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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Identifying candidate Aspergillus pathogenicity factors by annotation frequency.

Kayla K Pennerman1, Guohua Yin2, Anthony E Glenn3

  • 1United States Department of Agriculture, Toxicology and Mycotoxin Research Unit, Athens, GA, 30605, USA. kkpennerman@gmail.com.

BMC Microbiology
|November 12, 2020
PubMed
Summary
This summary is machine-generated.

Comparative genomics of Aspergillus species reveals distinct functional gene profiles linked to plant or animal pathogenicity. Hexokinase genes in Aspergillus fumigatus were upregulated during host immune cell interactions, suggesting roles in animal pathogenesis.

Keywords:
AspergillusComparative gene annotationComparative protein annotationHexokinasePathogenicity factors

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Area of Science:

  • Mycology
  • Genomics
  • Pathogenomics

Background:

  • The genus Aspergillus encompasses species with diverse lifestyles, including plant and animal pathogens.
  • Genome sequencing facilitates comparative '-omics' analyses to identify genes contributing to pathogenicity.
  • This study analyzed 216 genomes from 12 Aspergillus species, comparing gene structures and functional annotations.

Purpose of the Study:

  • To compare structural and functional genomic features across Aspergillus species.
  • To identify gene profiles associated with plant versus animal pathogenicity.
  • To investigate potential pathogenicity factors in Aspergillus fumigatus.

Main Methods:

  • Predicted protein-coding genes from 216 Aspergillus genomes.
  • Compared gene structural aspects (exon/intron counts/lengths, GC content, codon usage).
  • Analyzed functional annotations (InterPro, Gene Ontology, KEGG) and RNA-Seq data.

Main Results:

  • Species clustered based on functional annotations, separating by plant pathogenicity.
  • Phytopathogenic Aspergillus species showed enrichment for pectinase and secondary metabolite genes.
  • Animal-pathogenic Aspergillus fumigatus strains had more genes related to phosphate transferases and carbohydrate/amino-sugar metabolism.
  • A hexokinase gene in A. fumigatus was upregulated during co-culture with human immune cells.

Conclusions:

  • Genomic and functional comparisons can delineate pathogenicity traits in Aspergillus.
  • Hexokinases and other identified genes are potential targets for understanding and manipulating Aspergillus pathogenicity.
  • Specific metabolic pathways are associated with different host specificities within the Aspergillus genus.