Rapid mini‐chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

Liu, Sanzhen; Lin, Guifang; Ramachandran, Sowmya R.; Daza, Lidia Calderon; Cruppe, Giovana; Tembo, Batiseba; Singh, Pawan Kumar; Cook, David; Pedley, Kerry F.; Valent, Barbara

doi:10.1111/nph.19402

Cited by 6 publications

(1 citation statement)

References 54 publications

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“…The importance of mini-chromosomes for virulence on plant hosts has been demonstrated in several fungal pathogens including Fusarium oxysporum f.sp. lycopersici [15], Magnaporthe oryzae [16], C. lentis [12] and C. higginsianum [17].…”

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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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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The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance

Zaccaron,

Stergiopoulos

2024

Journal of Genetics and Genomics

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Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases

Gyawali,

Hao,

Lin

et al. 2024

NAR Genomics and Bioinformatics

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The genomes of the fungus Magnaporthe oryzae that causes blast diseases on diverse grass species, including major crops, have indispensable core-chromosomes and may contain supernumerary chromosomes, also known as mini-chromosomes. These mini-chromosomes are speculated to provide effector gene mobility, and may transfer between strains. To understand the biology of mini-chromosomes, it is valuable to be able to detect whether a M. oryzae strain possesses a mini-chromosome. Here, we applied recurrent neural network models for classifying DNA sequences as arising from core- or mini-chromosomes. The models were trained with sequences from available core- and mini-chromosome assemblies, and then used to predict the presence of mini-chromosomes in a global collection of M. oryzae isolates using short-read DNA sequences. The model predicted that mini-chromosomes were prevalent in M. oryzae isolates. Interestingly, at least one mini-chromosome was present in all recent wheat isolates, but no mini-chromosomes were found in early isolates collected before 1991, indicating a preferential selection for strains carrying mini-chromosomes in recent years. The model was also used to identify assembled contigs derived from mini-chromosomes. In summary, our study has developed a reliable method for categorizing DNA sequences and showcases an application of recurrent neural networks in predictive genomics.

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Rapid mini‐chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia

Cited by 6 publications

References 54 publications

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

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

The dynamics of fungal genome organization and its impact on host adaptation and antifungal resistance

Using recurrent neural networks to detect supernumerary chromosomes in fungal strains causing blast diseases

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