Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis. Supplementary Materials.

Additional materials linked to submitted paper "Adaptive protein evolution through length variation of short tandem repeats in Arabidopsis" In this repository, there are data necessary to run the scripts provided in the Jupyter Notebook 'AdaptiveProteinEvolutionNotebook.ipynb' Additional File 1: HipSTR variant calling of Arabidopsis accessions formatted as a zipped zarr folder. Additional File 2: A python dictionary containing a map of STRs IDs and the amino acid tract the sites encode (at least four repeated amino acids required). Additional File 3: The version of the TAIR10 peptide sequences used in the manuscript (FASTA text file). Additional File 4: Map of STR coordinates to coordinates in the protein sequence (TSV). Additional File 5: STR IDs in different IDR regions (TSV). Additional File 6: Disorder predictions from d2p2 (BED). Additional File 7: Disorder predictions, protein binding from DisoRDPbind (BED). Additional File 8: Disorder predictions, DNA binding from DisoRDPbind (BED). Additional File 9: Disorder predictions, RNA binding from DisoRDPbind (BED). Additional File 10: Disorder predictions, MoRF regions from fMoRFpred (BED). Additional File 11: Disorder predictions, ANCHOR2 regions from IUpred2a (BED). Additional File 12: Protein coding STR unit counts, 770 accessions (TSV). Additional File 13: STR lengts vs. gene expression LIMIX model results (TSV) (from ref 9. in the manuscript). Additional File 14: Metadata on accessions (SRA run table) (TSV). Additional File 15: BCFtools variant calling of Arabidopsis genes after mapping with BWA-MEM. Additional File 16. Lists of ecotypes and group/subpopulation-designations (TSV). Additional File 17. Variance-covariance matrix of the 770 accessions (TSV). Additional File 18. Scaled mean environmental values per group/subpopulation (TSV). Additional File 19: Bayenv2.0 results of the second poly-Q tract in TCP14 (TSV). Additional File 20: Zipped OLS results folder. Additional File 21: Bayenv2.0 results, all protein coding STRs. Additional File 22: FST results, all protein coding STRs. Additional File 23: Environmental variables retrieved for the Arabidopsis accessions from data produced by ref 17 (CSV). Additional File 24: Alelle counts, most common allele and less common alleles (combined if multiallelic) for STRs used in Bayenv2.0.