Deyholos, M. | Search bioRxiv

bioRxiv2025

A haplotype-phased male genome sequence of the stinging nettle, Urtica dioica ssp. dioica

Stinging nettle (Urtica dioica L.) is a widespread weed of economic significance with a dioecious mating system. Previously, we generated a high-quality genome assembly of a diploid female plant, which showed extreme levels of structural variation between haplotypes. Here, we present a chromosome-level, haplotype-resolved sequence of a diploid male plant; since the male is believed to be the heterogametic sex in Urtica dioica, this assembly represents a first step towards elucidating the control of sex determination in this species. This completely independently assembled genome also allows confirmation of previously reported features of the nettle genome, including (1) a high degree of structural variation between haplotypes, including large inversions, (2) the likely existence of polycentric centromeres, and (3) the presence of urticaceous "pain peptide" sequences. Chromosome 8 stands out for its multiple large, nested inversions and high levels of repetitive sequences, features that are often associated with sex determining regions (SDRs). This chromosome is therefore a candidate for further investigations to characterize the sex determination in nettle.

genomics↗

bioRxiv2020

A Single Nucleotide Polymorphism assay sheds light on the extent and distribution of genetic diversity, population structure and functional basis of key traits in cultivated North American Cannabis

BackgroundThe taxonomic classification of the Cannabis genus has been delineated through three main types: sativa (long and less branched plant with long and narrow leaves), indica (short but highly branched plant with broader leaves) and ruderalis (wild type with short stature, less branching and small thick leaves). While still under discussion, particularly whether the genus is polytypic or monotypic, this broad classification reflects putative geographical origin of each group and putative chemotypic and pharmacology. MethodsHere we describe a thorough investigation of cannabis accessions using a set of 22 highly informative and polymorphic SNP markers associated with important traits such as cannabinoid and terpenoid expression as well as fibre and resin production. The assay offers insight into cannabis population structure, phylogenetic relationship, population genetics and correlation to secondary metabolite concentrations and demonstrate the utility of this assay for rapid, repeatable and cost-efficient genotyping of commercial and industrial cannabis accessions for use in product traceability, breeding programs, regulatory compliance and consumer education. ResultsThe main outcomes are the identification of 5 clusters in the sample set available, including industrial hemp, resin hemp which likely underwent a bottleneck to stabilize CBDA accumulation (Type II & III). THC resin (type I) make up the other three clusters with terpinolene (colloquial "sativa" or "NLD"), myrcene/pinene and myrcene/limonene (colloquial "indica", "BLD"), which also putatively harbour an active CBCAS. ConclusionThe functional basis of key traits is also discussed as recently enabled by the NCBI Cannabis sativa Annotation Release 100, allowing for hypothesis testing with regards to secondary metabolite production as well as other key traits of importance for adaptable and compliant large-scale seed production under the new US Domestic Hemp Production Program.

plant biology↗