Code for Clusia genomes shed light on the evolution and diversity of CAM physiotypes

Supplementary Code accompanying the manuscript Clusia genomes shed light on the evolution and diversity of CAM physiotypes (Nature Communications, 2026) Final release for publication. Full Changelog (peer-review):https://github.com/hanneskramml/Clusia/compare/Manuscript1_v1.0.0-alpha...Manuscript1_v1.4.1 Content Pipelines and scripts to build and explore the Clusia genome assemblies, annotations, and multiomics analyses. The clusia_panomics_database handles data processing and integration (from raw data to figures and tables). Clusia/ ├── assembly/ # Genome assembly, scaffolding, and ploidy/subgenome identification scripts ├── annotation/ # Pipelines for gene, repeat, and pseudogene annotation ├── comparative_genomics/ # Orthogroup sampling, alignments, features incl. cis-regulatory motifs ├── rnaseq/ # RNA-seq/gene expression workflow ├── greenhouse_experiment/ # Environmental monitoring app written in Python/C (RaspberryPi/Arduino) ├── clusia_panomics_database/ # R pipeline for data processing and integration (figure and table generation) └── README.md # Project documentation A dedicated compute capsule including all dependencies, input data, and final results is published on CodeOcean: https://doi.org/10.24433/CO.2105665.v2