Biology subjects

Vergara, D.

Publications and source records attributed to Vergara, D..

10 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

The evolution of heteromorphic sex chromosomes in plants

Sex chromosomes in cannabis and hop were identified a century ago because of their obvious visible differences in size (heteromorphy). However, we know little about the genes they contain that control the development of the inflorescences. Here we assembled genomes, with phased sex chromosomes, for hop and cannabis. The XY chromosomes share an origin prior to the divergence between the genera >36 MYA. Due to the inheritance patterns of the XYs, the male-specific region of the Y is highly-degenerated, with substantial gene loss, while the X shows faster rates of molecular evolution. Consistent with the theory that these species lack an active-Y system, no clear sex-determining genes reside on the Y. Instead, an X-linked homolog of aminocyclopropane-1-carboxylate synthase (ACS), that is involved in the ethylene biosynthesis pathway, determines the fate of the female inflorescence. Beyond sex determination, the sex chromosomes contribute to the sexual dimorphism in ecology and physiology and have played a role in the domestication and breeding of these species.

evolutionary biology↗

bioRxiv2023

M1-derived extracellular vesicles polarize recipient macrophages into M2 and alter skeletal muscle homeostasis in a hyper-glucose environment

BackgroundMacrophages release not only cytokines but also extracellular vesicles (EVs). EVs are small lipid-derived vesicles with virus-like properties transferring lipids, RNA and proteins between cells. Until now, the consequences of macrophage plasticity on the release and the composition of EVs have been poorly explored. In this study, we determined the impact of high-glucose (HG) concentrations on macrophage metabolism, and characterized their derived EV subpopulations. Finally, we determined whether HG-treated macrophage-derived EVs participate in immune responses and in metabolic alterations of skeletal muscle cells. MethodsTHP1-macrophages (M0) were treated with 15mM (MG15) or 30mM (MG30) glucose. M1 or M2 canonical markers, pro- and anti-inflammatory cytokines and lactate production were evaluated. Macrophage-derived EVs were characterized by TEM, flow cytometry, and 1H-Nuclear magnetic resonance spectroscopy for lipid composition. M0 macrophages or C2C12 muscle cells were used as recipients of MG15 and MG30-derived EVs. The lipid profiles of recipient cells were determined, as well as protein and mRNA levels of relevant genes for macrophage polarization or muscle metabolism. ResultsM0 released 2 populations of small and large EVs (sEVs, lEVs) with specific lipid profiles. Proportionally to the glucose concentration, glucose-treatment induced glycolysis in M0 macrophages which consequently shifted into a pro-inflammatory M1 phenotype, containing increased triacylglycerol and cholesterol content. Glucose also affected macrophage sphingolipid and phospholipid compositions. The lipid profile differences between sEVs and lEVs were abolished and represented the lipid profile alterations of MG15 and MG30 macrophages. Both sEVs and lEVs from M15 and M30 macrophages polarized M0 into anti-inflammatory M2, with increased contents of triacylglycerol and cholesterol. MG15 lEVs and sEVs induced insulin-induced AKT hyper-phosphorylation and accumulation of triacylglycerol in muscle cells, a state observed in pre-diabetes. Conversely, MG30 lEVs and sEVs induced insulin resistance in myotubes. ConclusionsAs inflammation involves first M1 macrophages, then the activation of M2 macrophages to attenuate inflammation, this study demonstrates that the dialog between macrophages through the EV route is an intrinsic part of the inflammatory response. In a hyperglycemic context, EV macrophages could participate in the development of muscle insulin-resistance and chronic inflammation.

cell biology↗

bioRxiv2022

Genomic description of critical upstream cannabinoid biosynthesis genes

Cannabinoid production is one of the key attributes of the plant Cannabis sativa and the characterization of the genes involved is an essential first step to develop tools for their optimization. We used bioinformatic approaches to annotate and explore variation in the coding genes for critical enzymes comprising the cannabinoid pathway: Olivetol Synthase (OLS), Olivetolic Acid Cyclase (OAC), and Cannabigerolic Acid Synthase (CBGAS), in multiple C. sativa genomes. These upstream genes of the Cannabinoid Oxidocyclase Genes THCAS, CBDAS, and CBCAS generate the necessary precursor molecules to produce the cannabinoids THC and CBD. We found that these genes vary in copy number and confirm that OLS, OAC, CBGAS, and the Cannabinoid Oxidocyclases are on separate chromosomes, while homologs are found in proximity. CBGAS, located on Chromosome X, suggests potential dosage effects in female plants. Except for the Cannabinoid Oxidocyclase genes, the other genes have multiple exons, up to 10 in CBGAS. Through differential exon usage explorations in CBGAS we found evidence for potential regulatory differences. This study provides valuable insight on the genomic identity and variation of cannabinoid biosynthesis genes that will benefit future research on the origin and evolution of this pathway, driver of economic, social, and medicinal value.

genomics↗

bioRxiv2021

The Phytochemical Diversity of Commercial Cannabis in the United States

The legal status of Cannabis is changing, fueling an increased diversity of Cannabis-derived products. Because Cannabis contains dozens of chemical compounds with potential psychoactive or medicinal effects, understanding its phytochemical diversity is crucial. The legal Cannabis industry heavily markets products to consumers based on widely used labelling systems purported to predict the effects of different Cannabis "strains." We analyzed the cannabinoid and terpene content of tens of thousands of commercial Cannabis samples across six US states, finding distinct chemical phenotypes (chemotypes) which are reliably present. After careful descriptive analysis of the phytochemical diversity and comparison to the commercial labels commonly attached to Cannabis samples, we show that commercial labels do not consistently align with the observed chemical diversity. However, certain labels are statistically overrepresented for specific chemotypes. These results have important implications for the classification of commercial Cannabis, the design of animal and human research, and the regulation of legal Cannabis marketing.

plant biology↗

bioRxiv2021

Genomic evidence that governmentally produced Cannabis sativa poorly represents genetic variation available in state markets

The National Institute on Drug Abuse (NIDA) is the sole producer of Cannabis for research purposes in the United States, including medical investigation. Previous research established that cannabinoid profiles in the NIDA varieties lacked diversity and potency relative to the Cannabis produced commercially. Additionally, microsatellite marker analyses have established that the NIDA varieties are genetically divergent form varieties produced in the private legal market. Here, we analyzed the genome of multiple Cannabis varieties from diverse lineages including two produced by NIDA, and we provide further support that NIDAs varieties differ from widely available medical, recreational, or industrial Cannabis. Furthermore, our results suggest that NIDAs varieties lack diversity in the single copy portion of the genome, the maternally inherited genomes, the cannabinoid genes, and in the repetitive content of the genome. Therefore, results based on NIDAs varieties are not generalizable regarding the effects of Cannabis after consumption. For medical research to be relevant, material that is more widely used would have to be studied. Clearly, having research to date dominated by a single, non-representative source of Cannabis has hindered scientific investigation.

genomics↗

bioRxiv2020

Variation in mtDNA haplotypes suggests a complex history of reproductive strategy in Cannabis sativa

Cannabis is one example in angiosperms that appears to have a recent origin of dioecy and X/Y sex chromosomes. Several evolutionary explanations for this transition have been proposed, with the most parsimonious beginning with a mitochondrial mutation leading to cytoplasmic male sterility (CMS). Our study utilized 73 Cannabis sativa whole genome shotgun libraries to reveal eight different mtDNA haplotypes. The most common haplotype contained 60 of the 73 individuals studied and was composed of only dioecious individuals. However, other haplotypes contained a mix of dioecious and monoecious individuals, so haplotype alone does not predict dioecy. From these haplotype groupings we further examined the fully annotated mitochondrial genomes of four hemp individuals and looked for genetic variation affecting reproductive strategy (e.g., monoecious vs. dioecious strategies). Specifically, we searched for markers associated with CMS and for gene rearrangements within these mitochondrial genomes. Our results revealed highly syntenic mitochondrial genomes that contained approximately 60 identifiable sequences for protein coding genes, tRNAs and rRNAs and no obvious rearrangements or chimeric genes. We find no clear evidence that the different reproductive patterns are due to easily identifiable CMS mutations. Our results refute the simplest hypothesis that there was a single recent origin of dioecy in a monoecious ancestor. Instead, the story of the evolution of dioecy is likely much more complex. Further exploration of the nuclear and mitochondrial genomes and their interaction is required to fully understand Cannabis mating strategies and the possible existence of CMS in this species.

genomics↗

bioRxiv2020

Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes

The accelerating legalization of Cannabis has opened the industry to using contemporary analytical techniques. The gene regulation and pharmacokinetics of dozens of cannabinoids remain poorly understood. Because retailers in many medical and recreational jurisdictions are required to report chemical concentrations of cannabinoids, commercial laboratories have growing chemotype datasets of diverse Cannabis cultivars. Using a data set of 17,600 cultivars tested by Steep Hill Inc., we apply machine learning techniques to interpolate missing chemotype observations and cluster cultivars together based on similarity. Our results show that cultivars cluster based on their chemotype, and that some imputation methods work better than others at grouping these cultivars based on chemotypic identity. However, due to the missing data for some of the cannabinoids their behavior could not be accurately predicted. These findings have implications for characterizing complex interactions in cannabinoid biosynthesis and improving phenotypical classification of Cannabis cultivars.

plant biology↗

bioRxiv2019

Gene copy number is associated with phytochemistry in Cannabis sativa

Gene copy number variation is known to be important in nearly every species where it has been examined. Alterations in gene copy number may provide a fast way of acquiring diversity, allowing rapid adaptation under strong selective pressures, and may also be a key component of standing genetic variation within species. Cannabis sativa plants produce a distinguishing set of secondary metabolites, the cannabinoids, many having medicinal utility. Two major cannabinoids -- THCA and CBDA -- are products of a three-step biochemical pathway. Using genomic data for 69 Cannabis cultivars from diverse lineages within the species, we found that genes encoding the synthases in this pathway vary in copy number, and that the cannabinoid paralogs may be differentially expressed. We also found that copy number partially explains variation in cannabinoid content levels among Cannabis plants.

genomics↗

bioRxiv2016

Compromised External Validity: Federally Produced Cannabis Does Not Reflect Legal Markets

As the most widely used illicit drug, the basis of the fastest growing major industry in the US, and as a source of numerous under-studied psychoactive compounds, understanding the psychological and physiological effects of Cannabis is essential. The National Institute on Drug Abuse (NIDA) is designated as the sole legal producer of Cannabis for use in US research studies. We sought to compare the chemical profiles of Cannabis varieties that are available to consumers in states that have state-legalized use versus what is available to researchers interested in studying the plant and its effects. Our results demonstrate that the federally produced Cannabis has significantly less variety and lower concentrations of cannabinoids. Current research, which has focused on material that is far less diverse and less potent than that used by the public, limits our understanding of the plants chemical, biological, psychological, medical, and pharmacological properties. Investigation is urgently needed on the diverse forms of Cannabis used by the public in state-legal markets.

plant biology↗