Scientists have produced some of the most complete cannabis genome sequences assembled to date, revealing new details about how the plant evolved the genetic machinery responsible for making THC, CBD and CBC. The research fills in difficult sections of Cannabis sativa DNA that earlier sequencing projects struggled to reconstruct and provides a clearer evolutionary history of the genes that determine some of the plant’s most important chemical traits.
Published October 22 in Plant Biotechnology Journal, the study was led by researchers from the Chinese Academy of Agricultural Sciences, Huazhong Agricultural University and Yangzhou University. By assembling two essentially gap-free versions of the chromosomes inherited by a single female cannabis plant, the team was able to examine cannabinoid synthase genes inside the repetitive genomic regions where they evolved. The results suggest that the pathway eventually responsible for THC, CBD and CBC emerged through a series of ancient gene duplications, losses and specializations rather than through a recent duplication of the entire cannabis genome.
Scientists Built Two Gap-Free Cannabis Genomes
The researchers studied a CBD-dominant plant they designated Golden Cannabis sativa, or GCS, derived from Chinese cannabis germplasm. Because cannabis is diploid, each plant carries two sets of chromosomes inherited from its parents. Instead of collapsing those two versions into a single reference sequence, the researchers assembled them separately, producing two haplotype-resolved genomes measuring approximately 741 million and 745 million DNA base pairs.
Each genome contained 10 fully assembled chromosomes with no sequence gaps. The researchers identified 27,365 predicted genes in one haplotype and 27,776 in the other, while standard genome-completeness scores exceeded 99 percent. The assemblies were built using a combination of PacBio high-fidelity sequencing, longer continuous reads and Hi-C data that help determine how pieces of DNA are physically arranged inside chromosomes.
This level of resolution matters because cannabis has an unusually repetitive genome. About 78.5 percent of the DNA in the new assemblies consisted of repetitive sequences. Long stretches of nearly identical DNA can confuse genome-assembly algorithms in much the same way that reconstructing a book becomes difficult if most of its pages contain repeated paragraphs. Earlier cannabis genomes frequently contained gaps or uncertain arrangements in exactly the regions scientists most wanted to study.
Cannabinoid Genes Sit Inside Some of Cannabis’ Most Complicated DNA
The genes responsible for the final steps in cannabinoid production are concentrated in structurally complex regions containing repeated DNA, transposable elements and duplicated genes. These regions can differ dramatically among cannabis varieties, which is one reason earlier studies sometimes produced conflicting pictures of where cannabinoid genes were located and how they were related.
The new genome allowed researchers to follow these genes across complete chromosomes rather than working around unresolved sequence gaps. The most important cannabinoid synthase genes are found primarily on chromosome 7, where duplicated members of the same larger gene family have evolved into enzymes associated with THCA, CBDA and CBCA production. Those acidic cannabinoids later convert into THC, CBD and CBC, respectively, through decarboxylation caused by heat, time or other conditions.
The study also identified related genes on chromosome 2. Those chromosome 2 genes appear to preserve a more ancestral branch of the family, while the chromosome 7 branch underwent additional duplication and diversification. That distinction became crucial in reconstructing when cannabis first acquired the genetic foundation that would eventually produce its characteristic cannabinoid chemistry.
The Story Appears to Begin Before Cannabis and Hops Separated
Cannabis belongs to the Cannabaceae family and is closely related to Humulus, the genus containing hops. Researchers estimated that the cannabis and Humulus lineages separated approximately 17 million years ago. Yet the new genetic analysis indicates that an important duplication of the ancestral gene family occurred before that split.
The researchers reconstructed a model in which an ancestral gene duplicated in the common ancestor shared by cannabis and hops. Cannabis ultimately retained two descendant lineages corresponding broadly to genes now found on chromosomes 2 and 7. The Humulus lineage examined in the study retained only a relative resembling the cannabis chromosome 2 branch. Following the separation of cannabis and hops, the chromosome 7 lineage in cannabis underwent additional local duplications and evolutionary changes.
Those later changes created the cluster from which the modern cannabinoid synthases emerged. In other words, cannabis did not suddenly acquire separate THC, CBD and CBC genes in one evolutionary event. The evidence points toward a gradual process in which duplicated genes accumulated mutations, diverged in function and eventually became specialized enzymes capable of turning the same precursor molecule into different cannabinoids.
THC, CBD and CBC All Begin With the Same Chemical Precursor
The genetic differences among cannabinoid synthases are especially important because THC, CBD and CBC begin from the same biochemical branch point. Cannabis first produces cannabigerolic acid, or CBGA, through a series of upstream metabolic reactions. CBGA is sometimes described as a “mother cannabinoid” because several major cannabinoid pathways diverge from it.
THCA synthase converts CBGA primarily into tetrahydrocannabinolic acid. CBDA synthase directs it toward cannabidiolic acid, while CBCA synthase produces cannabichromenic acid. The acidic molecules are not chemically identical to the compounds consumers normally call THC, CBD and CBC. Heating or aging removes a carboxyl group, creating the neutral cannabinoids better known outside plant science.
The new analysis found that the THC- and CBC-associated synthase genes are particularly closely related, while the modern CBD synthase lineage occupies an earlier branching position within the cannabinoid synthase group. That family relationship helps explain why THCAS and CBCAS share substantial genetic similarity despite producing different cannabinoid profiles.
Earlier Research Brought Ancient Cannabis Enzymes Back to Life
The new genomic study fits remarkably well with separate research published earlier in 2026 by scientists at Wageningen University & Research. That team used ancestral sequence reconstruction to infer the genetic sequences of extinct cannabinoid enzymes and then synthesized those sequences in the laboratory. The reconstructed proteins were produced in yeast and tested to determine what cannabinoids they could actually make.
Those experiments showed that early cannabinoid enzymes were less specialized than their modern descendants. An ancestral enzyme could process CBGA into all three major products—THCA, CBDA and CBCA. Over evolutionary time, gene duplication allowed different copies to accumulate mutations without eliminating the original function entirely. Those copies gradually became more selective, eventually producing the highly specialized THCAS and CBDAS enzymes found in modern cannabis.
Together, the enzyme-resurrection study and the new gap-free genome provide complementary pieces of the same evolutionary story. One study experimentally demonstrated how ancestral enzymes behaved, while the other provides a high-resolution map showing where the gene lineages arose and how chromosome-scale duplication and rearrangement shaped their modern organization.
Cannabis Did Not Need a Recent Whole-Genome Duplication
One longstanding question in cannabis genomics has involved whether the plant experienced one or more relatively recent whole-genome duplication events. Whole-genome duplication occurs when an organism effectively acquires an additional copy of every chromosome, providing enormous amounts of duplicated genetic material that evolution can later modify.
Some earlier cannabis studies interpreted patterns in the genome as evidence for such additional duplication events. The new gap-free analysis found no convincing evidence for a cannabis-specific whole-genome duplication after the lineage separated from its relatives. Instead, researchers recovered evidence of the much older gamma whole-genome triplication shared broadly by core eudicot flowering plants.
The authors concluded that much of cannabis’ later genetic diversification resulted from smaller and more targeted events: individual gene duplications, tandem gene expansions, structural rearrangements and the movement of repetitive transposable elements. Cannabinoid biosynthesis appears to be a particularly good example. Rather than duplicating the entire genome, cannabis repeatedly copied and modified selected genes within a specialized region, allowing new chemical functions to evolve without requiring a genome-wide event.
Cannabis Varieties Can Organize the Same Genes Very Differently
Comparing the new assemblies with previously sequenced cannabis varieties revealed striking structural differences around the cannabinoid genes. In the Golden Cannabis genomes and the Yushe reference, the regions associated with THCAS and CBDAS were separated by approximately 10 million to 30 million DNA base pairs. In other assemblies, including Cannbio-2 and the CBD-rich Cs10 reference, the same functional regions were only about 4 million to 5 million base pairs apart.
These differences illustrate why cannabis genetics can be difficult to interpret using a single reference genome. Two plants can belong to the same species and possess related cannabinoid pathways while organizing large sections of their chromosomes differently. Human breeding for fiber, seed, THC, CBD and other traits has added another layer of selection onto millions of years of natural evolution.
The researchers also found many cannabinoid-synthase-related gene sequences that appear incomplete or nonfunctional. No more than one intact principal THCAS or CBDAS copy was found in each haploid genome examined, even though numerous related copies and pseudogenes were present. The finding reinforces the idea that cannabinoid chemistry depends not simply on how many synthase-like sequences a plant carries, but on whether the relevant genes are intact and actively expressed.
Gene Activity Helps Determine What a Cannabis Plant Actually Produces
Possessing a cannabinoid-related gene does not guarantee that a cannabis plant will produce large quantities of the corresponding compound. Genes must also be activated at the right time and in the appropriate tissues. The new study examined expression during flowering and found strong CBDAS activity in CBD-dominant accessions including Golden Cannabis, Cannbio-2 and Finola.
CBCAS behaved differently. Although CBC-related gene sequences were present in some genomes, CBCAS expression remained comparatively low during flowering. Many other duplicated synthase-like genes were weakly expressed or effectively silent. This may help explain why CBC is generally found at lower concentrations than THC or CBD in modern commercial cannabis.
The findings align with recent work on the cannabis chemotype-determining region showing that structural variation, gene presence and gene expression interact to produce very different cannabinoid profiles. Breeders therefore cannot reliably predict a plant’s chemistry merely by counting genes. They need to know which version of the gene is present, whether it is functional, where it sits within the chromosome and how strongly it is expressed.
The Research Could Improve Cannabis Breeding
A clearer map of cannabinoid genetics could eventually make breeding much more precise. Traditional cannabis breeding relies heavily on crossing plants, growing offspring and chemically testing flowers to determine which individuals produce the desired cannabinoid profile. Genetic markers can accelerate that process, but they work best when scientists understand the underlying chromosome structure accurately.
Gap-free genomes could help breeders distinguish intact cannabinoid synthases from inactive pseudogenes and identify structural arrangements associated with particular chemotypes. That could improve selection for high-CBD, THC-dominant or unusual minor-cannabinoid varieties while reducing the number of generations needed to identify promising plants.
CBC is an especially interesting target. Because commercial cannabis rarely produces very high CBC concentrations, breeders interested in CBC-rich cultivars have fewer natural starting points than breeders working with THC or CBD. Understanding CBCAS evolution, expression and genomic location could eventually help scientists identify naturally favorable germplasm or develop more efficient breeding strategies for CBC production.
Biotechnology Could Benefit From Ancient and Modern Cannabinoid Genes
The research also has implications beyond growing cannabis plants. Biotechnology companies increasingly use microorganisms such as yeast to manufacture cannabinoids through fermentation. Instead of extracting compounds from flowers, engineers introduce genes encoding cannabinoid-pathway enzymes into microbial cells and turn those cells into miniature chemical factories.
Modern cannabinoid synthases can be difficult proteins to manufacture efficiently in microorganisms. The earlier Wageningen study found that reconstructed ancestral enzymes were easier to produce in yeast and possessed unusually broad catalytic capabilities. Researchers were even able to engineer hybrid enzymes with altered cannabinoid selectivity.
Combining those findings with better chromosome-level genetic maps could expand the toolkit available for metabolic engineering. Scientists may eventually design enzymes optimized for particular cannabinoids, improve production of rare compounds or create cannabinoid molecules that cannabis itself produces only in tiny amounts. Those possibilities remain research objectives rather than immediate commercial outcomes, but the evolutionary information provides a rational starting point for engineering rather than relying on trial and error.
The Genome Is Still Not the Complete Story of Cannabis
The new assemblies are exceptionally complete, but no single cannabis plant can represent the genetic diversity of the entire species. Cannabis has been cultivated and moved across continents for thousands of years, with humans selecting dramatically different plants for fiber, seed, medicine and psychoactive effects. Modern marijuana, hemp, landrace and wild or feral populations contain extensive structural and genetic variation.
A major cannabis pangenome published in 2025 assembled genomic information from nearly 200 genomes and revealed extensive variation across the species. Another 2026 study created a reference-free graph containing 66 haplotypes and concluded that additional sampling—particularly from regions associated with cannabis’ geographic origins—is still needed. The Golden Cannabis assemblies add valuable Asian-derived material to that growing genomic archive but do not close the book on cannabis evolution.
Future studies will need to connect complete genome sequences with detailed cannabinoid measurements, gene-expression data and environmental information. Two genetically similar plants can produce different metabolite concentrations depending on development, cultivation conditions and stress, meaning DNA establishes biological potential rather than guaranteeing one fixed chemical outcome.
Cannabis’ Famous Chemistry Emerged Through Millions of Years of Genetic Experimentation
The new study provides one of the clearest genomic explanations yet for how cannabis became capable of producing its signature cannabinoids. An ancestral gene duplication occurred before cannabis and hops went their separate evolutionary ways roughly 17 million years ago. Cannabis retained multiple branches of that ancestral family, and one branch on chromosome 7 continued duplicating and diverging until specialized THC-, CBD- and CBC-producing enzymes emerged.
That history challenges any simple picture of cannabinoid production as the result of one unique “THC gene” appearing suddenly in cannabis. The modern cannabinoid pathway is the product of repeated duplication, mutation, structural rearrangement, gene loss and functional specialization unfolding across millions of years. Human cultivation later intensified the process by favoring plants with particular chemical profiles.
With gap-free genome assemblies finally exposing regions that remained difficult to read for years, scientists can now examine that evolutionary machinery with much greater precision. The result is not only a better explanation for where THC, CBD and CBC came from, but a genomic framework that could eventually help breeders and biotechnologists decide where cannabis chemistry goes next.
