Related Experiment Video

Updated: Feb 7, 2026

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
08:31

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

11.5K

Genome-Wide Comparative Analysis of Aspergillus fumigatus Strains: The Reference Genome as a Matter of Concern

Rocio Garcia-Rubio1, Sara Monzon2, Laura Alcazar-Fuoli3

  • 1Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain. rgarciar@isciii.es.

Genes
|July 22, 2018
PubMed

Insights

Choosing the right reference genome is crucial for accurate whole genome sequencing (WGS) analysis of Aspergillus fumigatus strains. Proper selection prevents misleading conclusions regarding antifungal resistance and genetic diversity in this important pathogen.

Area of Science:

  • Medical Mycology
  • Genomics
  • Antimicrobial Resistance

Background:

  • Aspergillus fumigatus is a common mold and a significant pathogen, particularly in immunocompromised individuals.
  • The efficacy of triazole antifungal drugs against A. fumigatus is increasingly compromised by widespread azole resistance.
  • Whole genome sequencing (WGS) is a powerful tool for understanding A. fumigatus genetic variation and resistance mechanisms.

Purpose of the Study:

  • To evaluate the impact of reference genome selection on WGS analysis of Aspergillus fumigatus.
  • To assess the genetic diversity and identify single nucleotide variants (SNVs) across a collection of A. fumigatus genomes.
  • To highlight the importance of appropriate reference genome choice for reliable WGS data interpretation.

Main Methods:

  • Analysis of 28 in-house and 73 publicly available Aspergillus fumigatus genomes using whole genome sequencing.
  • Comparative genomic analysis focusing on single nucleotide variant (SNV) calling.
  • Clustering of genomes based on genetic relatedness and evaluation of SNV counts using two different reference genomes (Af293 and A1163).

Main Results:

  • The analyzed Aspergillus fumigatus genomes clustered into four distinct groups.
  • The number of identified single nucleotide variants (SNVs) varied significantly depending on the chosen reference genome.
  • Each of the two reference genomes (Af293 and A1163) belonged to a different genomic cluster, indicating potential bias.

Conclusions:

  • The selection of an appropriate reference genome is critical for accurate whole genome sequencing analysis of Aspergillus fumigatus.
  • Using a genetically distant reference genome can lead to an overestimation or underestimation of genetic variations (SNVs).
  • Careful consideration of reference genome choice is essential to avoid erroneous conclusions in studies of A. fumigatus evolution and antifungal resistance.
Keywords:
Aspergillus fumigatusazole resistancecyp51Areference genomeswhole genome sequencing

More Related Videos

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer07:50

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

6.2K
Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets11:19

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

15.0K

Related Concept Videos

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
16.4K
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
40.8K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
15.7K
Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
37.2K
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
9.2K
Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
48.7K