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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Pilon is a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions, which is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains.
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
Comparison of genomes of three phenotypically diverse Fusarium species revealed lineage-specific genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome, putting the evolution of fungal pathogenicity into a new perspective.
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea, and shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating.
Evolution of pathogenicity and sexual reproduction in eight Candida genomes
There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence in Candida albicans species.
Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses
- S. Lockhart, K. Etienne, +16 authors A. Litvintseva
- Biology, MedicineClinical infectious diseases : an official…
- 15 January 2017
Candida auris is an emerging healthcare-associated pathogen associated with high mortality, and WGS analysis suggests nearly simultaneous, and recent, independent emergence of different clonal populations on 3 continents.
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution, and a comparative study with Aspergillus fumigatus and As pergillus oryzae, used in the production of sake, miso and soy sauce, provides new insight into eukaryotic genome evolution and gene regulation.
Obligate biotrophy features unraveled by the genomic analysis of rust fungi
- S. Duplessis, C. Cuomo, +47 authors F. Martin
- Biology, MedicineProceedings of the National Academy of Sciences
- 2 May 2011
The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition.
The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization
The genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals, was sequenced and annotated and many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination.
Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps
This work shows that purified RAG1 and RAG2 proteins are sufficient to carry out formation of double-strand breaks at recombination signal sequences and makes a hairpin structure at the coding end and a blunt, 5'-phosphorylated signal end.
Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens
Insight is revealed into the genetic mechanisms of niche adaptation of fungal wilt pathogens, advances the understanding of the evolution and development of their pathogenesis, and sheds light on potential avenues for the development of novel disease management strategies to combat destructive wilt diseases.