Mutation in the tropical tree canopy.
My analyses and participation as a postdoc in the TreeMutation project that led to the following publications:
- Schmitt, S., Heuret, P., Troispoux, V., Beraud, M., Cazal, J., Chancerel, É., ... & Tysklind, N. (2024). Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra. Proceedings of the National Academy of Sciences, 121(10), e2313312121. 10.1073/pnas.2313312121
- Schmitt, S., Leroy, T., Heuertz, M., & Tysklind, N. (2022). Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks. Peer Community Journal, 2. 10.24072/pcjournal.187
Have a nice reading.
Sylvain
Links and statistics can be found (not exhaustive) on Altmetric.
- First paper peer-review
- First paper preprint (with version history)
- Second paper preprint (with version history)
- The Conversation (french 🇫🇷)
- Sciences et Vies (french 🇫🇷)
- Technology Networks
- Science Mag
- Bioengineer
- France Culture (coming soon, french 🇫🇷)
- Natura Sciences (coming soon, french 🇫🇷)
- INRAE (french 🇫🇷)
- CIRAD (french 🇫🇷)
- CNRS (french 🇫🇷)
- CEBA (french 🇫🇷)
- INRAE first paper (french 🇫🇷)
All codes have been summarised in a single repository sylvainschmitt/treemutation_codes. This repository includes:
- genomeAnnotation: singularity & snakemake workflow to annotate genomes transposable elements (TE) and genes
- detectMutations - Angela: singularity & snakemake workflow to detect mutation with Strelka2 in the D. guianensis tree
- detectMutations - Sixto: singularity & snakemake workflow to detect mutation with Strelka2 in the S. rubra tree
- detectMutations - fruits: singularity & snakemake workflow to detect mutation with GATK in the fruits of the D. guianensis and the S. rubra trees
- treemutation: R code for all the project and manuscript analyses (this repository)
Genomic and transcriptomic reads from leaf, cambium, and fruits and corresponding genomes are available in GenBank. Results and intermediary files are available on Zenodo.