Plant-Pathogen Interactions

Volume 1127 of the series Methods in Molecular Biology pp 29-51


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

  • Diane G. O. SaundersAffiliated withThe Sainsbury Laboratory
  • , Joe WinAffiliated withThe Sainsbury Laboratory
  • , Sophien KamounAffiliated withThe Sainsbury Laboratory
  • , Sylvain RaffaeleAffiliated withThe Sainsbury Laboratory, Norwich Research ParkLaboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441 INRA—UMR2594 CNRS Email author 

* Final gross prices may vary according to local VAT.

Get Access


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.

Key words

Genome architecture Data binning Intergenic R Visualization Heatmap Effectors Filamentous plant pathogen