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

https://doi.org/10.1101/458083
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences
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GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality
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Endocannabinoids and Lipid Mediators in Brain Functions
inferredcites →https://doi.org/10.1007/bf01386390openalex-snapshot
A note on two problems in connexion with graphs
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Shape constrained additive models
inferredcites →https://doi.org/10.1007/s12231-016-9351-1openalex-snapshot
Ancient Cannabis Burial Shroud in a Central Eurasian Cemetery
inferredcites →https://doi.org/10.1016/0031-9422(80)85004-7openalex-snapshot
Deviations from michaelis-menten behaviour of plant glutamate dehydrogenase with ammonium as variable substrate
inferredcites →https://doi.org/10.1016/j.jbiotec.2016.05.038openalex-snapshot
An influence of the copy number of biosynthetic gene clusters on the production level of antibiotics in a heterologous host
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Sequence heterogeneity of cannabidiolic- and tetrahydrocannabinolic acid-synthase in Cannabis sativa L. and its relationship with chemical phenotype
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Beyond Cannabis: Plants and the Endocannabinoid System
inferredcites →https://doi.org/10.1038/166247a0openalex-snapshot
Genetical Structure of Populations
inferredcites →https://doi.org/10.1038/nbt.3122openalex-snapshot
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
inferredcites →https://doi.org/10.1038/ng.1028openalex-snapshot
De novo assembly and genotyping of variants using colored de Bruijn graphs
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity
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Regulatory activities of transposable elements: from conflicts to benefits
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High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
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The diverse CB 1 and CB 2 receptor pharmacology of three plant cannabinoids: Δ 9 ‐tetrahydrocannabinol, cannabidiol and Δ 9 ‐tetrahydrocannabivarin
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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot
CD-HIT: accelerated for clustering the next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btv383openalex-snapshot
Bandage: interactive visualization of de novo genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btw152openalex-snapshot
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/database/bax009openalex-snapshot
HopBase: a unified resource for Humulus genomics
inferredcites →https://doi.org/10.1093/nar/gkl842openalex-snapshot
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
inferredcites →https://doi.org/10.1093/nar/gkm286openalex-snapshot
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
inferredcites →https://doi.org/10.1093/nar/gkt418openalex-snapshot
WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes
inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot
Fast model-based estimation of ancestry in unrelated individuals
inferredcites →https://doi.org/10.1101/gr.214270.116openalex-snapshot
Fast and accurate de novo genome assembly from long uncorrected reads
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1111/j.1469-1809.1943.tb02321.xopenalex-snapshot
THE ESTIMATION OF MAP DISTANCES FROM RECOMBINATION VALUES
inferredcites →https://doi.org/10.1111/j.1558-5646.1984.tb05657.xopenalex-snapshot
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
inferredcites →https://doi.org/10.1111/nph.13562openalex-snapshot
Gene duplication and divergence affecting drug content in Cannabis sativa
inferredcites →https://doi.org/10.1126/science.1086949openalex-snapshot
Major Ecological Transitions in Wild Sunflowers Facilitated by Hybridization
inferredcites →https://doi.org/10.1126/science.1115740openalex-snapshot
Identification and Functional Characterization of Brainstem Cannabinoid CB2Receptors
inferredcites →https://doi.org/10.1126/science.1190371openalex-snapshot
Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
inferredcites →https://doi.org/10.1152/physrev.00004.2003openalex-snapshot
Role of Endogenous Cannabinoids in Synaptic Signaling
inferredcites →https://doi.org/10.1186/gb-2008-9-1-r7openalex-snapshot
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
inferredcites →https://doi.org/10.1186/gb-2011-12-10-r102openalex-snapshot
The draft genome and transcriptome of Cannabis sativa
inferredcites →https://doi.org/10.1186/gb-2013-14-1-r10openalex-snapshot
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
inferredcites →https://doi.org/10.1186/s12859-015-0654-5openalex-snapshot
Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
inferredcites →https://doi.org/10.1186/s12864-017-3879-zopenalex-snapshot
Scaffolding of long read assemblies using long range contact information
inferredcites →https://doi.org/10.1201/9781315367583openalex-snapshot
Cannabis
inferredcites →https://doi.org/10.12688/f1000research.12232.1openalex-snapshot
BlobTools: Interrogation of genome assemblies
inferredcites →https://doi.org/10.1270/jsbbs.56.371openalex-snapshot
AntMap: Constructing Genetic Linkage Maps Using an Ant Colony Optimization Algorithm
inferredcites →https://doi.org/10.1371/journal.pgen.1006529openalex-snapshot
A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy
inferredcites →https://doi.org/10.1371/journal.pone.0085118openalex-snapshot
Molecular Cytogenetic Characterization of the Dioecious Cannabis sativa with an XY Chromosome Sex Determination System
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.1515/sagmb-2012-0039openalex-snapshot
The mid p-value in exact tests for Hardy-Weinberg equilibrium
inferredcites →https://doi.org/10.1520/jfs14636jopenalex-snapshot
Potency Trends of Δ9-THC and Other Cannabinoids in Confiscated Marijuana from 1980–1997
inferredcites →https://doi.org/10.1534/genetics.115.182071openalex-snapshot
Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data
inferredcites →https://doi.org/10.2174/092986710790980005openalex-snapshot
Endocannabinoid Binding to the Cannabinoid Receptors: What Is Known and What Remains Unknown
inferredcites →https://doi.org/10.4103/sni.sni_45_18openalex-snapshot
Review of the neurological benefits of phytocannabinoids

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Cannabis Science and Therapeutics: An Overview for Clinicians
inferred← citeshttps://doi.org/10.1002/tpg2.20072openalex-snapshot
A draft phased assembly of the diploid Cascade hop ( Humulus lupulus ) genome
inferred← citeshttps://doi.org/10.1002/tpg2.70031openalex-snapshot
Discovery of major QTL and a massive haplotype associated with cannabinoid biosynthesis in drug‐type Cannabis
inferred← citeshttps://doi.org/10.1002/tpg2.70243openalex-snapshot
Genetic architecture of phenological, morphological, and phytochemical traits in Cannabis landraces
inferred← citeshttps://doi.org/10.1007/978-3-031-05144-9_10openalex-snapshot
Selective Breeding for Cannabis Variety
inferred← citeshttps://doi.org/10.1007/s00425-020-03522-yopenalex-snapshot
Comparative RNA-Seq analysis reveals genes associated with masculinization in female Cannabis sativa
inferred← citeshttps://doi.org/10.1007/s00425-023-04104-4openalex-snapshot
Identification of circular RNAs of Cannabis sativa L. potentially involved in the biosynthesis of cannabinoids
inferred← citeshttps://doi.org/10.1007/s00425-026-05043-6openalex-snapshot
Transcriptomic dissection of floral identity and trichome-derived metabolite pathways in Cannabis sativa L.
inferred← citeshttps://doi.org/10.1007/s10528-025-11166-4openalex-snapshot
Early Detection of Sex and Cannabinoid Chemotypes in Cannabis sativa: SCAR Marker Validation in Indigenous Indian Germplasm
inferred← citeshttps://doi.org/10.1007/s10722-025-02700-9openalex-snapshot
Exploring phenotypic and genetic variability in hemp (Cannabis sativa)
inferred← citeshttps://doi.org/10.1007/s11627-021-10178-0openalex-snapshot
Development of a robust transient expression screening system in protoplasts of Cannabis
inferred← citeshttps://doi.org/10.1016/j.forsciint.2020.110634openalex-snapshot
Rapid identification of drug-type and fiber-type cannabis by allele specific duplex PCR
inferred← citeshttps://doi.org/10.1016/j.indcrop.2020.113026openalex-snapshot
Recent advances in cannabis biotechnology
inferred← citeshttps://doi.org/10.1016/j.isci.2021.103391openalex-snapshot
Cannabis sativa research trends, challenges, and new-age perspectives
inferred← citeshttps://doi.org/10.1016/j.pbi.2019.12.009openalex-snapshot
Building near-complete plant genomes
inferred← citeshttps://doi.org/10.1016/j.pbi.2020.03.005openalex-snapshot
Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae
inferred← citeshttps://doi.org/10.1016/j.plantsci.2020.110571openalex-snapshot
Comprehending and improving cannabis specialized metabolism in the systems biology era
inferred← citeshttps://doi.org/10.1038/s41598-019-47812-2openalex-snapshot
Complex Patterns of Cannabinoid Alkyl Side-Chain Inheritance in Cannabis
inferred← citeshttps://doi.org/10.1038/s41598-019-53023-6openalex-snapshot
Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis
inferred← citeshttps://doi.org/10.1038/s41598-020-75271-7openalex-snapshot
An extreme-phenotype genome‐wide association study identifies candidate cannabinoid pathway genes in Cannabis
inferred← citeshttps://doi.org/10.1038/s41598-023-29148-0openalex-snapshot
Using a global diversity panel of Cannabis sativa L. to develop a near InfraRed-based chemometric application for cannabinoid quantification
inferred← citeshttps://doi.org/10.1038/s41598-024-58931-wopenalex-snapshot
Genetic insights into agronomic and morphological traits of drug-type cannabis revealed by genome-wide association studies
inferred← citeshttps://doi.org/10.1038/s41598-025-92168-5openalex-snapshot
Genome-specific association study (GSAS) for exploration of variability in hemp (Cannabis sativa)
inferred← citeshttps://doi.org/10.1071/cp22212openalex-snapshot
Agronomic, phytochemical and drought tolerance evaluation of Iranian cannabis (Cannabis sativa L.) ecotypes under different soil moisture levels: a step towards identifying pharmaceutical and industrial populations
inferred← citeshttps://doi.org/10.1073/pnas.1904094116openalex-snapshot
Genomics blazes a trail to improved cannabis cultivation
inferred← citeshttps://doi.org/10.1093/aobpla/plz074openalex-snapshot
Gene copy number is associated with phytochemistry in Cannabis sativa
inferred← citeshttps://doi.org/10.1093/gbe/evab130openalex-snapshot
Origin and Evolution of the Cannabinoid Oxidocyclase Gene Family
inferred← citeshttps://doi.org/10.1093/jxb/eraa263openalex-snapshot
Oxford Nanopore sequencing: new opportunities for plant genomics?
inferred← citeshttps://doi.org/10.1101/2020.01.03.894428openalex-snapshot
Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes
inferred← citeshttps://doi.org/10.1101/2020.05.25.114355openalex-snapshot
Development of genetic markers for sexing Cannabis sativa seedlings
inferred← citeshttps://doi.org/10.1101/2020.12.28.424591openalex-snapshot
Variation in mtDNA haplotypes suggests a complex history of reproductive strategy in Cannabis sativa
inferred← citeshttps://doi.org/10.1101/2022.08.01.501243openalex-snapshot
Transcriptome Response of Cannabis ( Cannabis sativa L.) to the Pathogenic fungus Golovinomyces ambrosiae
inferred← citeshttps://doi.org/10.1101/2024.05.07.593022openalex-snapshot
Population genomics of a natural Cannabis sativa L. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping
inferred← citeshttps://doi.org/10.1101/2025.08.11.669697openalex-snapshot
Predicting flowering time using integrated morphophysiological and genomic data with machine learning models
inferred← citeshttps://doi.org/10.1101/2025.09.22.677808openalex-snapshot
Transcription-based dissection of floral identity and trichome biosynthesis pathways in Cannabis sativa L
inferred← citeshttps://doi.org/10.1101/721324openalex-snapshot
A high-throughput segregation analysis identifies the sex chromosomes of Cannabis sativa
inferred← citeshttps://doi.org/10.1101/gr.251207.119openalex-snapshot
An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa
inferred← citeshttps://doi.org/10.1111/1556-4029.15045openalex-snapshot
Evaluation of tetrahydrocannabinolic acid ( THCA ) synthase polymorphisms for distinguishing between marijuana and hemp
inferred← citeshttps://doi.org/10.1111/nph.16122openalex-snapshot
Genome‐wide analysis of MIKC ‐type MADS ‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization
inferred← citeshttps://doi.org/10.1111/nph.17140openalex-snapshot
Recent advances in Cannabis sativa genomics research
inferred← citeshttps://doi.org/10.1111/nph.17243openalex-snapshot
A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana
inferred← citeshttps://doi.org/10.1111/nph.17456openalex-snapshot
Plant genera Cannabis and Humulus share the same pair of well‐differentiated sex chromosomes
inferred← citeshttps://doi.org/10.1111/ppl.70010openalex-snapshot
Cannabis Expression Atlas: a comprehensive resource for integrative analysis of Cannabis sativa L. gene expression
inferred← citeshttps://doi.org/10.1139/gen-2020-0087openalex-snapshot
The genetics of Cannabis—genomic variations of key synthases and their effect on cannabinoid content
inferred← citeshttps://doi.org/10.1146/annurev-arplant-081519-040203openalex-snapshot
The Genomics of Cannabis and Its Close Relatives
inferred← citeshttps://doi.org/10.1186/s12870-021-03079-2openalex-snapshot
The characterization of key physiological traits of medicinal cannabis (Cannabis sativa L.) as a tool for precision breeding
inferred← citeshttps://doi.org/10.1186/s12870-023-04630-zopenalex-snapshot
Transcriptomic and metabolomic analyses reveal the differential accumulation of phenylpropanoids and terpenoids in hemp autotetraploid and its diploid progenitor
inferred← citeshttps://doi.org/10.1186/s12870-024-04841-yopenalex-snapshot
Characterization of indigenous populations of cannabis in Iran: a morphological and phenological study
inferred← citeshttps://doi.org/10.1186/s12870-025-06045-4openalex-snapshot
Population genomics of a natural Cannabis sativa L. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping
inferred← citeshttps://doi.org/10.1186/s42238-020-00036-yopenalex-snapshot
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
inferred← citeshttps://doi.org/10.1371/journal.pone.0222363openalex-snapshot
Genomic characterization of the complete terpene synthase gene family from Cannabis sativa
inferred← citeshttps://doi.org/10.1371/journal.pone.0236878openalex-snapshot
Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes
inferred← citeshttps://doi.org/10.1371/journal.pone.0247607openalex-snapshot
Can public online databases serve as a source of phenotypic information for Cannabis genetic association studies?
inferred← citeshttps://doi.org/10.1371/journal.pone.0253387openalex-snapshot
Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms
inferred← citeshttps://doi.org/10.3389/fgene.2020.566314openalex-snapshot
Elucidating the Genetic Architecture of Fiber Quality in Hemp (Cannabis sativa L.) Using a Genome-Wide Association Study
inferred← citeshttps://doi.org/10.3389/fpls.2019.00495openalex-snapshot
Closing the Yield Gap for Cannabis: A Meta-Analysis of Factors Determining Cannabis Yield
inferred← citeshttps://doi.org/10.3389/fpls.2021.668315openalex-snapshot
Genomic Evidence That Governmentally Produced Cannabis sativa Poorly Represents Genetic Variation Available in State Markets
inferred← citeshttps://doi.org/10.3389/fpls.2021.773474openalex-snapshot
Manipulation of Cannabinoid Biosynthesis via Transient RNAi Expression
inferred← citeshttps://doi.org/10.3390/ijms20225630openalex-snapshot
A Multiple Protease Strategy to Optimise the Shotgun Proteomics of Mature Medicinal Cannabis Buds
inferred← citeshttps://doi.org/10.3390/ijms21030965openalex-snapshot
The Cannabis Proteome Draft Map Project
inferred← citeshttps://doi.org/10.3390/ijms232314531openalex-snapshot
Genetic Variants Associated with Long-Terminal Repeats Can Diagnostically Classify Cannabis Varieties
inferred← citeshttps://doi.org/10.3390/ijms26073445openalex-snapshot
Effect of Hormonal Treatments on Cannabinoid Content Levels in Female Hemp (Cannabis sativa L.) Inflorescences
inferred← citeshttps://doi.org/10.3390/molecules24040659openalex-snapshot
Optimisation of Protein Extraction from Medicinal Cannabis Mature Buds for Bottom-Up Proteomics
inferred← citeshttps://doi.org/10.3390/plants11030327openalex-snapshot
Tobacco Rattle Virus as a Tool for Rapid Reverse-Genetics Screens and Analysis of Gene Function in Cannabis sativa L.
inferred← citeshttps://doi.org/10.3390/plants14193050openalex-snapshot
Genotyping of Commercial European Cannabis Seeds Based on Multiple Mapped Marker Loci: A Comparative Study of Drug and Hemp Varieties
inferred← citeshttps://doi.org/10.3390/plants9111540openalex-snapshot
In Silico Identification of MYB and bHLH Families Reveals Candidate Transcription Factors for Secondary Metabolic Pathways in Cannabis sativa L.
inferred← citeshttps://doi.org/10.3390/proteomes8020013openalex-snapshot
The Power of Three in Cannabis Shotgun Proteomics: Proteases, Databases and Search Engines
inferred← citeshttps://doi.org/10.3897/phytokeys.144.46700openalex-snapshot
A classification of endangered high-THC cannabis (Cannabis sativa subsp. indica) domesticates and their wild relatives
inferred← citeshttps://doi.org/10.4018/978-1-6684-5718-4.ch006openalex-snapshot
Role of Cannabis sativa L. in the Cosmetic Industry
inferred← citeshttps://doi.org/10.46471/gigabyte.10openalex-snapshot
A new and improved genome sequence of Cannabis sativa
inferred← citeshttps://doi.org/10.70675/fa6f00eaze5e0z4b5cza87ez249151c8882aopenalex-snapshot
How to produce your furanocoumarins : the hidden pathway ~ From the characterisation of new P450s to the evolution of the furanocoumarin pathway and the development of tools allowing the study of furanocoumarins’ metabolic cost
inferred← citeshttps://doi.org/10.7287/peerj.10672v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Widely assumed phenotypic associations in Cannabis sativa lack a shared genetic basis (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10672v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Widely assumed phenotypic associations in Cannabis sativa lack a shared genetic basis (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10672v0.1/reviews/3openalex-snapshot
Peer Review #3 of "Widely assumed phenotypic associations in Cannabis sativa lack a shared genetic basis (v0.1)"
inferred← citeshttps://doi.org/10.7717/peerj.10672openalex-snapshot
Widely assumed phenotypic associations in Cannabis sativa lack a shared genetic basis
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.