Supplementary files from paper "Revisiting the evolution and function of NIP2 paralogs in the Rhynchosporium spp. complex"

This dataset contains additional files related with the "Revisiting the evolution and function of NIP2 parologs in the Rhynchosporium spp. complex" paper. The second version contains four additional files: EarlGrey_annotation.bed, The_RIPper_annotation.gff3, Figure_S7_alignment.fasta, and WAI_strains_attributes.xlsx

Folder 1: R script for differential gene expression analysis and RPKM calculation (EdgeR_WAI453.html) including the input files (gene_count_matrix.csv and for_RPKM_featureCounts.csv).

Folder 2: Genome assembly (R.communeWAI453_20contigs.fasta), gene annotation of R. commune WAI453 (R.communeWAI453.gff3), transposable elements annotation of R. commune WAI453 (EarlGrey_annotation.bed), and RIP-affected region annotation of R. commune WAI453 (The_RIPper_annotation.gff3).

Folder 3: Sequence of NIP2 and NLP paralogs from R. commune global populations and R. commune sister species used in this study (nip2.1.all.fasta-nlp4.all.fasta) the summary of presence-absence polymorphism of all NIP2 and NLP genes in R. commune and three R. commune sister species (gene_summary.csv), alignment of NIP2 and NLP genes (Figure_S7_alignment.fasta), and attributes of all R. commune WAI strains used in this study (WAI_strains_attributes.xlsx).

Folder 4: Pdb files of structural prediction of NIP2 proteins generated by AlphaFold 2 (nip2.1.pdb, nip2.3.pdb, and nip2.6.pdb).

Folder 5: A python script to parse local blast result into fasta file (BLASTtoGFF_multiple.py).