Two-dimensional data binning for the analysis of genome architecture in filamentous plant pathogens and other eukaryotes

Saunders, Diane G O, Win, Joe, Kamoun, Sophien and Raffaele, Sylvain (2014) Two-dimensional data binning for the analysis of genome architecture in filamentous plant pathogens and other eukaryotes. Methods in Molecular Biology, 1127. pp. 29-51. ISSN 1064-3745

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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.

Item Type: Article
Uncontrolled Keywords: data binning,effectors,filamentous plant pathogen,genome architecture,heatmap,intergenic,r,visualization
Faculty \ School:
Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: Pure Connector
Date Deposited: 06 Jun 2016 16:00
Last Modified: 22 Apr 2020 01:28
URI: https://ueaeprints.uea.ac.uk/id/eprint/59237
DOI: 10.1007/978-1-62703-986-4_3

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