Minimizing detection bias of somatic mutations in a highly heterozygous oak genome

Somatic mutations are particularly relevant for long-lived organisms. Sources of somatic mutations include imperfect DNA repair, replication errors, and exogenous damage such as ultraviolet radiation. A previous study estimated a surprisingly low number of somatic mutations in a 234-year-old individ...

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Detalles Bibliográficos
Autores: Xian, Wenfei, Carbonell-Bejerano, Pablo [0000-0002-7266-9665], Rabanal, Fernando A., Bezrukov, Ilja, Reymond, Philippe, Weigel, Detlef
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Universidad de La Rioja (UR)
Repositorio:RIUR. Repositorio Institucional de la Universidad de La Rioja
OAI Identifier:oai:portal.dialnet.es:doc/68b33d7d2f359d6e8f724e4f
Acceso en línea:https://investigacion.unirioja.es/documentos/68b33d7d2f359d6e8f724e4f
Access Level:acceso abierto
Palabra clave:Quercus robur
HiFi assembly
Somatic mutations
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spelling Minimizing detection bias of somatic mutations in a highly heterozygous oak genomeXian, WenfeiCarbonell-Bejerano, Pablo [0000-0002-7266-9665]Rabanal, Fernando A.Bezrukov, IljaReymond, PhilippeWeigel, DetlefQuercus roburHiFi assemblySomatic mutationsSomatic mutations are particularly relevant for long-lived organisms. Sources of somatic mutations include imperfect DNA repair, replication errors, and exogenous damage such as ultraviolet radiation. A previous study estimated a surprisingly low number of somatic mutations in a 234-year-old individual of the pedunculate oak (Quercus robur), known as the Napoleon Oak. It has been suggested that the true number of somatic mutations was underestimated due to gaps in the reference genome and too conservative filtering of potential mutations. We therefore generated new high-fidelity long-read data for the Napoleon Oak (n = 12) to produce both a pseudo-haploid genome assembly and a partially phased diploid assembly. The high heterozygosity allowed for complete reconstruction of phased and gapless centromeres for 22 of the 24 chromosomes. On the other hand, the high heterozygosity posed challenges for short-read alignments. Use of only the pseudo-haploid assembly as a reference led to potential misalignments, while use of only the diploid assembly reduced variant detection sensitivity. Since most somatic mutations are layer-specific, the fraction of reads covering a specific somatic mutation is expected to be relatively low, even where all cells in a single layer contain a specific mutation. To address this challenge, we employed a read assignment strategy, selecting the appropriate reference sequence (pseudo-haploid or diploid) based on alignment score and mapping quality. Ultimately, we identified 198 high-confidence somatic mutations, compared with 17 somatic mutations identified before with the same set of short reads. Our approach thus increased the total estimated annual mutation rate by a factor of 5.2025info:eu-repo/semantics/articleSubtype: Articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://investigacion.unirioja.es/documentos/68b33d7d2f359d6e8f724e4freponame:RIUR. Repositorio Institucional de la Universidad de La Riojainstname:Universidad de La Rioja (UR)Inglésinfo:eu-repo/semantics/altIdentifier/doi/10.1093/G3JOURNAL/JKAF143info:eu-repo/semantics/altIdentifier/pmid/40543050info:eu-repo/semantics/altIdentifier/eissn/2160-1836Minimizing detection bias of somatic mutations in a highly heterozygous oak genome, 2025, vol. 15, núm. 8info:eu-repo/semantics/openAccessoai:portal.dialnet.es:doc/68b33d7d2f359d6e8f724e4f2026-06-14T12:47:17Z
dc.title.none.fl_str_mv Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
title Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
spellingShingle Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
Xian, Wenfei
Quercus robur
HiFi assembly
Somatic mutations
title_short Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
title_full Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
title_fullStr Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
title_full_unstemmed Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
title_sort Minimizing detection bias of somatic mutations in a highly heterozygous oak genome
dc.creator.none.fl_str_mv Xian, Wenfei
Carbonell-Bejerano, Pablo [0000-0002-7266-9665]
Rabanal, Fernando A.
Bezrukov, Ilja
Reymond, Philippe
Weigel, Detlef
author Xian, Wenfei
author_facet Xian, Wenfei
Carbonell-Bejerano, Pablo [0000-0002-7266-9665]
Rabanal, Fernando A.
Bezrukov, Ilja
Reymond, Philippe
Weigel, Detlef
author_role author
author2 Carbonell-Bejerano, Pablo [0000-0002-7266-9665]
Rabanal, Fernando A.
Bezrukov, Ilja
Reymond, Philippe
Weigel, Detlef
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Quercus robur
HiFi assembly
Somatic mutations
topic Quercus robur
HiFi assembly
Somatic mutations
description Somatic mutations are particularly relevant for long-lived organisms. Sources of somatic mutations include imperfect DNA repair, replication errors, and exogenous damage such as ultraviolet radiation. A previous study estimated a surprisingly low number of somatic mutations in a 234-year-old individual of the pedunculate oak (Quercus robur), known as the Napoleon Oak. It has been suggested that the true number of somatic mutations was underestimated due to gaps in the reference genome and too conservative filtering of potential mutations. We therefore generated new high-fidelity long-read data for the Napoleon Oak (n = 12) to produce both a pseudo-haploid genome assembly and a partially phased diploid assembly. The high heterozygosity allowed for complete reconstruction of phased and gapless centromeres for 22 of the 24 chromosomes. On the other hand, the high heterozygosity posed challenges for short-read alignments. Use of only the pseudo-haploid assembly as a reference led to potential misalignments, while use of only the diploid assembly reduced variant detection sensitivity. Since most somatic mutations are layer-specific, the fraction of reads covering a specific somatic mutation is expected to be relatively low, even where all cells in a single layer contain a specific mutation. To address this challenge, we employed a read assignment strategy, selecting the appropriate reference sequence (pseudo-haploid or diploid) based on alignment score and mapping quality. Ultimately, we identified 198 high-confidence somatic mutations, compared with 17 somatic mutations identified before with the same set of short reads. Our approach thus increased the total estimated annual mutation rate by a factor of 5.
publishDate 2025
dc.date.none.fl_str_mv 2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
Subtype: Article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://investigacion.unirioja.es/documentos/68b33d7d2f359d6e8f724e4f
url https://investigacion.unirioja.es/documentos/68b33d7d2f359d6e8f724e4f
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1093/G3JOURNAL/JKAF143
info:eu-repo/semantics/altIdentifier/pmid/40543050
info:eu-repo/semantics/altIdentifier/eissn/2160-1836
Minimizing detection bias of somatic mutations in a highly heterozygous oak genome, 2025, vol. 15, núm. 8
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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dc.source.none.fl_str_mv reponame:RIUR. Repositorio Institucional de la Universidad de La Rioja
instname:Universidad de La Rioja (UR)
instname_str Universidad de La Rioja (UR)
reponame_str RIUR. Repositorio Institucional de la Universidad de La Rioja
collection RIUR. Repositorio Institucional de la Universidad de La Rioja
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