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

Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Two emerging challenges for the C. sativa research community are to 1) comprehensively capture the genomic diversity of the species and 2) reconcile and leverage the large amounts of genomic data to make meaningful contributions to fundamental research and commercial production systems. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We used a kmer-based pangenome analysis to place these new assemblies in the context of more than 200 existing assemblies. We leveraged linkage maps constructed from F2 progeny of two of the assembled genotypes to characterize the recombination rate across the genome. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus Early1 to several of the new assemblies to evaluate the impact of reference bias on the mapping results. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for C. sativa to accelerate future research efforts.