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


Ontology type: schema:Chapter     


Chapter Info

DATE

2014

AUTHORS

Diane G. O. Saunders , Joe Win , Sophien Kamoun , Sylvain Raffaele

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. More... »

PAGES

29-51

References to SciGraph publications

Book

TITLE

Plant-Pathogen Interactions

ISBN

978-1-62703-985-7
978-1-62703-986-4

Author Affiliations

From Grant

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-62703-986-4_3

DOI

http://dx.doi.org/10.1007/978-1-62703-986-4_3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1003574460

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24643550


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