A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie.

ABSTRACT: With the advent of long-read DNA sequencing technologies, assembling eukaryotic genomes has become routine; however, properly phasing the maternal and paternal contributions, which is of great value for breeding programs, remains technically challenging. Here, we use the trio-binning approach to separate Oxford Nanopore reads derived from a Cannabis F1 wide cross, made between the Colombian landrace Punto Rojo and the Colorado CBD clone Cherry Pie #16. Reads were obtained from a single PromethION flow cell, generating assemblies with coverage of just 18 × per haplotype, but with good contiguity and gene completeness, demonstrating that it is a cost-effective approach for genome-wide and high-quality haplotype phasing. Evaluated through the lenses of disease resistance and secondary metabol

SUBMITTER: Pike B 

PROVIDER: S-EPMC12869074 | biostudies-literature | 2026 Feb

REPOSITORIES: biostudies-literature