Microbiome analysis for phosphate-defense interaction
The code in this repository was used to analyze the microbial community assembled on roots of plants growing in a wild soil (census) or on plates with a synthetic community (SynCom).
The census directory contains code used to analyze the microbial community composition of
plants gorwing in wild Mason Farm soil.
The syncom directory contains code used to analyze the microbial community composition,
and the plant phenotypes, of plants growing on agar plates with a well-defined but complex
synthetic bacterial community, under different phosphate conditions.
The misc directory contains intermediate files that have been made available after
publication upon request. The misc/unifrac subdirectory contains UniFrac distance
matrices as calculated in QIIME/1.5.0 (described in Castrillo et al. 2017).
The raw sequencing reads that underlie the data in these analysis are publicly available in the European Nucleotide Archive's Short Read Archive under study accession: PRJEB15671.
Most scripts load one or two different functions.r files. Those two files are located at the main directory.
The file that is referenced as "~/rhizogenomics/src/trunk/phosphate_code/functions.r" is
simply named functions.r.
The file that is referenced as "~/rhizogenomics/src/trunk/immune_code/PRR_propep/functions.r"
is named functions_prrpropep.r.
If you use this code or the data associated with it please cite:
Castrillo G, Teixeira PJPL, Herrera Paredes S, Law TF, de Lorenzo L, Feltcher ME, et al. "Root microbiota drive direct integration of phosphate stress and immunity" (2017). Nature 543(7646):513–8. Available from: http://www.nature.com/doifinder/10.1038/nature21417
A BibTex entry for this publication is:
@article{Castrillo2017,
author = {Castrillo, Gabriel and Teixeira, Paulo Jos{\'{e}} Pereira Lima and {Herrera Paredes}, Sur and Law, Theresa F. and de Lorenzo, Laura and Feltcher, Meghan E. and Finkel, Omri M. and Breakfield, Natalie W. and Mieczkowski, Piotr and Jones, Corbin D. and Paz-Ares, Javier and Dangl, Jeffery L},
doi = {10.1038/nature21417},
issn = {0028-0836},
journal = {Nature},
month = {mar},
title = {{Root microbiota drive direct integration of phosphate stress and immunity}},
url = {http://www.nature.com/doifinder/10.1038/nature21417},
year = {2017}
}(C) Copyright 2016 Sur Herrera Paredes
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