Cannabis sativa comparative hub

Cannabis sativa assemblies aligned to cs10, with pairwise chains, nets and a multiz alignment

This hub currently serves assembled sequence for 217 Cannabis sativa assembly/ies, with cs10_NCBI_RefSeq_softmasked as the alignment reference. Assemblies are aligned to the reference; the list below says which tracks are on how many genomes.

Tracks

• 217-way multiz alignment: cs10_NCBI_RefSeq_softmasked only
• Alignment depth and variant frequency: cs10_NCBI_RefSeq_softmasked only
• K-mer sharing (Panagram): cs10_NCBI_RefSeq_softmasked only
• Pairwise chains to cs10: 216 of 217 genomes
• Reciprocal-best chains to cs10: every genome
• Alignment nets on cs10: cs10_NCBI_RefSeq_softmasked only
• Gene models: 182 of 217 genomes
• Genes from cs10: 215 of 217 genomes
• Terpene and cannabinoid synthase arrays: cs10_NCBI_RefSeq_softmasked only
• Cannabinoid synthases: 202 of 217 genomes
• Terpene synthases: 8 of 217 genomes
• NLR genes: 8 of 217 genomes
• Repeats: every genome
• Assembly gaps: 104 of 217 genomes
• GC percent: every genome
• Ideogram: every genome

Where to start

Open cs10_NCBI_RefSeq_softmasked (cs10, CBDRx) to see the multiple alignment: the other assemblies are aligned to it. Gene names, RefSeq accessions and words from a gene's product (for example cannabidiolic) can be typed into the position box on cs10 and on every genome that carries cs10's projected genes. Each assembly's own page credits its source and licence.

Sequence is soft-masked. Assemblies in this panel vary widely in contiguity: 93 of 217 carry more than 1,000 sequences, so the default view for those opens on the longest sequence rather than a chromosome.

Data sources and credits

Each assembly's page gives its citation, data holder, licence and original location. By source:

• Lynch, R.C., Padgitt-Cobb, L.K., Garfinkel, A.R., et al. (2025). Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome. Nature, 643, 1001–1010. doi:10.1038/s41586-025-09065-0 — 127 assemblies; Creative Commons Zero v1.0 Universal
• Lynch, R.C., Padgitt-Cobb, L.K., Garfinkel, A.R., et al. (2025). Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome. Nature, 643, 1001–1010. doi:10.1038/s41586-025-09065-0 — 40 assemblies; Creative Commons Attribution 4.0 International
• NCBI (INSDC): cite each original submission (accession on the assembly's page) — 27 assemblies; no licence stated
• Lynch, R.C., Padgitt-Cobb, L.K., Garfinkel, A.R., et al. (2025). Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome. Nature, 643, 1001–1010. doi:10.1038/s41586-025-09065-0 — 14 assemblies; CC BY 4.0
• NGDC Genome Warehouse: cite each original submission (accession on the assembly's page) — 5 assemblies; no licence stated
• CoGe (genomevolution.org) — 4 assemblies; no licence stated

Contact: rcb112@psu.edu