#36 · Genomics

Haplotype-resolved genome assemblies tie haplotype diversity to resistance traits in…

The dominant thread is haplotype-aware genome representation applied to wild and related plant germplasm. The Carya glabra preprint reports a first haplotype-resolved, chromosome-scale assembly of an autotetraploid, with organelle genomes and annotation. The Aegilops caudata study pairs genome assembly and optical mapping with k-mer GWAS across 95 accessions, identifying stem rust resistance gene SrAect1. The Vitis work assembles four chromosome-scale diploid genomes and applies sequence graph analysis to map PdR1 haplotype diversity and candidate defense genes against Pierce's disease. What is new is the direct linkage of haplotype-aware representation to trait variation, through graph-based analysis in Vitis and assembly-plus-k-mer association in Aegilops. The Carya summary reports assembly and annotation only. The items do not share one organism or trait, so the shared element is methodological.