Talk:Cannabis genome

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Discussion for: Cannabis genome • View • Links • Related changes

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Page scope

Cannabis genome covers the chromosomes, genome size, published assemblies and what each was built from, repeats, the cannabinoid synthase region, the sex chromosomes and the organelle genomes. Heredity in general belongs to Cannabis genetics, the sex system and how sex is set to Sex determination in cannabis, the inheritance of chemotype to Genetic traits, and heterozygosity values to Heterozygosity.

Data verification

Record source conflicts, figures that differ between studies and sources not used here. Keep narrative content on the article.

Discussion

Sources

Sakamoto and colleagues (1998), Cytologia 63: 459–464: the flow cytometry values of 818 and 843 Mb. Divashuk and colleagues (2014), PLoS ONE 9: e85118: the karyotype. Razumova and colleagues (2016), Protoplasma 253: 895–901: monoecious hemp. Faux and colleagues (2014), Euphytica 196: 183–197, and Balant and colleagues (2022), Plants 11: 2736: genome size by flow cytometry.
van Bakel and colleagues (2011), Laverty and colleagues (2019), Gao and colleagues (2020), Braich and colleagues (2020), Grassa and colleagues (2021), Wei and colleagues (2024, 2026), Ryu and colleagues (2024), Stack and colleagues (2025), Lynch and colleagues (2025), Pike and colleagues (2026, two papers) and Ni and colleagues (2026): the assemblies.
Pisupati and colleagues (2018), BMC Genomics 19: 156: repeats from raw reads. Alexandrov and colleagues (2022), Plants 11: 1396: the CS-237 repeat.
van Velzen and Schranz (2021), Genome Biology and Evolution 13: evab130: origin of the synthase family. Vergara and colleagues (2019), AoB PLANTS 11: plz074: copy number. Ren and colleagues (2021), Science Advances 7: eabg2286: synthases across accessions.
Prentout and colleagues (2020, 2021): the sex chromosomes and their age. Carey and colleagues (2026), Nature Communications 17: 6866: age and an X-linked candidate gene.
White and colleagues (2016) and Liu and colleagues (2023): organelle genomes.

Where the sources disagree

Size of CBDRx. Grassa and colleagues give a k-mer prediction of 639 Mb and an assembly of 737 Mb and attribute the difference to residual heterozygosity. Their discussion also gives a size of 736 Mb "matching predictions from kmer frequency". Braich and colleagues list the same assembly at 854 Mb with gaps and 714 Mb without.
Largest chromosome. The abstract of Divashuk and colleagues calls the X the largest of all. Their Table 1 gives relative lengths of 6.5 per cent for the Y, 6.1 for the X and 5.6 for the largest autosome. Lynch and colleagues call the Y the largest.
Y against X. About 30 per cent larger in the pangenome (108–113 against 83–85 Mb). Under the microscope the two differ by 0.4 of a percentage point of relative length. Prentout and colleagues (2020) call the pair roughly homomorphic.
X-specific region. 30 to 105 Mb on chromosome 1 of the 2018 CBDRx assembly, so about 75 Mb (Prentout 2020). 53 to 55 Mb in the phased assemblies of the pangenome. The first was inferred from sex-linked transcripts mapped to an XX assembly, the second from assembled X and Y chromosomes.
Age of the sex chromosomes. Prentout and colleagues (2020) state about 12 to 29 million years; their 2021 abstract restates this as 12–28. Carey and colleagues wrote ">36 MYA" in their 2024 preprint, which Lynch and colleagues cite, and "around 36 MYA" in the 2026 paper. The later estimates are in the article.
Flow cytometry standards. Faux and colleagues (2014) report 1.835 pg for males with soybean and 1.883 pg with maize, and call the soybean values the more accurate. They set their values above Sakamoto and colleagues' (1998), which used Arabidopsis and DAPI.
Shape of the sex chromosomes. Sakamoto and colleagues (1998) call the X submetacentric and the Y subtelocentric. The karyotype formula of Divashuk and colleagues (2014) has both as metacentric.
Plants or cultivars. The abstract of Vergara and colleagues (2019) writes of 69 cultivars. Its methods describe two assemblies and 67 sequence libraries from individuals, several of them from one cultivar.
Share of repeats in one paper. Lynch and colleagues write of approximately 79 per cent transposable elements in their introduction and report an average of 68 per cent in their results. Laverty and colleagues cite Pisupati and colleagues for about 70 per cent of the draft genome; Pisupati and colleagues report 64 to 65 per cent.
Low-complexity repeats. Pisupati and colleagues give 29 per cent in the abstract, approximately 27 in the results and approximately 25 in the discussion.
Whole-genome duplication. Three events in Gao and colleagues, two in Wei and colleagues (2024), none since an event about 100 million years ago in Lynch and colleagues.
Pseudogenes in CBDRx. Grassa and colleagues write that all but two of the 13 homologues are pseudogenes, and also describe three full-length sequences: CBCAS at 26 Mb, one CBDAS-like copy at 29 Mb and CBDAS at 31 Mb.
Size of the synthase units. 31 to 45 kilobases in Grassa and colleagues. Lynch and colleagues, citing that paper, write 70 to 80 kilobases.
Sex of the assembled plants. Grassa and colleagues write that CBDRx and other available assemblies came from female plants. Laverty and colleagues sequenced a male Finola.
Pink Pepper. The abstract of Ryu and colleagues reads 770 Gbp. Their chromosome table sums to 770 Mb.
Mitochondrial genes. White and colleagues give 54 genes and a breakdown of 38, 15 and 3, which sums to 56.

How far the evidence goes

Repeat shares and gene counts come from different programs and thresholds, so the table does not rank assemblies. A blank cell means the figure is not stated in the main text of the paper.
"Wild" is the word of the authors for JL and for the accession of Ni and colleagues. Lynch and colleagues call for a careful separation of wild from feral plants, and Ren and colleagues treat feral plants they sampled as historical escapes.
Punto Rojo is called a landrace by Pike and colleagues. Its haplotype comes from a single F₁ plant, so it stands for one parental chromosome set.
Balant and colleagues concede that secondary metabolites may have interfered with staining, though they used young leaves to reduce the effect.
The chromosome numbering of one assembly does not carry over to another. Each number in the article belongs to the assembly named beside it.

Terms

Contig and scaffold: a contig is an unbroken run of assembled sequence; a scaffold joins contigs in order, often with gaps between them.
Haplotype-resolved or phased: the two chromosome sets of a diploid plant assembled separately.
Hi-C: a method that measures which stretches of DNA touch inside the nucleus, used to order contigs along chromosomes.
k-mer: a short DNA word of fixed length, counted in reads to estimate genome size and heterozygosity.
Pseudoautosomal region: the part of the X and Y that still pairs and recombines. Sex-determining region: the part of the Y that does not.
Pg/2C: picograms of DNA in a diploid nucleus.