Comparative chromosome-scale genomics of the ayahuasca liana Banisteriopsis caapi reveals paleopolyploid ancestry and recent tandem-gene expansions as candidate signatures of ethnovariety differentiation
Background: Banisteriopsis caapi is the Amazonian liana that provides the {beta}-carboline-rich vine component of ayahuasca, a traditional Amazonian psychoactive preparation used in Indigenous and ceremonial contexts. The species encompasses culturally recognized ethnovarieties, some differing in stem architecture. Despite its cultural, ecological, and pharmacological importance, B. caapi remains largely unexplored at the genomic level. Here, we generated chromosome-scale genome assemblies for the caupuri and tucunaca ethnovarieties and used them to investigate genome evolution, structural variation, repeat composition, and candidate genomic features associated with ethnovariety-level differentiation. Results: Caupuri and tucunaca assemblies span 1.16 and 1.13 Gb, respectively, each organized into ten high-quality chromosome-scale pseudomolecules. Both genomes retain signatures of two ancient post-gamma duplication components, with related signals also detected in Malpighia emarginata, suggesting that at least part of this paleopolyploid history may predate the divergence of these Malpighiaceae lineages. Against this conserved chromosomal framework, the sampled caupuri and tucunaca genomes differ in structural variation, repeat composition, and gene-family profiles. Transposable element-associated insertions and deletions dominate the structural-variant landscape, while both genomes are highly repetitive, with approximately 78% of their assemblies composed of repetitive DNA largely shaped by LTR retrotransposons, including Gypsy/Retand and Copia/Ale, Copia/Tork, and Copia/Ivana lineages, together with non-autonomous large retrotransposon derivatives (LARDs). Most genes belong to shared orthogroups, indicating a largely conserved gene repertoire. However, candidate ethnovariety-biased differences emerge from the combined remodeling of gene families, LARD and LTR-associated genomic neighborhoods, and comparatively recent local expansions of tandem-duplicated gene arrays encoding signaling receptors, transporters, hormone-associated genes, cell wall and secondary wall functions, and meristem or organ-development pathways. Conclusions: These results indicate that the sampled caupuri and tucunaca genomes differ mainly through localized remodeling of shared genomic modules, including comparatively recent repeat turnover and local tandem-gene expansions. These assemblies provide the first large-scale nuclear genomic resource for B. caapi and a foundation for investigating paleopolyploid evolution in Malpighiaceae and candidate mechanisms of ethnovariety diversification.