Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights allopolyploidy-mediated innovations in N-acylnornicotine metabolism

preprint available at: https://doi.org/10.1101/2022.09.12.507566

supplementatry data at :

# Running QCxmS on the singularity container (ubuntu.sif) with the qcxms.py script 
# —> singularity exec ubuntu.sif python qcxms.py -o $outdir -nt $nr_trajectories -i $inchi  

# Sending it 
module load singularity
srun -p public singularity exec ubuntu.sif python qcxms.py -o mol1 -nt 5 -i "InChI=1S/C23H38N2O3/c1-2-3-5-11-20(26)12-6-4-7-13-21(27)17-23(28)25-16-9-14-22(25)19-10-8-15-24-18-19/h8,10,15,18,20-22,26-27H,2-7,9,11-14,16-17H2,1H3"

Workflow:

Scripts used in this publication:

• S1_openbabel_conversion.ipynb Converts Smiles to Inchi
• S2_reformater.R Clean Databases
• S3_add_openbabel_info.R Merge Databases and drop duplicates
• S4_run_cfmid_mesocenter.sh & cfmid_commands.txt Used to run CFM on HPC Cluster
• S5_Process_mgf.ipynb Used to create composite Spectra from CFM Collision Energies
• S6_matchms_spec2vec.py Used for Database Matching of CFM ID on HPC Cluster
• S7_matchms_scores_analysis.py Used for Database Matching of CFM ID on HPC Cluster
• S8_MatchMS-v1-cosine-msp.ipynb Used for Database Matching of Nicotiana DB
• S9_MatchMS-v1-cosine.ipynb Used for Database Matching of Jassbi
• S10_Batch-QTOF-sens-v3.xml Used for Batch Mode processing of Dataset
• S11_mgf-rem-redundancy-v4.ipynb Remove redundant features
• S12_Sirius-removev2.ipynb Remove redundant IDs from Sirius mgf file
• S13_run_sirius.sh Used to run Sirius on HPC Cluster
• S14_degree-unsaturation-sirius.ipynb Restore Feature ID from Sirius ID and Calculate degree of unsaturation, requires molmass package
• S15_compound-id-sirius.ipynb Restore Feature ID from Sirius ID
• S16_canopus_consensus_ms2lda.ipynb merge the outputs of all the tools into one big table also get consensus substructures( based on ms2lda motifs) for insilico-tools and propagate canopus within networks
• S17_MSLDAmerge-motfs.ipynb Get Motifcount based on Presence of Feature
• S18_MSLDAmerge-motfs-sumall.ipynb Get Motifcount based on Presence of Feature within all Tissues
• S19_canopus_consensus.ipynb Script to merge the outputs of all the tools into one big table also get consensus substructures for insilico-tools and propagate canopus within networks
• S20_phylometabo.ipynb Calculate Pairwise Distance Matrix based on Data of Motif Figure and Network Figure
• S21_phylo.Rmd Plot Phylogenies from pairwise Distance Matrix based on APE package
• S22_sum_molformula_areas.ipynb Sum Areas of NANNs based on identical Molecular Formula
• S23_nann_bubbles.ipynb Sum Areas based on Carbon Chain of NANNs, split by hydroxylation or not
• S24_Networkclustermap.ipynb Sum all areas of Networks per Samples
• S25_ASR-single.Rmd Ancestral State reconstruction based on MBASR
• S26_dbsearch.py Script to run cosine score based search on big in-silico db
• S27_run_db.py Script to run cosine score based search on big in-silico db
• S28_group_for_treemap.ipynb Used to group and sum canopus classes peak areas
• S29_alpha_diversity.ipynb Calculate alpha diversity based on shannon entropy
• S30_Vegan_calculations.Rmd NMDS using vegan package
• S31_cosine_distance_sp_canopus.ipynb Calculate distances between species and CANOPUS classes