Data and codes used to perform genome re-annotation, weighted gene co-expression analyses, and differential gene expression analyses of below paper

Environmental gradients reveal stress hubs predating plant terrestrialization Armin Dadras, Janine M. R. Fürst-Jansen, Tatyana Darienko, Denis Krone, Patricia Scholz, Tim P. Rieseberg, Iker Irisarri, Rasmus Steinkamp, Maike Hansen, Henrik Buschmann, Oliver Valerius, Gerhard H. Braus, Ute Hoecker, Marek Mutwil, Till Ischebeck, Sophie de Vries, Maike Lorenz, Jan de Vries bioRxiv 2022.10.17.512551; doi: https://doi.org/10.1101/2022.10.17.512551

Sequences used as inputs

If we used any publicly available sequence for an analysis, we gathered them from this sources (sorted by the priorities):

1. Phytozome
2. The supplamentary files of the paper which sequenced or annotated a genome
3. Any website mentioned on the paper which sequenced or annotated a genome

To save space, we just put a file containing the name of files (organisms) which were used for each genome re-annotation step. All RNAseq reads have been uploaded to NCBI SRA and can be accessed under Bioproject PRJNA832564 and SRA accessions SRR18936040 to SRR18936170.

Improvements that has happened during the review process

The files (codes and results) that we gathered while we were compiling the response letters to the reviewers' concerns and improving the manuscript are available here: https://doi.org/10.5281/zenodo.8109118 The files are too big to be published in GitHub without a paid plan.