This repository contains supplementary materials relating to the manuscript "The chemoevolution of diterpenoids in Euphorbia across the world" by M. Ernst (@madeleineernst), L.-F. Nothias (@lfnothias), J. J. J. van der Hooft, R. R. Silva (@rsilvabioinfo), C. H. Saslis-Lagoudakis, O. M. Grace, K. Martinez-Swatson, G. Hassemer, L. A. Funez, H. T. Simonsen, M. H. Medema, D. Staerk, N. Nilsson, P. Lovato, P. C. Dorrestein & N. Rønsted.
Please cite this supplementary material through: https://doi.org/10.1101/323014.
The file called Cytoscape_SummaryTable.csv is a summary table of the mass spectral molecular network data described in the the manuscript and the supplementary material.
The file called Euphorbia_Network.cys is a file, which can be opened in Cytoscape version 3.4.0 (Shannon et al., 2003) and visualizes the mass spectral molecular network and associated data as described in the manuscript and the supplementary material.
The folder called 3DMolecularCartography contains R scripts and data files used for analyses associated with the 3D mass spectral molecular cartography. For more details see 3DMolecularCartography/README.
The folder called ClassyFire contains R scripts and data files used for performing automated chemical classification of the in silico annotated structures using ClassyFire (Djoumbou Feunang et al., 2016).
The folder called Figure 1 contains R scripts and data files used for creating Figure 1 of the manuscript.
The folder called Figure 4 and subfolders Figure4A and Figures4BtoD contain R scripts and data files used for creating Figures 4A to D of the manuscript.
The folder called Mass2Motifs_2_MolecularNetwork contains R scripts and data files used for mapping Mass2Motifs (Van der Hooft et al., 2016; Wandy et al., 2018) on the mass spectral molecular networks (Wang et al., 2016; Watrous et al., 2012).
The folder called Optimus contains data files used and retrieved from LC-MS/MS data preprocessing through Optimus (https://github.com/MolecularCartography/Optimus).
The folder called PGLS contains R scripts and data files used for performing the phylogenetic generalized least squares regression analysis (PGLS).
The folder called Sirius_CSIFingerID contains data files used and retrieved from in silico structure annotation through SIRIUS+CSI:FingerID (Dührkop and Böcker, 2016; Dührkop et al., 2015). For more details see Sirius_CSIFingerID/README.
- Euphorbia horrida (Model 1)
- Euphorbia horrida (Model 2)
- Euphorbia horrida (Model 3)
- Euphorbia hirta (Model 1)
- Euphorbia hirta (Model 2)
- Euphorbia lathyris (Model 1)
- Euphorbia lathyris (Model 2)
- Euphorbia milii (Model 1), milliamine C derivative, m/z 749.3005, RT 4.4042
- Euphorbia milii (Model 2), milliamine C derivative, m/z 749.3005, RT 4.4042
- Euphorbia milii (Model 1), milliamine C derivative, m/z 778.33, RT 3.7326
- Euphorbia milii (Model 2), milliamine C derivative, m/z 778.33, RT 3.7326
- Euphorbia milii (Model 1), milliamine C derivative, m/z 778.3291, RT 5.1918
- Euphorbia milii (Model 2), milliamine C derivative, m/z 778.3291, RT 5.1918
- Euphorbia milii (Model 1), milliamine C derivative, m/z 792.3451, RT 2.6119
- Euphorbia milii (Model 2), milliamine C derivative, m/z 792.3451, RT 2.6119