simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants
- 1Technical University of Munich
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.
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BibTeX
@misc{johannes2026simsoma,
title = {{simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants}},
author = {F. Johannes},
howpublished = {bioRxiv},
year = {2026},
month = jun,
doi = {10.64898/2026.06.28.735079},
url = {https://www.biorxiv.org/content/10.64898/2026.06.28.735079v2},
note = {CC BY},
}
RIS
TY - UNPB
TI - simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants
AU - F. Johannes
PY - 2026
DA - 2026/06/28
PB - bioRxiv
DO - 10.64898/2026.06.28.735079
UR - https://www.biorxiv.org/content/10.64898/2026.06.28.735079v2
AB - 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.
ER -