Biology subjects

Grassa, C. J.

Publications and source records attributed to Grassa, C. J..

4 recordsLinked to original sources

bioRxiv2025

Unraveling Cross-Cellular Communication in Cannabis sativa Sex Determination: A Network Ontology Transcript Annotation (Nota) Analysis.

Cannabis sativa L. (marijuana, hemp, cannabis) is an angiosperm species currently evolving sex chromosomes. Genetic mechanisms, primarily an XY chromosome system, dictate cannabis sex expression in dioecious populations. However, sexual expression is also governed by the interplay of hormone regulatory gene networks, influenced by both genetic and environmental factors. Within the species, some populations exhibit dioecy, monoecy, or a gradient of both. Dioecious individuals produce exclusively male or female flowers, while monoecious plants bear both male and female flowers. Remarkably, through interruption of phytohormone signal transduction via abiotic stressors, genetically male or female cannabis are able to produce flowers of the opposite sex. Previous transcriptomic analysis have identified genes associated with masculinization through the application of phytohormone signal disruption using silver thiosulfate treatment. We analyzed transcriptomic data from cannabis treated with colloidal silver to similarly induce masculinization. Using Nota (Network Ontology Transcript Annotation), a multilayer network analysis (random walk with restart) tool, we identified candidate genes involved in sex-determination. Nota and a companion program Jack facilitate multi-layer network analyses, enabling discovery and annotation of gene-trait associations. Our findings highlight Notas robust application to enrich the genetic architecture of complex traits, particularly in non-model systems like cannabis, and complex traits such as sex determination. Our analyses identified genes associated with cell wall morphogenesis and embryogenic tissue homeostasis, indicating that silver ion treatment perturbs phytohormone signal transduction through metal ion imbalance. In this reproductive strategy, cannabis is able to make use of its widely investigated sex-determining genetic architecture to navigate transient changes in co-expression and cross-cellular signaling driving embryogenic cell wall re-patterning.

systems biology↗

bioRxiv2024

A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication

The Streptanthoid complex, a clade of primarily Streptanthus and Caulanthus genera in the Thelypodieae tribe (Brassicaceae) is an emerging model system for ecological and evolutionary studies. This Complex spans the full range of the California Floristic Province including desert, foothill, and mountain environments. The ability of these related species to radiate into dramatically different environments makes them a desirable study subject for exploring how plant species expand their ranges and adapt to new environments over time. Ecological and evolutionary studies for this complex have revealed fascinating variation in serpentine soil adaptation, defense compounds, germination, flowering, and life history strategies. Until now a lack of available genomic resources has hindered the ability to relate these phenotypic observations to their underlying genetic and molecular mechanisms. To help remedy this situation we present here a chromosome-level genome assembly of Streptanthus diversifolius, a member of the Streptanthoid Complex, developed using Illumina, Hi-C, and HiFi sequencing technologies. Construction of this assembly also provides further evidence to support the previously reported recent whole genome duplication unique to the Thelypodieae tribe. This whole genome duplication may have provided individuals in the Streptanthoid Complex the genetic arsenal to rapidly radiate throughout the California Floristic Province and to occupy commonly inhospitable environments including serpentine soils.

genomics↗

bioRxiv2020

Back to the future: a refined single user photostation for massively scaling herbarium digitization

The digitization and online mobilization of herbarium specimens has greatly facilitated their access and helped ignite a revolution in the biodiversity sciences (Drew et al., 2017; Hedrick et al., 2020; Nelson et al., 2015; Soltis, 2017; Sweeney et al., 2018; Thiers et al., 2016). These efforts have mobilized millions of specimens with significant economies of scale and accelerated advances in scientific investigations, including phenological studies of climate change, species range assessments, and biotic interactions (Hedrick et al., 2020; Meineke et al., 2019; Meineke et al., 2018; Pearson et al., 2020; Willis et al., 2017). In addition, the use of natural history collections to answer scientific questions using only their digitized representation, rather than the physical specimen itself-i.e., Digitization 2.0 sensu Hedrick et al. (2020)-has sparked the integration and development of new scholarly disciplines and lines of inquiry not previously possible. Despite these exciting new directions, however, Digitization 1.0 sensu Hedrick et al. (2020)-i.e., the generation of digitized products from the physical specimen-remains an active area of innovation and development. This relates to both hardware and workflow innovations as well as their integration with advancements in software. Along these lines, innovations in these areas have greatly increased the cost-effectiveness of digitizing herbarium specimens and enabled the successful mobilization of entire collections and whole floristic regions (Heerlien et al., 2015; Pignal and Michiels, 2012; Schorn et al., 2016; Slijkhuis, 2014; Sweeney et al., 2018; van Oever and Gofferje, 2012). Here, we present a novel photostation and workstation design for imaging herbarium specimen that represents a dramatic improvement upon existing approaches and is scalable for large and small institutions alike.

plant biology↗

bioRxiv2018

A complete Cannabis chromosome assembly and adaptive admixture for elevated cannabidiol (CBD) content

Cannabis has been cultivated for millennia with distinct cultivars providing either fiber and grain or tetrahydrocannabinol. Recent demand for cannabidiol rather than tetrahydrocannabinol has favored the breeding of admixed cultivars with extremely high cannabidiol content. Despite several draft Cannabis genomes, the genomic structure of cannabinoid synthase loci has remained elusive. A genetic map derived from a tetrahydrocannabinol/cannabidiol segregating population and a complete chromosome assembly from a high-cannabidiol cultivar together resolve the linkage of cannabidiolic and tetrahydrocannabinolic acid synthase gene clusters which are associated with transposable elements. High-cannabidiol cultivars appear to have been generated by integrating hemp-type cannabidiolic acid synthase gene clusters into a background of marijuana-type cannabis. Quantitative trait locus mapping suggests that overall drug potency, however, is associated with other genomic regions needing additional study.\n\nResources available online at: http://cannabisgenome.org\n\nSummaryA complete chromosome assembly and an ultra-high-density linkage map together identify the genetic mechanism responsible for the ratio of tetrahydrocannabinol (THC) to cannabidiol (CBD) in Cannabis cultivars, allowing paradigms for the evolution and inheritance of drug potency to be evaluated.

genomics↗