Mosaicism in old trees and its patterns

Zahradníková, Eva; Ficek, Andrej; Brejová, Bronislava; Vinař, Tomáš; Mičieta, Karol

doi:10.1007/s00468-019-01921-7

Cited by 18 publications

(14 citation statements)

References 28 publications

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“…2018, we further filtered out candidate somatic mutations by using a cross-validation procedure to keep a coherent temporal pattern among mutations following the original publication (Plomion et al ., 2018). Contrary to a general expectation and a common view in the field (Schmid-Siegert et al ., 2017, Orr et al ., 2019), detected mutations do not always accumulate following the developing plant architecture (Zahradníková et al ., 2020; Ren et al ., 2021). As a consequence, our cross-validation represents a conservative strategy for the mutation detection, but it should be noted that this strategy could have removed some true somatic mutations.…”

Section: Methodsmentioning

confidence: 99%

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

Schmitt

Leroy²,

Heuertz³

et al. 2021

Preprint

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Mutation, the source of genetic diversity, is the raw material of evolution; however, it remains an understudied process in plants. Using simulations, we demonstrate that generic variant callers, commonly used to detect mutations in plants, are outperformed by methods developed for cancer research. Reanalysis of published data identified up to 7x more somatic mutations than initially reported, advocating the use of cancer research callers to boost mutation research in plants.

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Section: Methodsmentioning

confidence: 99%

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

Schmitt

Leroy²,

Heuertz³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…For the data from Plomion et al 2018, we further filtered out candidate somatic mutations by using a crossvalidation procedure to keep a coherent temporal pattern among mutations following the original publication (Plomion et al, 2018). Contrary to a general expectation and a common view in the field (Schmid-Siegert et al, 2017, Orr et al, 2019, detected mutations do not always accumulate following the developing plant architecture (Zahradníková et al, 2020;Ren et al, 2021). As a consequence, our crossvalidation represents a conservative strategy for the mutation detection, but it should be noted that this strategy could have removed some true somatic mutations.…”

Section: Oak Data Reanalysesmentioning

confidence: 99%

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

Schmitt¹,

Leroy²,

Heuertz³

et al. 2022

Peer Community Journal

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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 withinindividual variation in long-lived pedunculate oaks. 3. Based on thein 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.

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“…However, the pattern of chimerism doesn't have to follow the branching of the tree and depends on the layering of meristems and patterns of branching (Fig. 1, from Zahradníková et al 2020). and type of branching.…”

Section: Technologie Pěstebních Opatřenímentioning

confidence: 99%

Významné stromy ve venkovské krajině: Sborník z konference

2022

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Ľudové piesne odzrkadľujú vzájomný vzťah medzi človekom a prírodou a predstavujú významný zdroj etnobiologických informácií. V príspevku sú predstavené najvýznamnejšie stromy v ľudových piesňach Slovenska, ich symbolický význam, aj praktické využitie. Cel kovo bolo analyzovaných 4 341 slovenských ľudových piesní. Stromy boli spomínané v 14 % pie sní, pričom bolo identifikovaných 31 rastlinných druhov a rodov (24 voľne rastúcich a 8 pestovaných), ktoré patria do 12 rastlinných čeľadí. Najviac spomínanými boli javor, dub, jabloň, lipa a buk. Ľudové piesne prispievajú k zachovaniu tradičných ekologických poznatkov a pomáhajú lepšie pochopiť dávny vzťah našich predkov k prírode.

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Mosaicism in old trees and its patterns

Cited by 18 publications

References 28 publications

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

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

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

Významné stromy ve venkovské krajině: Sborník z konference

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