ArticleMolecular biology and evolution2017
Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
- Lineage-Specific Gene Family Innovations Underpin the Pathogenicity of Woody-Plant Pathogens in Botryosphaeriaceae.Genome biology and evolution · 2026Article
- Gene presence-absence and evolutionary signals of positive selection associated with virulence divergence inMicrobial genomics · 2026Article
- Article
- Global genomic and antimicrobial resistance profiling of Neisseria gonorrhoeae: Insights from whole genome sequencing and minimum inhibitory concentration analysis.PLoS neglected tropical diseases · 2025Article
- Navigating Host Immunity and Concurrent Ozone Stress: Strain-Resolved Metagenomics Reveals Maintenance of Intraspecific Diversity and Genetic Variation inEvolutionary applications · 2025Article
- Copy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen.Nature communications · 2024Article
- Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogenCurrent research in food science · 2024Article
- Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen.Frontiers in cellular and infection microbiology · 2023Article
- Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen.BMC biology · 2022Article
- How large and diverse are field populations of fungal plant pathogens? The case ofEvolutionary applications · 2022Article
- Cryptic genetic structure and copy-number variation in the ubiquitous forest symbiotic fungus Cenococcum geophilum.Environmental microbiology · 2021Article
- Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogenMicrobial genomics · 2021Article
- A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen.eLife · 2021Article
- Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen.Microbial genomics · 2021Article
- Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae.Genome biology and evolution · 2021Article
- Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen.Nature communications · 2021Article
- Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen.BMC genomics · 2021Article
- Allopatric Plant Pathogen Population Divergence following Disease Emergence.Applied and environmental microbiology · 2021Article
- Gene Copy Number Variation Does Not Reflect Structure or Environmental Selection in Two Recently Diverged California Populations ofG3 (Bethesda, Md.) · 2020Article
- The Effect of Virulence and Resistance Mechanisms on the Interactions between Parasitic Plants and Their Hosts.International journal of molecular sciences · 2020Review
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2 authors.
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Abstract
Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence-absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence-absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories.
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