Building pangenomes for domesticated and wild tree species: genomic complexity and strategies

Long-read sequencing and pangenomics are revolutionizing crop research by providing more complete genome information and revealing crucial structural variations linked to important agricultural traits. Building on recent advances in intraspecific pangenome construction, this study addresses the challenge of creating broader, cross-taxon pangenomes, using the Armeniaca taxonomic section as a model. Leveraging a diverse panel of genome assemblies, we constructed a pangenome graph and cataloged associated single nucleotide polymorphisms (SNPs) and structural variants. We characterized the diversity of these variants and assessed the extent to which different taxa contribute to overall pangenome expansion. Additionally, we evaluated the performance of low-depth sample mapping to the graph-based reference, highlighting key technical limitations that may affect the quality of downstream analyses. We further identified specific subsets of SVs that exhibit associations with particular classes of transposable elements. As a case study illustrating the potential functional and phenotypic relevance of graph-derived SVs, we examined the genomic configuration of the DAM locus within the Armeniaca pangenome.