This dataset contains supplementary files associated with the analyses presented in the manuscript. The data include genome annotations, molecular modeling coordinate files, and structural docking resources that support the identification and characterization of biosynthetic gene clusters and stereochemistry-inverting enzymes involved in monoterpenoid indole alkaloid (MIA) biosynthesis.

Description of the data and file structure

The dataset is organized into individual compressed archives. Each archive corresponds to a specific analysis described in the manuscript.

• Rauvolfia_tetraphylla.gff3.zip
  Contains the genome annotation file (.gff3) for Rauvolfia tetraphylla, generated with GeMoMa (reference-based annotation modeler). The annotation is aligned to the R. tetraphylla genome assembly (NCBI accession: ASM3051222v1).
• CrTHAS2_for_XYZ.zip
  Contains .xyz coordinate files for docking analyses of Catharanthus roseus tetrahydroalstonine synthase 2 (CrTHAS2) with ligands. Files were generated using Molecular Operating Environment (MOE).
• HpHYC3O_for_XYZ.zip
  Contains .xyz coordinate files for Hameliapatens HYC3O (HpHYC3O) enzyme with ligands, generated in MOE.
• RsHYC3R(CAD7)_for_XYZ.zip
  Contains .xyz coordinate files for Rauvolfia serpentina C3-reductase (RsHYC3R, also referred to as CAD7) with ligands, generated in MOE.
• RtHYC3O_for_XYZ.zip
  Contains .xyz coordinate files for Rauvolfia tetraphylla HYC3O (RtHYC3O) enzyme with ligands, generated in MOE.

All XYZ files contain Cartesian atomic coordinates for enzyme–ligand complexes used in substrate docking and structural analyses. These are intended for reuse in molecular modeling workflows.

Variable and file definitions

• .gff3 annotation file
  • seqid: Chromosome or scaffold identifier
  • source: Annotation source (GeMoMa)
  • type: Feature type (e.g., gene, mRNA, exon, CDS)
  • start, end: Genomic coordinates (base pairs)
  • score: Alignment/annotation score (NA if not applicable)
  • strand: + / – strand
  • phase: CDS phase (0–2; NA if not CDS)
  • attributes: Gene ID, transcript ID, functional annotations
• .xyz coordinate files
  • ATOM: List of atoms in the modeled complex
  • X, Y, Z: Cartesian coordinates (Ångströms)
  • element: Atomic symbol (C, N, O, H, etc.)
  • Each file corresponds to a specific enzyme–ligand docking pose.

Sharing/Access information

• Genome assembly reference: Rauvolfia tetraphylla genome (ASM3051222v1) is publicly available on NCBI.
• Experimental context and analyses are described in the associated publication.

Code/Software

• Genome annotation: Generated with GeMoMa (v1.9). Open-source software available at: https://github.com/JStrozzi/GeMoMa.
• Molecular modeling and docking: Performed using Molecular Operating Environment (MOE), 2022.02 (Chemical Computing Group Inc.).
• Viewing files:
  • .gff3: Open with any genome browser or text editor (e.g., IGV, Apollo, Artemis, or command-line parsing).
  • .xyz: Can be viewed with free/open-source molecular visualization tools, such as PyMOL (open-source edition), Avogadro, or VMD.

Notes for reuse

• The .gff3 annotation is specific to the R. tetraphylla genome assembly ASM3051222v1 and may not align properly to other assemblies.
• XYZ coordinate files represent modeled docking poses; they are not experimentally determined structures. They can be used as starting points for comparative docking, energy minimization, or structural refinement.
• No additional preprocessing is required to use these files.