Integrating target capture with whole genome sequencing of recent and natural history collections to explain the phylogeography of wild-growing and cultivated cannabis
Manica Balant, Daniel Vitales, Zhiqiang Wang, Zoltán Barina, Lin Fu, Tiangang Gao, Teresa Garnatje, Airy Gras, Muhammad Q. Hayat, Marine Oganesian, Jaume Pellicer, Alireza S. Salami, Alexey P. Seregin, Nina Stepanyan-Gandilyan, Nusrat Sultana, Shagdar Tsooj, Magsar Urgamal, Joan Vallès, Robin van Velzen, Lisa Pokorny
Plants, People, Planet· 2025
Phylogeographic study using a Hyb-Seq approach that combines target capture (with the universal Angiosperms353 enrichment panel) and shotgun whole-genome sequencing on the same data, applied to wild-growing accessions, cultivars and herbarium specimens drawn from natural history collections. Phylogenomic and population genomic workflows on the integrated dataset support treating Cannabis as a monotypic genus and recover three main genetic groups: East Asia, Paleotropis, and Boreal. Paleotropis is further divided into Iranian Plateau, Central and South China–Himalayas, and Indoafrica subgroups. Boreal is divided into Eurosiberia–West Mongolia and Caucasus–Mediterranean subgroups. The dominant signal is geographic rather than use-type, with cultivars clustering by region of origin rather than by hemp/drug distinction. Iranian and Central Asian wild-growing populations are reported as distinctive and morphogenetically diverse. The authors demonstrate that herbarium specimens, including older natural history collections, can be integrated with fresh material to recover phylogenetic signal.
2025-02-06
2026-05-04
Integrating target capture with whole genome sequencing of recent and natural history collections to explain the phylogeography of wild-growing and cultivated cannabis
Journal article
Manica Balant, Daniel Vitales, Zhiqiang Wang, Zoltán Barina, Lin Fu, Tiangang Gao, Teresa Garnatje, Airy Gras, Muhammad Q. Hayat, Marine Oganesian, Jaume Pellicer, Alireza S. Salami, Alexey P. Seregin, Nina Stepanyan-Gandilyan, Nusrat Sultana, Shagdar Tsooj, Magsar Urgamal, Joan Vallès, Robin van Velzen, Lisa Pokorny
Plants, People, Planet
2025
10.1002/ppp3.70043
https://nph.onlinelibrary.wiley.com/doi/10.1002/ppp3.70043
https://nph.onlinelibrary.wiley.com/doi/pdf/10.1002/ppp3.70043
Global phylogeographic study using a Hyb-Seq approach that combines target capture (with the universal Angiosperms353 enrichment panel) and shotgun whole-genome sequencing on the same data, applied to wild-growing accessions, cultivars and herbarium specimens drawn from natural history collections. Phylogenomic and population genomic workflows on the integrated dataset support treating Cannabis as a monotypic genus and recover three main genetic groups: East Asia, Paleotropis, and Boreal. Paleotropis is further divided into Iranian Plateau, Central and South China–Himalayas, and Indoafrica subgroups. Boreal is divided into Eurosiberia–West Mongolia and Caucasus–Mediterranean subgroups. The strongest signal in the data is geographic rather than use-type, with cultivars clustering by region of origin rather than by hemp/drug distinction. Iranian and Central Asian wild-growing populations emerge as particularly distinctive and morphogenetically diverse, consistent with the idea that this region functions as a genetic melting pot. The study is the first global landrace-inclusive phylogeography of cannabis after Ren et al. 2021 and is methodologically significant for showing that herbarium specimens (including older natural history collections) can be integrated with fresh material to recover phylogenetic signal in a genus where field sampling is legally difficult. Provides the geographic backbone against which any landrace genotype on the wiki can be situated, complements the Lynch et al. 2025 pangenome at the population scale, and supports the conservation case that wild-growing populations from understudied regions hold diversity not represented in modern cultivars.
