European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility

Files associated with the publication "European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility" Preprint: https://doi.org/10.1101/2025.07.16.665114 Final doi to be added upon publication #Files BATG-1.0_annotation_v1.0.gtf - gtf file for BATG-1.0 annotation. Genes named FexB00001, FexB00002 etc. FexPG_v1.0_SVs.bcf - bcf file of SVs used to construct pangenome, alongside BATG-1.0 fasta FexPG_v1.0_graph.vg - graph pangenome constructed from bcf above and BATG-1.0 fasta using vg construct FexPG_annotation.bed - bed file outlining the location of the total gene set in the pangenome. Second and third columns are locations in BATG-1.0 co-ordinate space. Fourth and Fifth columns correspond to start and end locations of a feature including within SVs: i) location in BATG-1.0, ii) a "+", iii) SV type, iv) location within the SV (distance from start of breakpoint). FexPG_annotation.proteins.fa - protein coding sequences for the total gene set in the pangenome. Genes not already present in BATG-1.0 are named FexPG000001, FexPG00002 etc. FexPG_All_SVs.bcf - complete set of SVs called across all samples (i..e before filtering for SVs called in more than 3 individuals). Low_ADB_associated_SNPs - genomics locations of 220 SNPs associated low ADB susceptibility Revised_Source_Data_R3.1 - Source Data files for producing manuscript plots - see Source Data file README for complete descriptions Note: Gene names for the FexPG and BATG-1.0_v1.0 were renamed to more concise versions; the underlying annotation is identical, but some files may contain the original gene names (and some of the initial genes, such as those that were putatively dispensable but not supported by underlying SVs, are removed from the final gene sets). For clarity, files outlining the relationships bewteen the original and cleaned names are below: FexPG_annotation_renaming_to_v1.0BATG1.0_annotation_renaming_to_v1.0.txt BATG1.0_cpDNA.fasta - Chloroplast assembly for BATG-1.0 Note - the BATG-1.0 fasta is available at https://ashgenome.org/uk-reference-genome/