#39 · Genomics

Gap-free assemblies and pangenomes expose structural variation across crop lineages

Across these three studies, long-read, gap-free or chromosome-scale assemblies serve as the substrate for variation-aware comparison across crop and grass lineages. The longan study pairs a T2T gap-free genome and graph pangenome from 101 accessions with SV calling, selective sweep detection, and SV-GWAS that links structural variation to a DlDAZ-proximal region. The grain amaranth pangenome catalogs over 100,000 structural variants and reports domestication-associated changes in SV diversity and function alongside flowering-time QTL. The diploid Bromus assemblies, with contig N50 up to 294.76 Mb, characterize centromeric and sub-telomeric satellite repeats. What is new is trait association performed directly on structural variation within graph representations of lineage-level variation, while the Bromus work contributes assembly-level resolution of repeat architecture.