Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in Cannabis sativa Using Seven De Novo Genome Assemblies

Genomic characterization of <i>Cannabis sativa</i> has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of <i>C. sativa</i>. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We performed a <i>k</i>-mer-based pangenome analysis to contextualize these assemblies within over 200 existing assemblies. This allowed us to identify unique haplotypes and genomic diversity among <i>Cannabis sativa</i> genotypes. We leveraged linkage maps constructed from F₂ progeny of two of the assembled genotypes to characterize the recombination rate across the genome showing strong periphery-biased recombination. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus <i>Early1</i> to several of the new assemblies to evaluate the impact of reference bias on the mapping results and narrow the locus to a smaller region of the chromosome. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for <i>C. sativa</i> to accelerate future research efforts.