Bacterial and Archeal GC Content by Metabolism
his is a figure from a chapter from my PhD dissertation (still a work in progress) about open access and open notebooks in the sciences. I am interested in seeing what large scale patterns in microbiology ecology fall out from large whole genome datasets.
I read somewhere (need to find the source) that G and C are more energy intensive to make. I am curious if high energy metabolic pathways are coupled to GC content in bacteria and archaea.
References
R software
R Core Team (2014). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/
H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York, 2009.
Genome data provided by:
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates.
Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I, Smirnova T, Grigoriev IV, Dubchak I. Nucleic Acids Res. 2014,42(1):D26-31.
The Genome Portal of the Department of Energy Joint Genome Institute
Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I.Nucleic Acids Res. 2012 Jan;40(Database issue):D26-32.
IMG: the integrated microbial genomes database and comparative analysis system Victor M. Markowitz1, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova and Nikos C. Kyrpides
"These sequence data were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the user community."
