LoFi drafts to map to: 4 haplotype-resolved Cannabis genomes enable characterization of large structural variants

We present fully-phased, chromosome-scale genome assemblies of 4 genotypes of Cannabis sativa. These assemblies were built from Oxford Nanopore R9.4.1 long reads, which previously have been considered insufficiently accurate for proper phasing. Contigs produced by the Phased Error Correction and Assembly Tool (PECAT), in combination with Hi-C libraries, were used by GreenHill to develop intermediate data structures that permit accurate phasing of the dual contigs, which were then scaffolded by the advanced algorithm of Yet another Hi-C Scaffolder (YaHS). These assemblies, while low in QV, are comparable to recent HiFi assemblies in their contiguity and gene content, and also show good macrosynteny with them. We compare these 8 haplotypes with 77 others recently produced and present a phylogenetic analysis, as well as a first draft of the Cannabis pan-NLRome.