GEO accession GSE246592.C. destructivumgenome assembly and annotation are available under the NCBI BioProject PRJNA1029933 with sequence accessionsCP137305-CP137317.Supplementary data (genomic and annotation files, genome browser) are available from the INRAE BIOGER Bioinformatics platform (https://bioinfo.bioger.inrae.fr/). Transposable Elements consensus sequences are also available from the French national data repository, research.data.gouv.fr with doi 10.57745/TOO1JS.Impact statementColletotrichum is a large genus of fungal phytopathogens that cause major economic losses on a wide range of crop plants throughout the world. These pathogens vary widely in their host specificity and may have either broad or narrow host ranges. Here, we report the first complete genome of the alfalfa (Medicago sativa) pathogen,Colletotrichum destructivum, which will facilitate the genomic analysis of host adaptation and comparison with other members of the Destructivum clade. We identified a species-specific 1.2 Mb region within chromosome 1 displaying all the hallmarks of fungal accessory chromosomes, which may have arisen through the integration of a mini-chromosome into a core chromosome and could be linked to the pathogenicity of this fungus. We show this region is also a focus for segmental duplications, which may contribute to generating genetic diversity for adaptive evolution. Finally, we report infection by this fungus of the model legume,Medicago truncatula, providing a novel pathosystem for studying fungal-plant interactions.

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The Many Questions about Mini Chromosomes in Colletotrichum spp.

Cited by 11 publications

References 96 publications

Comparative Genomics of Three Colletotrichum scovillei Strains and Genetic Analysis Revealed Genes Involved in Fungal Growth and Virulence on Chili Pepper

Comparative Genomics of Three Colletotrichum scovillei Strains and Genetic Analysis Revealed Genes Involved in Fungal Growth and Virulence on Chili Pepper

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

Complete genome of the Medicago anthracnose fungus,Colletotrichum destructivum, reveals a mini-chromosome-like region within a core chromosome

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