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

<p>This dataset contains additional files related with the "Revisiting the evolution and function of NIP2 parologs in the <em>Rhynchosporium</em> spp. complex" paper. The second version contains four additional files: EarlGrey_annotation.bed, The_RIPper_annotation.gff3,&nbsp;Figure_S7_alignment.fasta, and WAI_strains_attributes.xlsx</p> <p>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).</p> <p>Folder 2: Genome assembly (R.communeWAI453_20contigs.fasta), gene annotation of <em>R. commune</em> WAI453 (R.communeWAI453.gff3), <strong>transposable elements annotation of <em>R. commune</em> WAI453 (EarlGrey_annotation.bed)</strong>, and<strong> RIP-affected region annotation of <em>R. commune</em> WAI453 (The_RIPper_annotation.gff3)</strong>.</p> <p>Folder 3: Sequence of <em>NIP2</em> and <em>NLP</em> paralogs from <em>R. commune</em> global populations and <em>R. commune</em> sister species used in this study (nip2.1.all.fasta-nlp4.all.fasta) the summary of presence-absence polymorphism of all <em>NIP2</em> and <em>NLP</em> genes in <em>R. commune</em> and three <em>R. commune</em> sister species (gene_summary.csv),&nbsp;<strong>alignment of <em>NIP2 </em>and <em>NLP</em> genes (Figure_S7_alignment.fasta), </strong>and <strong>attributes of all <em>R. commune</em> WAI strains used in this study (WAI_strains_attributes.xlsx).</strong></p> <p>Folder 4: Pdb files of structural prediction of NIP2 proteins generated by AlphaFold 2 (nip2.1.pdb, nip2.3.pdb, and nip2.6.pdb).</p> <p>Folder 5: A python script to parse local blast result into fasta file&nbsp;(BLASTtoGFF_multiple.py).</p>