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A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism

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Publicado en:Nature Genetics vol. 57, no. 9 (Sep 2025), p. 2289-2319
Autor principal: Igolkina, Anna A.
Otros Autores: Vorbrugg, Sebastian, Rabanal, Fernando A., Liu, Hai-Jun, Ashkenazy, Haim, Kornienko, Aleksandra E., Fitz, Joffrey, Collenberg, Max, Kubica, Christian, Mollá Morales, Almudena, Jaegle, Benjamin, Wrightsman, Travis, Voloshin, Vitaly, Bezlepsky, Alexander D., Llaca, Victor, Nizhynska, Viktoria, Reichardt, Ilka, Bezrukov, Ilja, Lanz, Christa, Bemm, Felix, Flood, Pádraic J., Nemomissa, Sileshi, Hancock, Angela, Guo, Ya-Long, Kersey, Paul, Weigel, Detlef, Nordborg, Magnus
Publicado:
Nature Publishing Group
Materias:
Transcriptomes
Polymorphism
Gene polymorphism
Genomes
Gene mapping
Chromosomes
Mapping
Single-nucleotide polymorphism
Inbreeding
Satellites
Coordinates
Arabidopsis thaliana
Environmental
Acceso en línea:Citation/Abstract
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024 7 |a 10.1038/s41588-025-02293-0  |2 doi 
035 |a 3249515583 
045 2 |b d20250901  |b d20250930 
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100 1 |a Igolkina, Anna A.  |u Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852) 
245 1 |a A comparison of 27 <i>Arabidopsis thaliana</i> genomes and the path toward an unbiased characterization of genetic polymorphism 
260 |b Nature Publishing Group  |c Sep 2025 
513 |a Journal Article 
520 3 |a Making sense of whole-genome polymorphism data is challenging, but it is essential for overcoming the biases in SNP data. Here we analyze 27 genomes of Arabidopsis thaliana to illustrate these issues. Genome size variation is mostly due to tandem repeat regions that are difficult to assemble. However, while the rest of the genome varies little in length, it is full of structural variants, mostly due to transposon insertions. Because of this, the pangenome coordinate system grows rapidly with sample size and ultimately becomes 70% larger than the size of any single genome, even for n = 27. Finally, we show how short-read data are biased by read mapping. SNP calling is biased by the choice of reference genome, and both transcriptome and methylome profiling results are affected by mapping reads to a reference genome rather than to the genome of the assayed individual.New concepts for comparing the genomes of 27 naturally inbred Arabidopsis thaliana accessions provide essential insights into obtaining a less biased view of whole-genome polymorphism. 
653 |a Transcriptomes 
653 |a Polymorphism 
653 |a Gene polymorphism 
653 |a Genomes 
653 |a Gene mapping 
653 |a Chromosomes 
653 |a Mapping 
653 |a Single-nucleotide polymorphism 
653 |a Inbreeding 
653 |a Satellites 
653 |a Coordinates 
653 |a Arabidopsis thaliana 
653 |a Environmental 
700 1 |a Vorbrugg, Sebastian  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Rabanal, Fernando A.  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Liu, Hai-Jun  |u Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852) 
700 1 |a Ashkenazy, Haim  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Kornienko, Aleksandra E.  |u Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852) 
700 1 |a Fitz, Joffrey  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Collenberg, Max  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Kubica, Christian  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Mollá Morales, Almudena  |u Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852) 
700 1 |a Jaegle, Benjamin  |u Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852) 
700 1 |a Wrightsman, Travis  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Voloshin, Vitaly  |u Royal Botanic Gardens Kew, London, UK (ROR: https://ror.org/00ynnr806) (GRID: grid.4903.e) (ISNI: 0000 0001 2097 4353) 
700 1 |a Bezlepsky, Alexander D.  |u All-Russian Research Institute of Agricultural Microbiology, Saint Petersburg, Russia (ROR: https://ror.org/01f02ww36) (GRID: grid.466463.5) (ISNI: 0000 0004 0445 582X) 
700 1 |a Llaca, Victor  |u Corteva Agriscience, Johnston, IA, USA (ROR: https://ror.org/02pm1jf23) (GRID: grid.508744.a) (ISNI: 0000 0004 7642 3544) 
700 1 |a Nizhynska, Viktoria  |u Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852) 
700 1 |a Reichardt, Ilka  |u Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852) 
700 1 |a Bezrukov, Ilja  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Lanz, Christa  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Bemm, Felix  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125) 
700 1 |a Flood, Pádraic J.  |u Max Planck Institute for Plant Breeding Research, Cologne, Germany (ROR: https://ror.org/044g3zk14) (GRID: grid.419498.9) (ISNI: 0000 0001 0660 6765) 
700 1 |a Nemomissa, Sileshi  |u Addis Ababa University, Addis Ababa, Ethiopia (ROR: https://ror.org/038b8e254) (GRID: grid.7123.7) (ISNI: 0000 0001 1250 5688) 
700 1 |a Hancock, Angela  |u Max Planck Institute for Plant Breeding Research, Cologne, Germany (ROR: https://ror.org/044g3zk14) (GRID: grid.419498.9) (ISNI: 0000 0001 0660 6765) 
700 1 |a Guo, Ya-Long  |u Institute of Botany, Chinese Academy of Sciences, Beijing, China (ROR: https://ror.org/034t30j35) (GRID: grid.9227.e) (ISNI: 0000000119573309) 
700 1 |a Kersey, Paul  |u Royal Botanic Gardens Kew, London, UK (ROR: https://ror.org/00ynnr806) (GRID: grid.4903.e) (ISNI: 0000 0001 2097 4353) 
700 1 |a Weigel, Detlef  |u Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125); Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany (ROR: https://ror.org/03a1kwz48) (GRID: grid.10392.39) (ISNI: 0000 0001 2190 1447) 
700 1 |a Nordborg, Magnus  |u Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852) 
773 0 |t Nature Genetics  |g vol. 57, no. 9 (Sep 2025), p. 2289-2319 
786 0 |d ProQuest  |t Health & Medical Collection 
856 4 1 |3 Citation/Abstract  |u https://www.proquest.com/docview/3249515583/abstract/embedded/7BTGNMKEMPT1V9Z2?source=fedsrch