Two-Dimensional Data Binning for the Analysis of Genome Architecture in Filamentous Plant Pathogens and Other Eukaryotes

Abstract

Genome architecture often reflects an organism's lifestyle and can therefore provide insights into gene function, regulation, and adaptation. In several lineages of plant pathogenic fungi and oomycetes, characteristic repeat-rich and gene-sparse regions harbor pathogenicity-related genes such as effectors. In these pathogens, analysis of genome architecture has assisted the mining for novel candidate effector genes and investigations into patterns of gene regulation and evolution at the whole genome level. Here we describe a two-dimensional data binning method in R with a heatmap-style graphical output to facilitate analysis and visualization of whole genome architecture. The method is flexible, combining whole genome architecture heatmaps with scatter plots of the genomic environment of selected gene sets. This enables analysis of specific values associated with genes such as gene expression and sequence polymorphisms, according to genome architecture. This method enables the investigation of whole genome architecture and reveals local properties of genomic neighborhoods in a clear and concise manner.

Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range

“…8Flanking distance (3′ and 5′) between predicted genes of Venturia inaequalis Vi1. Intergenic distances for all predicted genes are represented in the underlying heatmap, with the number of genes in each bin shown as a colour-coded heat map (on orthogonal projection) generated as in Saunders et al [185]. Genes were sorted into two-dimensional bins on the basis of the lengths of flanking intergenic distances to neighbouring genes at their 5′ and 3′ ends; overlying this are scatterplots of a 423 Core Eukaryotic Genes ( white dots ) or b Venturia infection secretome ( V IS) gene set, plus AvrLm6- and Ave1 -like genes (coloured dots: dark pink  = SSPs with two or more cysteines (≤500 amino acids); light pink  = SSPs with one or no cysteines (≤500 amino acids); blue = peptidases; dark green  = CAZymes; light green  = putative cell wall-degrading enzymes (non-CAZyme); white  = cell wall associated and miscellaneous proteins >500 amino acids).…”

De novoassembly and phasing of dikaryotic genomes from two isolates ofPuccinia coronataf. sp.avenae, the causal agent of oat crown rust

“…This genome architecture may favor fast host adaptation by relieving constraints on effector diversification. To determine the distribution of genes in gene-rich or sparse regions, we used a two-dimensional genome-binning method (54) to plot intergenic distances for all genes in Pca ( Figure 5 ). Predicted effectors on primary contigs and haplotigs in both isolates showed no difference in location compared to the overall gene space.…”

“…Gene ontology (GO) enrichment analysis was carried out with the enrichGO function in the R package clusterProfiler version 3.4.4 (92) using the “Molecular function” ontology method and the Holm method to correct p -values for multiple comparisons. Local gene density was assessed using the method of Saunders et al (54), with updates from density-Mapr ( https://github.com/Adamtaranto/density-Mapr ) to plot the 5’ and 3’ intergenic distance for each gene. The R package GenometriCorr (55) was used to test for associations between effectors and various categories of repeats within 10 kbp regions using default parameters.…”

Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida

“…This property has been used to identify novel candidate virulence factors [ 44 ]. Calculating the distance between each gene and its nearest neighbours (the flanking intergenic regions) and comparing these values for all genes in a genome, can be used as a way of calculating whether a gene resides in a gene rich or gene sparse environment [ 45 ]. We therefore examined whether or not this pattern is also true in the G. pallida genome with a particular focus on the SPRYSECs as the nature of this substantial gene family and the absence of a similarly expanded family in other cyst nematodes suggested that it may be in the process of rapid evolution.…”