DOI: 10.5281/zenodo.15722582
title: Data and code for Brun et al. - Seed metabolites headstart haustoriogenesis and potentiate aggressiveness of parasitic weeds

description: Data, codes, and final outputs for the research article Brun et al., "Seed metabolites headstart haustoriogenesis and potentiate aggressiveness of parasitic weeds", containing raw data tables and R scripts for bioassays, RNAseq read mapping data and analysis code, MS raw files from LC-MS analysis, annotation details, as well as post-processing information as follows: 

1) Directory "Bioassays" : contains all raw data are available as Excel spreadhseet. The R scripts are organized per Figure panel or supplementary figure for easy processing.

 

2) Directory "LC-MS"

- Annotation : contains the four main files used as supplementary data S7-S10

- Post-processing : contains the two abundance files from each kinetic analysis and the R script to generate the final heatmap. 

- RAW MS files

- Conditioning_raw_files : all *.raw MS files pertaining to LC-MS quantification of exudome of P. ramosa seeds undergoing conditioning for 1, 4, 7, and 14 days (in five biological replicates each), and a series of 6 blank replicates corresponding to autoclaved distilled water supplemented with 0.1% PPM

- Haustoriogenesis_raw_files: all *.raw MS files pertaining to LC-MS quantification of exudome of P. ramosa conditioned and washed seeds stimulated with rac-GR24 for 0 (t_0_*), 3 (t_1_*), 6 (t_2_*), and 12 (t_3_*) days (in five biological replicates each), and a series of 5 blank replicates corresponding to autoclaved distilled water supplemented with 0.1% PPM.

 

3) Directory "RNASeq"

- Conditioning

- Assembly & Annotation

Trinity.filtered.estscan.vsearch.rmdup.fasta = reference transcriptome assembly encompassing all 15 samples of P. ramosa seeds collected over the first 24 hours of conditioning. 

Trinity.filtered.estscan.vsearch.rmdup.fasta.transdecoder.pep = translated assembly using Transdecoder

Trinotate_annotation_report.xls = Full transcriptome annotation report as output by Trinotate

trinotate_report_gene_ontology_with_parents.xls = GO strings per transcriptome unigene as output by Trinotate

- Count data

rsem_matrix.gene.* = count, TPM, and TMM matrices in gene mode (the one used for the DEG analysis)

rsem_matrix.isoform.* = count, TPM, and TMM matrices in isoform mode

- DEG analysis

conditioning_RNAseq_clustering+enrichment.R = the full R script to cluster kinetic RNAseq data and perform enrichment analyses. 

*.RData = intermediate RData files for lazy loading 

Fig*.R and fig*.R = R scripts to generate the corresponding figures. 

The remaining files are in/outfiles necessary for either script to execute. 

- Haustoriogenesis

- Assembly & Annotation

Trinity.filtered.estscan.vsearch.rmdup.fasta = reference transcriptome assembly encompassing all 42 samples of P. ramosa washed and unwashed seeds treated with rac-GR24 for 0 to 144 hours. 

Trinity.filtered.estscan.vsearch.rmdup.fasta.transdecoder.pep = translated assembly using Transdecoder

Trinotate_annotation_report.xls = Full transcriptome annotation report as output by Trinotate

trinotate_report_gene_ontology_with_parents.xls = GO strings per transcriptome unigene as output by Trinotate

- Count data

rsem_matrix.gene.* = count, TPM, and TMM matrices in gene mode (the one used for the DEG analysis)

rsem_matrix.isoform.* = count, TPM, and TMM matrices in isoform mode

- DEG analysis

haustoriogenesis_RNAseq_clustering+enrichment.R = the full R script to cluster kinetic RNAseq data and perform enrichment analyses. 

*.RData = intermediate RData files for lazy loading 

Fig*.R and fig*.R = R scripts to generate the corresponding figures. 

The remaining files are in/outfiles necessary for either script to execute.