Year: 2026
Type: preprint
Abstract: Plants accumulate somatic mutations during growth, some of which spread into branches, organs, or reproductive tissues. These variants are of growing interest because they underlie bud-sport traits in perennial crops, contribute to within-organism selection, and are a source of heritable genetic variation. Recent genomic sequencing of bulk or layer-enriched plant tissues has revealed complex variant allele-frequency (VAF) spectra. Interpreting these spectra requires modelling how somatic mutations are filtered or amplified by shoot growth, branching, and organ formation, a problem that is difficult to derive analytically. Here, we present simSOMA, a modular simulator linking plant topologies to shoot apical meristem cell-lineage dynamics. simSOMA models mutation accumulation during stem-cell self-renewal, clonal expansion to the meristem periphery, branch founding, and organ formation. We demonstrate how simSOMA isolates developmental processes that shape organ-level VAF spectra and among-organ variant sharing, and transforms spectra for bulk or layer-enriched sampling, phased or unphased readouts, and read-level sequencing noise. SAM layers can be simulated as independent cell lineages and combined into bulk tissue samples. simSOMA can be used to explore developmental hypotheses about the origin of somatic variation, and to design somatic sequencing experiments and variant-detection strategies. simSOMA is available at https://github.com/jlab-code/simSOMA .
Author: Frank Johannes
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7167025349