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Baranda P, Islam S, Modi A, Mistry H, Al Obaid S, Ansari MJ, Yadav VK, Patel A, Joshi M, Sahoo DK, Bariya H. Whole-genome sequencing of marine water-derived Curvularia verruculosa KHW-7: a pioneering study. Front Microbiol 2024; 15:1363879. [PMID: 38846574 PMCID: PMC11155457 DOI: 10.3389/fmicb.2024.1363879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
Marine microorganisms are renowned for being a rich source of new secondary metabolites that are significant to humans. The fungi strain KHW-7 was isolated from the seawater collected from the Gulf of Khambhat, India, and identified as Curvularia verruculosa KHW-7. On a next-generation sequencing platform, C. verruculosa KHW-7's whole-genome sequencing (WGS) and gene annotation were carried out using several bioinformatic methods. The 31.59 MB genome size, 52.3% GC, and 158 bp mean read length were discovered using WGS. This genome also contained 9,745 protein-coding genes, including 852 secreted proteins and 2048 transmembrane proteins. The antiSMASH algorithm used to analyze genomes found 25 secondary metabolite biosynthetic gene clusters (BGCs) that are abundant in terpene, non-ribosomal peptide synthetase (NRPS), and polyketides type 1 (T1PKS). To our knowledge, this is the first whole-genome sequence report of C. verruculosa. The WGS analysis of C. verruculosa KHW-7 indicated that this marine-derived fungus could be an efficient generator of bioactive secondary metabolites and an important industrial enzyme, both of which demand further investigation and development.
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Affiliation(s)
- Payal Baranda
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Shaikhul Islam
- Plant Pathology Division, Bangladesh Wheat and Maize Research Institute, Nashipur, Bangladesh
| | - Ashish Modi
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Harsh Mistry
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Sami Al Obaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Uttar Pradesh, India
| | - Virendra Kumar Yadav
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Ashish Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, India
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Himanshu Bariya
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
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Liu J, Ni Y, Liu C. Polymeric structure of the Cannabis sativa L. mitochondrial genome identified with an assembly graph model. Gene 2023; 853:147081. [PMID: 36470482 DOI: 10.1016/j.gene.2022.147081] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/14/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Cannabis sativa L. belongs to the family Cannabaceae in Rosales. It has been widely used as medicines, building materials, and textiles. Elucidating its genome is critical for molecular breeding and synthetic biology study. Many studies have shown that the mitochondrial genomes (mitogenomes) and even chloroplast genomes (plastomes) had complex polymeric structures. Using the Nanopore sequencing platform, we sequenced, assembled, and analyzed its mitogenome and plastome. The resulting unitig graph suggested that the mitogenome had a complex polymeric structure. However, a gap-free, circular sequence was further assembled from the unitig graph. In contrast, a circular sequence representing the plastome was obtained. The mitogenome major conformation was 415,837 bp long, and the plastome was 153,927 bp long. To test if the repeat sequences promote recombination, which corresponds to the branch points in the structure, we tested the sequences around repeats by long-read mapping. Among 208 pairs of predicted repeats, the mapping results supported the presence of cross-over around 25 pairs of repeats. Subsequent PCR amplification confirmed the presence of cross-over around 15 of the 25 repeats. By comparing the mitogenome and plastome sequences, we identified 19 mitochondria plastid DNAs, including seven complete genes (trnW-CCA, trnP-UGG, psbJ, trnN-GUU, trnD-GUC, trnH-GUG, trnM-CAU) and nine gene fragments. Furthermore, the selective pressure analysis results showed that five genes (atp1, ccmB, ccmC, cox1, nad7) had 19 positively selected sites. Lastly, we predicted 28 RNA editing sites. A total of 8 RNA editing sites located in the coding regions were successfully validated by PCR amplification and Sanger sequencing, of which four were synonymous, and four were nonsynonymous. In particular, the RNA editing events appeared to be tissue-specific in C. sativa mitogenome. In summary, we have confirmed the major confirmation of C. sativa mitogenome and characterized its structural features in detail. These results provide critical information for future variety breeding and resource development for C. sativa.
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Affiliation(s)
- Jingting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China.
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Padgitt-Cobb LK, Pitra NJ, Matthews PD, Henning JA, Hendrix DA. An improved assembly of the "Cascade" hop ( Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family. HORTICULTURE RESEARCH 2023; 10:uhac281. [PMID: 36818366 PMCID: PMC9930403 DOI: 10.1093/hr/uhac281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/22/2022] [Indexed: 06/16/2023]
Abstract
We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Nicholi J Pitra
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
| | - Paul D Matthews
- Department of Research and Development, Hopsteiner, S.S. Steiner, Inc., 1 West Washington Avenue, Yakima, Washington 98903, USA
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Balant M, Rodríguez González R, Garcia S, Garnatje T, Pellicer J, Vallès J, Vitales D, Hidalgo O. Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L. PLANTS (BASEL, SWITZERLAND) 2022; 11:2736. [PMID: 36297761 PMCID: PMC9607409 DOI: 10.3390/plants11202736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Cannabis sativa has been used for millennia in traditional medicine for ritual purposes and for the production of food and fibres, thus, providing important and versatile services to humans. The species, which currently has a worldwide distribution, strikes out for displaying a huge morphological and chemical diversity. Differences in Cannabis genome size have also been found, suggesting it could be a useful character to differentiate between accessions. We used flow cytometry to investigate the extent of genome size diversity across 483 individuals belonging to 84 accessions, with a wide range of wild/feral, landrace, and cultivated accessions. We also carried out sex determination using the MADC2 marker and investigated the potential of flow cytometry as a method for early sex determination. All individuals were diploid, with genome sizes ranging from 1.810 up to 2.152 pg/2C (1.189-fold variation), apart from a triploid, with 2.884 pg/2C. Our results suggest that the geographical expansion of Cannabis and its domestication had little impact on its overall genome size. We found significant differences between the genome size of male and female individuals. Unfortunately, differences were, however, too small to be discriminated using flow cytometry through the direct processing of combined male and female individuals.
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Affiliation(s)
- Manica Balant
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Roi Rodríguez González
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
| | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
| | - Joan Vallès
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació–Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació–Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., 08038 Barcelona, Catalonia, Spain
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
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5
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Sirangelo TM, Ludlow RA, Spadafora ND. Multi-Omics Approaches to Study Molecular Mechanisms in Cannabis sativa. PLANTS (BASEL, SWITZERLAND) 2022; 11:2182. [PMID: 36015485 PMCID: PMC9416457 DOI: 10.3390/plants11162182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Cannabis (Cannabis sativa L.), also known as hemp, is one of the oldest cultivated crops, grown for both its use in textile and cordage production, and its unique chemical properties. However, due to the legislation regulating cannabis cultivation, it is not a well characterized crop, especially regarding molecular and genetic pathways. Only recently have regulations begun to ease enough to allow more widespread cannabis research, which, coupled with the availability of cannabis genome sequences, is fuelling the interest of the scientific community. In this review, we provide a summary of cannabis molecular resources focusing on the most recent and relevant genomics, transcriptomics and metabolomics approaches and investigations. Multi-omics methods are discussed, with this combined approach being a powerful tool to identify correlations between biological processes and metabolic pathways across diverse omics layers, and to better elucidate the relationships between cannabis sub-species. The correlations between genotypes and phenotypes, as well as novel metabolites with therapeutic potential are also explored in the context of cannabis breeding programs. However, further studies are needed to fully elucidate the complex metabolomic matrix of this crop. For this reason, some key points for future research activities are discussed, relying on multi-omics approaches.
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Affiliation(s)
- Tiziana M. Sirangelo
- CREA—Council for Agricultural Research and Agricultural Economy Analysis, Genomics and Bioinformatics Department, 26836 Montanaso Lombardo, Italy
| | - Richard A. Ludlow
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
| | - Natasha D. Spadafora
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
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6
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The phytochemical diversity of commercial Cannabis in the United States. PLoS One 2022; 17:e0267498. [PMID: 35588111 PMCID: PMC9119530 DOI: 10.1371/journal.pone.0267498] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/08/2022] [Indexed: 02/07/2023] Open
Abstract
The legal status of Cannabis is changing, fueling an increasing diversity of Cannabis-derived products. Because Cannabis contains dozens of chemical compounds with potential psychoactive or medicinal effects, understanding this phytochemical diversity is crucial. The legal Cannabis industry heavily markets products to consumers based on widely used labeling systems purported to predict the effects of different "strains." We analyzed the cannabinoid and terpene content of commercial Cannabis samples across six US states, finding distinct chemical phenotypes (chemotypes) which are reliably present. By comparing the observed phytochemical diversity to the commercial labels commonly attached to Cannabis-derived product samples, we show that commercial labels do not consistently align with the observed chemical diversity. However, certain labels do show a biased association with specific chemotypes. These results have implications for the classification of commercial Cannabis, design of animal and human research, and regulation of consumer marketing-areas which today are often divorced from the chemical reality of the Cannabis-derived material they wish to represent.
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Schwabe AL, Hansen CJ, Hyslop RM, McGlaughlin ME. Comparative Genetic Structure of Cannabis sativa Including Federally Produced, Wild Collected, and Cultivated Samples. FRONTIERS IN PLANT SCIENCE 2021; 12:675770. [PMID: 34707624 PMCID: PMC8544287 DOI: 10.3389/fpls.2021.675770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
Currently in the United States, the sole licensed facility to cultivate Cannabis sativa L. for research purposes is the University of Mississippi, which is funded by the National Institute on Drug Abuse (NIDA). Studies researching Cannabis flower consumption rely on NIDA-supplied "research grade marijuana." Previous research found that cannabinoid levels of NIDA-supplied Cannabis do not align with commercially available Cannabis. We sought to investigate the genetic identity of Cannabis supplied by NIDA relative to common categories within the species. This is the first genetic study to include "research grade marijuana" from NIDA. Samples (49) were assigned as Wild Hemp (feral; 6) and Cultivated Hemp (3), NIDA (2), CBD drug type (3), and high THC drug type subdivided into Sativa (11), Hybrid (14), and Indica (10). Ten microsatellites targeting neutral non-coding regions were used. Clustering and genetic distance analyses support a division between hemp and drug-type Cannabis. All hemp samples clustered genetically, but no clear distinction of Sativa, Hybrid, and Indica subcategories within retail marijuana samples was found. Interestingly, the two analyzed "research grade marijuana" samples obtained from NIDA were genetically distinct from most drug-type Cannabis available from retail dispensaries. Although the sample size was small, "research grade marijuana" provided for research is genetically distinct from most retail drug-type Cannabis that patients and patrons are consuming.
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Affiliation(s)
- Anna L. Schwabe
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, United States
| | - Connor J. Hansen
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, United States
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO, United States
| | - Richard M. Hyslop
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO, United States
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Vergara D, Huscher EL, Keepers KG, Pisupati R, Schwabe AL, McGlaughlin ME, Kane NC. Genomic Evidence That Governmentally Produced Cannabis sativa Poorly Represents Genetic Variation Available in State Markets. FRONTIERS IN PLANT SCIENCE 2021; 12:668315. [PMID: 34594346 PMCID: PMC8476804 DOI: 10.3389/fpls.2021.668315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
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 genomes of multiple Cannabis varieties from diverse lineages including two produced by NIDA, and we provide further support that NIDA's varieties differ from widely available medical, recreational, or industrial Cannabis. Furthermore, our results suggest that NIDA's 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 NIDA's 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.
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Affiliation(s)
- Daniela Vergara
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Ezra L. Huscher
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Kyle G. Keepers
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Rahul Pisupati
- Austrian Academy of Sciences, Vienna Biocenter, Gregor Mendel Institute, Vienna, Austria
| | - Anna L. Schwabe
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, United States
| | | | - Nolan C. Kane
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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van Velzen R, Schranz ME. Origin and Evolution of the Cannabinoid Oxidocyclase Gene Family. Genome Biol Evol 2021; 13:evab130. [PMID: 34100927 PMCID: PMC8521752 DOI: 10.1093/gbe/evab130] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 12/21/2022] Open
Abstract
Cannabis is an ancient crop representing a rapidly increasing legal market, especially for medicinal purposes. Medicinal and psychoactive effects of Cannabis rely on specific terpenophenolic ligands named cannabinoids. Recent whole-genome sequencing efforts have uncovered variation in multiple genes encoding the final steps in cannabinoid biosynthesis. However, the origin, evolution, and phylogenetic relationships of these cannabinoid oxidocyclase genes remain unclear. To elucidate these aspects, we performed comparative genomic analyses of Cannabis, related genera within the Cannabaceae family, and selected outgroup species. Results show that cannabinoid oxidocyclase genes originated in the Cannabis lineage from within a larger gene expansion in the Cannabaceae family. Localization and divergence of oxidocyclase genes in the Cannabis genome revealed two main syntenic blocks, each comprising tandemly repeated cannabinoid oxidocyclase genes. By comparing these blocks with those in genomes from closely related species, we propose an evolutionary model for the origin, neofunctionalization, duplication, and diversification of cannabinoid oxidocycloase genes. Based on phylogenetic analyses, we propose a comprehensive classification of three main clades and seven subclades that are intended to aid unequivocal referencing and identification of cannabinoid oxidocyclase genes. Our data suggest that cannabinoid phenotype is primarily determined by the presence/absence of single-copy genes. Although wild populations of Cannabis are still unknown, increased sampling of landraces and wild/feral populations across its native geographic range is likely to uncover additional cannabinoid oxidocyclase sequence variants.
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Affiliation(s)
- Robin van Velzen
- Plant Sciences, Biosystematics Group, Wageningen University, Wageningen, The Netherlands
- Bedrocan International, Veendam, The Netherlands
| | - M Eric Schranz
- Plant Sciences, Biosystematics Group, Wageningen University, Wageningen, The Netherlands
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Hurgobin B, Tamiru‐Oli M, Welling MT, Doblin MS, Bacic A, Whelan J, Lewsey MG. Recent advances in Cannabis sativa genomics research. THE NEW PHYTOLOGIST 2021; 230:73-89. [PMID: 33283274 PMCID: PMC7986631 DOI: 10.1111/nph.17140] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/27/2020] [Indexed: 05/06/2023]
Abstract
Cannabis (Cannabis sativa L.) is one of the oldest cultivated plants purported to have unique medicinal properties. However, scientific research of cannabis has been restricted by the Single Convention on Narcotic Drugs of 1961, an international treaty that prohibits the production and supply of narcotic drugs except under license. Legislation governing cannabis cultivation for research, medicinal and even recreational purposes has been relaxed recently in certain jurisdictions. As a result, there is now potential to accelerate cultivar development of this multi-use and potentially medically useful plant species by application of modern genomics technologies. Whilst genomics has been pivotal to our understanding of the basic biology and molecular mechanisms controlling key traits in several crop species, much work is needed for cannabis. In this review we provide a comprehensive summary of key cannabis genomics resources and their applications. We also discuss prospective applications of existing and emerging genomics technologies for accelerating the genetic improvement of cannabis.
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Affiliation(s)
- Bhavna Hurgobin
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Muluneh Tamiru‐Oli
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Matthew T. Welling
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Monika S. Doblin
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - James Whelan
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Centre of Excellence for Plant Energy BiologyLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
| | - Mathew G. Lewsey
- La Trobe Institute for Agriculture and FoodDepartment of Animal, Plant and Soil SciencesSchool of Life SciencesLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
- Australian Research Council Research Hub for Medicinal AgricultureLa Trobe UniversityAgriBio BuildingBundooraVIC3086Australia
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11
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Padgitt-Cobb LK, Kingan SB, Wells J, Elser J, Kronmiller B, Moore D, Concepcion G, Peluso P, Rank D, Jaiswal P, Henning J, Hendrix DA. A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. THE PLANT GENOME 2021; 14:e20072. [PMID: 33605092 DOI: 10.1002/tpg2.20072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/03/2020] [Indexed: 05/25/2023]
Abstract
Hop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing and contain compounds of therapeutic interest including xanthohumol. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large (2.8 Gb), repetitive, and heterozygous genome of hop. We present a draft haplotype-phased assembly of the Cascade cultivar genome. Our draft assembly and annotation of the Cascade genome is the most extensive representation of the hop genome to date. PacBio long-read sequences from hop were assembled with FALCON and partially phased with FALCON-Unzip. Comparative analysis of haplotype sequences provides insight into selective pressures that have driven evolution in hop. We discovered genes with greater sequence divergence enriched for stress-response, growth, and flowering functions in the draft phased assembly. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is over 70% repetitive. We identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze the draft phased assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.
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Affiliation(s)
- Lillian K Padgitt-Cobb
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Sarah B Kingan
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Jackson Wells
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | | | | | - Paul Peluso
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - David Rank
- Pacific Biosciences of California, Menlo Park, CA, 94025, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | | | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
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12
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Aardema ML, DeSalle R. Can public online databases serve as a source of phenotypic information for Cannabis genetic association studies? PLoS One 2021; 16:e0247607. [PMID: 33621243 PMCID: PMC7901747 DOI: 10.1371/journal.pone.0247607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
The use of Cannabis is gaining greater social acceptance for its beneficial medicinal and recreational uses. With this acceptance has come new opportunities for crop management, selective breeding, and the potential for targeted genetic manipulation. However, as an agricultural product Cannabis lags far behind other domesticated plants in knowledge of the genes and genetic variation that influence plant traits of interest such as growth form and chemical composition. Despite this lack of information, there are substantial publicly available resources that document phenotypic traits believed to be associated with particular Cannabis varieties. Such databases could be a valuable resource for developing a greater understanding of genes underlying phenotypic variation if combined with appropriate genetic information. To test this potential, we collated phenotypic data from information available through multiple online databases. We then produced a Cannabis SNP database from 845 strains to examine genome wide associations in conjunction with our assembled phenotypic traits. Our goal was not to locate Cannabis-specific genetic variation that correlates with phenotypic variation as such, but rather to examine the potential utility of these databases more broadly for future, explicit genome wide association studies (GWAS), either in stand-alone analyses or to complement other types of data. For this reason, we examined a very broad array of phenotypic traits. In total, we performed 201 distinct association tests using web-derived phenotype data appended to 290 uniquely named Cannabis strains. Our results indicated that chemical phenotypes, such as tetrahydrocannabinol (THC) and cannabidiol (CBD) content, may have sufficiently high-quality information available through web-based sources to allow for genetic association inferences. In many cases, variation in chemical traits correlated with genetic variation in or near biologically reasonable candidate genes, including several not previously implicated in Cannabis chemical variation. As with chemical phenotypes, we found that publicly available data on growth traits such as height, area of growth, and floral yield may be precise enough for use in future association studies. In contrast, phenotypic information for subjective traits such as taste, physiological affect, neurological affect, and medicinal use appeared less reliable. These results are consistent with the high degree of subjectivity for such trait data found on internet databases, and suggest that future work on these important but less easily quantifiable characteristics of Cannabis may require dedicated, controlled phenotyping.
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Affiliation(s)
- Matthew L. Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- * E-mail:
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
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13
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Batista TM, Hilario HO, de Brito GAM, Moreira RG, Furtado C, de Menezes GCA, Rosa CA, Rosa LH, Franco GR. Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny. Genomics 2020; 112:2915-2921. [DOI: 10.1016/j.ygeno.2020.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022]
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14
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Kovalchuk I, Pellino M, Rigault P, van Velzen R, Ebersbach J, Ashnest JR, Mau M, Schranz ME, Alcorn J, Laprairie RB, McKay JK, Burbridge C, Schneider D, Vergara D, Kane NC, Sharbel TF. The Genomics of Cannabis and Its Close Relatives. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:713-739. [PMID: 32155342 DOI: 10.1146/annurev-arplant-081519-040203] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with ∼10% missing, 10-25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.
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Affiliation(s)
- I Kovalchuk
- Department of Biology, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - M Pellino
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - P Rigault
- Gydle Inc., Québec, Québec G1S 1E7, Canada
- Center for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - R van Velzen
- Biosystematics Group, Wageningen University, 6703 BD Wageningen, The Netherlands
- Bedrocan International, 9640 CA Veendam, The Netherlands
| | - J Ebersbach
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - J R Ashnest
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - M Mau
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
| | - M E Schranz
- Biosystematics Group, Wageningen University, 6703 BD Wageningen, The Netherlands
| | - J Alcorn
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - R B Laprairie
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
- Department of Pharmacology, College of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - J K McKay
- College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - C Burbridge
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - D Schneider
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - D Vergara
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - N C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - T F Sharbel
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada;
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15
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Li Q, Ramasamy S, Singh P, Hagel JM, Dunemann SM, Chen X, Chen R, Yu L, Tucker JE, Facchini PJ, Yeaman S. Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy. Nat Commun 2020; 11:1190. [PMID: 32132540 PMCID: PMC7055283 DOI: 10.1038/s41467-020-15040-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/10/2020] [Indexed: 02/08/2023] Open
Abstract
Genes in plant secondary metabolic pathways enable biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression of BIA genes increases within clusters and identify candidates with unknown function based on clustering and covariation in expression and alkaloid production. Copy number variation in critical BIA genes correlates with stark differences in alkaloid production, linking noscapine production with an 11-gene deletion, and increased thebaine/decreased morphine production with deletion of a T6ODM cluster. Our results show that the opium poppy genome is still dynamically evolving in ways that contribute to medically and industrially important phenotypes.
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Affiliation(s)
- Qiushi Li
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sukanya Ramasamy
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Sonja M Dunemann
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Xue Chen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Rongji Chen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Lisa Yu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Joseph E Tucker
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
- Willow Biosciences Inc., 3655 36 Street N.W., Calgary, Alberta, T2L 1Y8, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
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16
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Van-Lume B, Mata-Sucre Y, Báez M, Ribeiro T, Huettel B, Gagnon E, Leitch IJ, Pedrosa-Harand A, Lewis GP, Souza G. Evolutionary convergence or homology? Comparative cytogenomics of Caesalpinia group species (Leguminosae) reveals diversification in the pericentromeric heterochromatic composition. PLANTA 2019; 250:2173-2186. [PMID: 31696317 DOI: 10.1007/s00425-019-03287-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/25/2019] [Indexed: 05/02/2023]
Abstract
We demonstrated by cytogenomic analysis that the proximal heterochromatin of the Northeast Brazilian species of Caesalpinia group is enriched with phylogenetically conserved Ty3/Gypsy-Tekay RT, but diverge in the presence of Ty3/Gypsy-Athila RT and satDNA. The Caesalpinia Group includes 225 species and 27 monophyletic genera of which four occur in Northeastern Brazil: Erythrostemon (1 sp.), Cenostigma (7 spp.), Libidibia (1 sp.), and Paubrasilia (1 sp.). The last three genera are placed in different clades in the Caesalpinia Group phylogeny, and yet they are characterized by having a numerically stable karyotype 2n = 24 (16 M+8A) and GC-rich heterochromatic bands (chromomycin A3 positive/CMA+ bands) in the proximal chromosome regions. To characterize the composition of their heterochromatin and test for the homology of these chromosomal regions, genomic DNA was extracted from Cenostigma microphyllum, Libidibia ferrea, and Paubrasilia echinata, and sequenced at low coverage using the Illumina platform. The genomic repetitive fractions were characterized using a Galaxy/RepeatExplorer-Elixir platform. The most abundant elements of each genome were chromosomally located by fluorescent in situ hybridization (FISH) and compared to the CMA+ heterochromatin distribution. The repetitive fraction of the genomes of C. microphyllum, L. ferrea, and P. echinata were estimated to be 41.70%, 38.44%, and 72.51%, respectively. Ty3/Gypsy retrotransposons (RT), specifically the Tekay lineage, were the most abundant repeats in each of the three genomes. FISH mapping revealed species-specific patterns for the Tekay elements in the proximal regions of the chromosomes, co-localized with CMA+ bands. Other species-specific patterns were observed, e.g., for the Ty3/Gypsy RT Athila elements which were found in all the proximal heterochromatin of L. ferrea or restricted to the acrocentric chromosomes of C. microphyllum. This Athila labeling co-localized with satellite DNAs (satDNAs). Although the Caesalpinia Group diverged around 55 Mya, our results suggest an ancestral colonization of Tekay RT in the proximal heterochromatin. Thus, the present-day composition of the pericentromeric heterochromatin in these Northeast Brazilian species is a combination of the maintenance of an ancestral Tekay distribution with a species-specific accumulation of other repeats.
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Affiliation(s)
- Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Yennifer Mata-Sucre
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Mariana Báez
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Tiago Ribeiro
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
- Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Av. Fernando Correa da Costa, 2.367, Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | | | - Edeline Gagnon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil
| | - Gwilym P Lewis
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitária, Recife, PE, 50670-420, Brazil.
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17
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Vergara D, Huscher EL, Keepers KG, Givens RM, Cizek CG, Torres A, Gaudino R, Kane NC. Gene copy number is associated with phytochemistry in Cannabis sativa. AOB PLANTS 2019; 11:plz074. [PMID: 32010439 PMCID: PMC6986684 DOI: 10.1093/aobpla/plz074] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/19/2019] [Indexed: 05/22/2023]
Abstract
Gene copy number (CN) variation is known to be important in nearly every species where it has been examined. Alterations in gene CN 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 of which have medicinal utility. Two major cannabinoids-THCA (delta-9-tetrahydrocannabinolic acid) and CBDA (cannabidiolic acid)-are products of a three-step biochemical pathway. Using whole-genome shotgun sequence data for 69 Cannabis cultivars from diverse lineages within the species, we found that genes encoding the synthases in this pathway vary in CN. Transcriptome sequence data show that the cannabinoid paralogs are differentially expressed among lineages within the species. We also found that CN partially explains variation in cannabinoid content levels among Cannabis plants. Our results demonstrate that biosynthetic genes found at multiple points in the pathway could be useful for breeding purposes, and suggest that natural and artificial selection have shaped CN variation. Truncations in specific paralogs are associated with lack of production of particular cannabinoids, showing how phytochemical diversity can evolve through a complex combination of processes.
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Affiliation(s)
- Daniela Vergara
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Ezra L Huscher
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Kyle G Keepers
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | | | | | | | | | - Nolan C Kane
- Kane Laboratory, Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
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18
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Tassorelli C, Greco R, Silberstein SD. The endocannabinoid system in migraine: from bench to pharmacy and back. Curr Opin Neurol 2019; 32:405-412. [DOI: 10.1097/wco.0000000000000688] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Res 2019. [PMID: 30409771 DOI: 10.1101/gr.242594.118.freely] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Cannabis sativa is widely cultivated for medicinal, food, industrial, and recreational use, but much remains unknown regarding its genetics, including the molecular determinants of cannabinoid content. Here, we describe a combined physical and genetic map derived from a cross between the drug-type strain Purple Kush and the hemp variety "Finola." The map reveals that cannabinoid biosynthesis genes are generally unlinked but that aromatic prenyltransferase (AP), which produces the substrate for THCA and CBDA synthases (THCAS and CBDAS), is tightly linked to a known marker for total cannabinoid content. We further identify the gene encoding CBCA synthase (CBCAS) and characterize its catalytic activity, providing insight into how cannabinoid diversity arises in cannabis. THCAS and CBDAS (which determine the drug vs. hemp chemotype) are contained within large (>250 kb) retrotransposon-rich regions that are highly nonhomologous between drug- and hemp-type alleles and are furthermore embedded within ∼40 Mb of minimally recombining repetitive DNA. The chromosome structures are similar to those in grains such as wheat, with recombination focused in gene-rich, repeat-depleted regions near chromosome ends. The physical and genetic map should facilitate further dissection of genetic and molecular mechanisms in this commercially and medically important plant.
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Affiliation(s)
- Kaitlin U Laverty
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jake M Stout
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mitchell J Sullivan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Navdeep Gill
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Larry Holbrook
- CanniMed Therapeutics Incorporated, Saskatoon, Saskatchewan S7K 3J8, Canada
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Jonathan E Page
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Anandia Labs, Vancouver, British Columbia V6T 1Z4, Canada
| | - Harm van Bakel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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20
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Laverty KU, Stout JM, Sullivan MJ, Shah H, Gill N, Holbrook L, Deikus G, Sebra R, Hughes TR, Page JE, van Bakel H. A physical and genetic map of Cannabis sativa identifies extensive rearrangements at the THC/CBD acid synthase loci. Genome Res 2018; 29:146-156. [PMID: 30409771 PMCID: PMC6314170 DOI: 10.1101/gr.242594.118] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/07/2018] [Indexed: 01/19/2023]
Abstract
Cannabis sativa is widely cultivated for medicinal, food, industrial, and recreational use, but much remains unknown regarding its genetics, including the molecular determinants of cannabinoid content. Here, we describe a combined physical and genetic map derived from a cross between the drug-type strain Purple Kush and the hemp variety “Finola.” The map reveals that cannabinoid biosynthesis genes are generally unlinked but that aromatic prenyltransferase (AP), which produces the substrate for THCA and CBDA synthases (THCAS and CBDAS), is tightly linked to a known marker for total cannabinoid content. We further identify the gene encoding CBCA synthase (CBCAS) and characterize its catalytic activity, providing insight into how cannabinoid diversity arises in cannabis. THCAS and CBDAS (which determine the drug vs. hemp chemotype) are contained within large (>250 kb) retrotransposon-rich regions that are highly nonhomologous between drug- and hemp-type alleles and are furthermore embedded within ∼40 Mb of minimally recombining repetitive DNA. The chromosome structures are similar to those in grains such as wheat, with recombination focused in gene-rich, repeat-depleted regions near chromosome ends. The physical and genetic map should facilitate further dissection of genetic and molecular mechanisms in this commercially and medically important plant.
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Affiliation(s)
- Kaitlin U Laverty
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jake M Stout
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mitchell J Sullivan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Navdeep Gill
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Larry Holbrook
- CanniMed Therapeutics Incorporated, Saskatoon, Saskatchewan S7K 3J8, Canada
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Jonathan E Page
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Anandia Labs, Vancouver, British Columbia V6T 1Z4, Canada
| | - Harm van Bakel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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