New Fungal Alignments Available in the Comparative Genome Viewer (CGV)

New Fungal Alignments Available in the Comparative Genome Viewer (CGV)

Recognizing Fungal Disease Awareness Week 

Fungal pathogens are a growing threat to global public health. To promote awareness of this issue, the Centers for Disease Control and Prevention (CDC) has established September 18 -22 as Fungal Disease Awareness Week 

In honor of this week, we’re highlighting whole genome alignments for fungal pathogens that are now available in the Comparative Genome Viewer (CGV) – NCBI’s latest genome visualization tool.  Alignment displays in CGV help you identify rearrangements and differences in genomic structure such as deletions, inversions, and translocations. These differences can be important for understanding genome plasticity, genetic diversity within species (PMC8640552) and the response to environmental stresses such as exposure to anti-fungal drugs (PMC5555451).    

CGV provides alignments for many species on the World Health Organization (WHO) prioritized list of fungal pathogens as well genome alignments of other fungi of medical, agricultural, or food production interest. 

You can explore cross-strain and cross-species genome alignments of several of these pathogens in CGV. Relevant species and some alignment partners are listed in the table below. 

Species Assemblies in CGV Cross-species WHO Priority  
Cryptococcus neoformans   5   No   Critical  
[Candida] auris   5   No   Critical  
Aspergillus fumigatus   2   No   Critical  
Candida albicans   3   Yes (C. dubliniensis)   Critical  
Nakaseomyces glabratus   4   No   High  
Fusarium oxysporum   4   No   High  
Cryptococcus gattii   2   No   Medium  
Pichia kudriavzevii   2   No   Medium  
Talaromyces marneffei   2   No   Medium  
Aspergillus flavus   3   Yes (A. oryzae)   N/A  
Aspergillus oryzae   1   Yes (A. flavus)   N/A  
Aspergillus niger   3   No   N/A  
Candida dubliniensis   2   Yes (C. albicans)   N/A  


Screenshot of the CGV comparing two aligned assemblies of fungal pathogensFigure 1: CGV alignment of a region of chromosome 5 for two Talaromyces marneffei clinical isolate assemblies from Vietnam. T. marneffei is a WHO medium priority pathogen that causes serious fungal infections. The two aligned assemblies are for strains associated with different disease severities. The alignment shows complex rearrangements in the region associated with the pathogenicity differences. See PMC6952663 for details. 

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CGV is a part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.     

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