Plant-Pathogen Interactions pp 29-51

Part of the Methods in Molecular Biology book series (MIMB, volume 1127)

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

  • Diane G. O. Saunders
  • Joe Win
  • Sophien Kamoun
  • Sylvain Raffaele
Protocol

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.

Key words

Genome architecture Data binning Intergenic Visualization Heatmap Effectors Filamentous plant pathogen 

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Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  • Diane G. O. Saunders
    • 3
  • Joe Win
    • 3
  • Sophien Kamoun
    • 3
  • Sylvain Raffaele
    • 1
    • 2
  1. 1.The Sainsbury LaboratoryNorwich Research ParkNorwichUK
  2. 2.Laboratoire des Interactions Plantes-Microorganismes (LIPM)UMR441 INRA—UMR2594 CNRSCastanet-TolosanFrance
  3. 3.The Sainsbury LaboratoryNorwichUK

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