On Variant Discovery in Genomes of Fungal Plant Pathogens

Abstract

Comparative genome analyses of eukaryotic pathogens including fungi and oomycetes have revealed extensive variability in genome composition and structure. The genomes of individuals from the same population can exhibit different numbers of chromosomes and different organization of chromosomal segments, defining so-called accessory compartments that have been shown to be crucial to pathogenicity in plant-infecting fungi. This high level of structural variation confers a methodological challenge for population genomic analyses. Variant discovery from population sequencing data is typically achieved using established pipelines based on the mapping of short reads to a reference genome. These pipelines have been developed, and extensively used, for eukaryote genomes of both plants and animals, to retrieve single nucleotide polymorphisms and short insertions and deletions. However, they do not permit the inference of large-scale genomic structural variation, as this task typically requires the alignment of complete genome sequences. Here, we compare traditional variant discovery approaches to a pipeline based on de novo genome assembly of short read data followed by whole genome alignment, using simulated data sets with properties mimicking that of fungal pathogen genomes. We show that the latter approach exhibits levels of performance comparable to that of read-mapping based methodologies, when used on sequence data with sufficient coverage. We argue that this approach further allows additional types of genomic diversity to be explored, in particular as longread third-generation sequencing technologies are becoming increasingly available to generate population genomic data.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

“…However, the mechanisms that enabled the formation of these regions of genomic innovations remain unclear. Very recently, Potgieter et al [ 65 ] revised the approaches of genome analyses to discovery the genetic variants that characterized the high structural variation among the accessory compartments of the effector genes. In their analyses, the authors have proposed a pipeline based on de novo genome assembly of short read data followed by whole genome alignment, using simulated data sets with properties mimicking that of fungal pathogen genomes.…”

Combined Pan-, Population-, and Phylo-Genomic Analysis of Aspergillus fumigatus Reveals Population Structure and Lineage-Specific Diversity

“…However, there is growing appreciation that a single reference genome is incapable of capturing the genetic variation present across a species. Whereas genes absent in the reference genome are likely to be ignored using reference based alignment, de novo strategies for genome assembly offer the possibility of capturing the full repertoire of genetic diversity (Potgieter et al ., 2020). Here, we used a combined genomics approach to leverage both reference-based and de novo strategies to illuminate population structure and genetic diversity across the A. fumigatus pan-genome.…”

Recent Advances in Molecular Diagnostics of Fungal Plant Pathogens: A Mini Review

“…A 51.4 Mb genome of the two host isolates showed a unique single nucleotide polymorphism for the two isolates and identified both as C. pseudonaviculata ( Malapi-Wight et al., 2016b ). Datasets from population genomics built on NGS can be exploited to recuperate variations including single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and structural variations ( Potgieter et al., 2020 ). Puccinia striiformis f. sp.…”