Section: Genomics
Topic: Genetics/Genomics, Plant biology

Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks

10.24072/pcjournal.187 - Peer Community Journal, Volume 2 (2022), article no. e68.

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1. Mutation, the source of genetic diversity, is the raw material of evolution; however, the mutation process remains understudied, especially in plants. Using both a simulation and reanalysis framework, we set out to explore and demonstrate the improved performance of variant callers developed for cancer research compared to single nucleotide polymorphism (SNP) callers in detecting de novo somatic mutations.

2. In an in silico experiment, we generated Illumina-like sequence reads spiked with simulated mutations at different allelic fractions to compare the performance of seven commonly-used variant callers to recall them. More empirically, we then reanalyzed two of the largest datasets available for plants, both developed for identifying within-individual variation in long-lived pedunculate oaks.

3. Based on the in silico experiment, variant callers developed for cancer research outperform SNP callers regarding plant mutation recall and precision, especially at low allele frequency. Such variants at low allelic fractions are typically expected for within-individual de novo plant mutations, which initially appear in single cells. Reanalysis of published oak data with Strelka2, the best-performing caller based on our simulations, identified up to 3.4x more candidate somatic mutations than reported in the original studies.

4. Our results advocate the use of cancer research callers to boost de novo mutation research in plants, and to reconcile empirical reports with theoretical expectations.

Published online:
DOI: 10.24072/pcjournal.187
Type: Research article

Schmitt, Sylvain 1; Leroy, Thibault 2, 3; Heuertz, Myriam 4; Tysklind, Niklas 5

1 CNRS, UMR EcoFoG (Agroparistech, Cirad, INRAE, Université des Antilles, Université de la Guyane), Campus Agronomique, 97310 Kourou, French Guiana
2 Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
3 IRHS-UMR1345, Université d’Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouzé, France
4 Université Bordeaux, INRAE, BIOGECO, 69 route d’Arcachon, CS 80227, 33612 Cestas Cedex, France
5 INRAE, UMR EcoFoG (Agroparistech, CNRS, Cirad, Université des Antilles, Université de la Guyane), Campus Agronomique, 97310 Kourou, French Guiana
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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     title = {Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks},
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%A Leroy, Thibault
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Schmitt, Sylvain; Leroy, Thibault; Heuertz, Myriam; Tysklind, Niklas. Somatic mutation detection: a critical evaluation through simulations and reanalyses in oaks. Peer Community Journal, Volume 2 (2022), article  no. e68. doi : 10.24072/pcjournal.187.

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.genomics.100024

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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