Data from: Comparative chromosome-scale genomics of the ayahuasca liana Banisteriopsis caapi reveals paleopolyploid ancestry and recent tandem-gene expansions as candidate signatures of ethnovariety differentiation

Abstract

README -- Banisteriopsis caapi Genome Resources Associated preprint: Trinca, V., Prosdocimi, F., Côrtes-Barros, P., de Moraes, A. P., Almeida, M. C., Paschoal, A. R., da Silva, S. R., Miranda, V. F. O., Barbosa, J. B. F., Oliveira, D. R., Lopes, S. S. S., and Varani, A. M. (2026). Comparative chromosome-scale genomics of the   ayahuasca liana Banisteriopsis caapi reveals paleopolyploid ancestry   and recent tandem-gene expansions as candidate signatures of   ethnovariety differentiation. bioRxiv , 2026.10.11.758337.  https://doi.org/10.64898/2026.10.11.758337 This dataset provides chromosome-scale genome assemblies and comprehensive annotations for two ethnovarieties of Banisteriopsis   caapi (Malpighiaceae), Caupuri and Tucuncá , together with comparative genomic resources for Malpighia emarginata . The B. caapi assemblies were generated using PacBio Revio HiFi long   reads and Arima Hi-C scaffolding. These resources support studies of genome evolution, paleopolyploidy, gene duplication, functional genomics, and specialized metabolism. The Zenodo record includes: Genome assemblies: chromosome-scale nuclear genome sequences and soft-masked assemblies. Structural and functional annotations: gene models (GFF3), coding sequences (CDS), transcripts (cDNA), proteins, and functional assignments, including GO, KEGG, Pfam, CAZy, transcription factors (TFs), and resistance-related gene catalogs where available. Transposable element (TE) annotations: repeat classifications, genomic coordinates, and sequence libraries generated with EDTA-GUI in AnnoTEP mode. Gene duplication analyses: WGD/segmental, tandem, proximal, transposed, and dispersed duplicates, retrocopies, and small-scale duplication categories, where available. Quality assessments: BUSCO, LTR Assembly Index (LAI), and assembly and annotation statistics. Biosynthetic gene clusters: plantiSMASH predictions of candidate specialized-metabolite biosynthetic gene clusters. Raw PacBio HiFi and Hi-C sequencing reads are not included because of their size. The corresponding NCBI BioProjects are listed below. Files are distributed in widely used formats, including FASTA, GFF3, and tabular reports, to facilitate reuse and interoperability. Files Description The dataset is organized into three compressed archives: Caupuri-complete.tar.gz -- Genome assembly and associated annotations for the B. caapi Caupuri ethnovariety. Tucunaca-complete.tar.gz -- Genome assembly and associated annotations for the B. caapi Tucuncá ethnovariety. Memarginata-complete.tar.gz -- Genome assembly and associated annotations for Malpighia emarginata , included as a comparative reference. Each archive contains the corresponding genome assembly and available structural, functional, and repeat annotations. File prefixes identify the respective genome. Depending on the archive, individual files may be compressed ( .gz ) or uncompressed. Genome Assemblies *.fa.gz -- Nuclear genome assembly in FASTA format. *-Softmasked.fasta.gz -- Genome assembly with repetitive regions soft-masked (lowercase nucleotides), suitable for gene prediction and repeat-aware analyses. Structural and Functional Annotation *-Annotation.gff3.gz -- Structural gene annotation in GFF3 format, retaining predicted transcript isoforms and available functional annotation attributes. *-Annotation.prot.gz -- Predicted protein sequences in FASTA format. *-Annotation.CDS.gz -- Coding sequences (CDS) in nucleotide FASTA format. *-Annotation.cDNA.gz -- Predicted transcript (cDNA) sequences in nucleotide FASTA format. *-Annotation.gene.gz -- Gene sequences or gene-associated records. *-Annotation.stats -- Gene annotation summary statistics. *-Annotation.BUSCO -- BUSCO completeness assessment of the corresponding gene set. *-Annotation.annot -- Blast2GO plain-text functional annotation, including GO terms where assigned. *-Annotation.b2g -- Blast2GO annotation file. *-Annotation.tRNA.gff3.gz -- Transfer RNA (tRNA) annotation. *-Annotation.rRNA.gff3 -- Ribosomal RNA (rRNA) annotation. *-NoAnnotation.gff3 -- Structural-only annotation corresponding to the HQ gene set, without functional annotation attributes. Alternative gene annotation datasets: Annotation-Primary_Transcripts -- Complete gene annotation retaining only the longest transcript isoform per gene. Annotation-HQ -- High-confidence gene annotation excluding predicted genes without detectable database matches and without evidence of expression. Annotation-HQ-Primary_Transcripts -- High-confidence gene annotation retaining only the longest transcript isoform per gene. These subsets may include corresponding GFF3, protein, CDS, cDNA, BUSCO, and annotation statistics files. The HQ designation refers to the filtering criteria applied to the predicted gene set. Repeats and Transposable Elements *TEanno.gff3.gz -- Genome-wide transposable element annotations in GFF3 format. *TElib.fa.gz -- Custom TE consensus sequence library in FASTA format. *.LAI -- LTR Assembly Index (LAI) results for evaluating assembly quality in LTR-rich regions. TEs-report-lite.tbl -- Summary of transposable element classifications and abundances. TEs-report-complete.tbl -- Detailed transposable element annotation report. TE annotation and classification were performed using EDTA-GUI in   AnnoTEP mode . Gene Duplication and Comparative Genomics Where included, gene-family classification files identify duplicated genes associated with whole-genome duplication (WGD), tandem, proximal, transposed, and dispersed duplication, as well as retrocopies and small-scale duplications. These results support analyses of gene-family evolution and comparisons between the two B. caapi ethnovarieties. Functional Annotation and Biosynthetic Gene Clusters *-PlantiSMASH.zip -- Predicted plant biosynthetic gene clusters identified using plantiSMASH, including candidate clusters associated with specialized metabolism. Functional annotations may additionally include GO, KEGG, Pfam, CAZy, transcription factor, and resistance-associated gene assignments, according to the files provided for each genome. GenBank Availability Genome and sequencing resources are associated with the following NCBI BioProjects: Caupuri:   PRJNA1497017 Tucuncá:   PRJNA997335 Please refer to the respective BioProject records for available raw sequencing data and genome accessions. Citation If you use these genomic resources, please cite the associated preprint: Trinca et al. (2026). Comparative chromosome-scale genomics of the ayahuasca liana Banisteriopsis caapi reveals paleopolyploid ancestry and recent tandem-gene expansions as candidate signatures of ethnovariety differentiation. bioRxiv .  https://doi.org/10.64898/2026.10.11.758337

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