ArticleMolecular plant pathology2018
Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust.
Article in Molecular plant pathology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 45 citations in OpenAlex.
- A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy.G3 (Bethesda, Md.) · 2026Article
- Tracking the Evolutionary Trajectory of a Young Hybrid Plant Pathogen.Genome biology and evolution · 2026Article
- Organization of neuropeptide systems in the human brain.Nature neuroscience · 2026Article
- Genome-wide subgenome-resolved analysis validates chromosome 4 differentiation and prioritizes introgressedFrontiers in plant science · 2026Article
- The Role of Coffee Microbiomes in Pathogen Resistance Across Varieties and Ecological Niches.Microorganisms · 2025Article
- Article
- GlobalFrontiers in plant science · 2025Article
- Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia.International microbiology : the official journal of the Spanish Society for Microbiology · 2024Article
- A roadmap to understanding diversity and function of coral reef-associated fungi.FEMS microbiology reviews · 2022Article
- Current Status and Future Perspectives of Genomics Research in the Rust Fungi.International journal of molecular sciences · 2022Review
- Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade.Nature communications · 2022Article
- Spatial and Temporal Genetic Diversity and Population Structure of Hemileia vastatrix from Peruvian Coffee Plantations.The plant pathology journal · 2021Article
- Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence.Molecular biology and evolution · 2020Article
- Genome-scale data reveal the role of hybridization in lichen-forming fungi.Scientific reports · 2020Article
- On the hunt for the alternate host ofEcology and evolution · 2019Article
- Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist.Environmental microbiology · 2019Article
- Fungal species boundaries in the genomics era.Fungal genetics and biology : FG & B · 2019Review
- Article
- Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coffee leaf rust, caused by Hemileia vastatrix (Hv), represents the biggest threat to coffee production worldwide and ranks amongst the most serious fungal diseases in history. Despite a recent series of outbreaks and emergence of hypervirulent strains, the population evolutionary history and potential of this pathogen remain poorly understood. To address this issue, we used restriction site-associated DNA sequencing (RADseq) to generate ∼19 000 single nucleotide polymorphisms (SNPs) across a worldwide collection of 37 Hv samples. Contrary to the long-standing idea that Hv represents a genetically unstructured and cosmopolitan species, our results reveal the existence of a cryptic species complex with marked host tropism. Using phylogenetic and pathological data, we show that one of these lineages (C3) infects almost exclusively the most economically valuable coffee species (tetraploids that include Coffea arabica and interspecific hybrids), whereas the other lineages (C1 and C2) are severely maladapted to these hosts, but successfully infect diploid coffee species. Population dynamic analyses suggest that the C3 group may be a recent 'domesticated' lineage that emerged via host shift from diploid coffee hosts. We also found evidence of recombination occurring within this group, which could explain the high pace of pathotype emergence despite the low genetic variation. Moreover, genomic footprints of introgression between the C3 and C2 groups were discovered and raise the possibility that virulence factors may be quickly exchanged between groups with different pathogenic abilities. This work advances our understanding of the evolutionary strategies used by plant pathogens in agro-ecosystems with direct and far-reaching implications for disease control.
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