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Teran, W.

Publications and source records attributed to Teran, W..

2 recordsLinked to original sources
bioRxiv2026

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. CoreWe assembled four fully-phased and chromosome-scale diploid genomes of Cannabis sativa, using Oxford Nanopore Technology readsets. These new assemblies are comparable to recent PacBio HiFi assemblies in terms of contiguity and gene content. We present a phylogenomic analysis, using whole-genome alignments after including 77 other publicly available Cannabis genomes, as well as a draft pan-NLRome. Gene and Accession NumbersAssemblies are archived at NCBI as BioProjects PRJNA1301983 (ANC), PRJNA1301963 (HAW), PRJNA1301984 (SRI), and PRJNA1301985 (TRC). Assemblies, annotations, and Supplemental Tables are also available on Zenodo: https://doi.org/10.5281/zenodo.16456638.

plant biology↗
bioRxiv2025

A trio-binning approach for Cannabis genome de novo assembly reveals extensive structural variation, and defines paralog cohorts with very good resolution

With the advent of long read DNA sequencing technologies, assembling eukaryotic genomes has become routine; however, properly phasing the maternal and paternal contributions 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 18x 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, which is of great value for crop breeding programs. Evaluated through the lenses of disease resistance and secondary metabolite synthesis, both being traits of interest for the Cannabis industry, we report copy number and structural variation that, as has recently been shown for other major crops, may contribute to phenotypic variation along several relevant dimensions.

plant biology↗