A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.
Name
s41588-025-02293-0__1_.pdf
Description
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Size
19.68 MB
Format
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Resource type
Journal article
Creator (person)
Igolkina, Anna A.
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
Date published
August 19, 2025
Abstract
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 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 = 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.
Project(s)
Priority 2: Trait Diversity and Function
Funder
| Funder name | Awards |
Max-Planck-Gesellschaft, Germany | Open access funding |
Journal title
Nature Genetics
Publisher
Springer Science and Business Media LLC
Place of publication
Berlin/Heidelberg, Germany
ISSN
1061-4036
eISSN
1546-1718
Date accepted
July 10, 2025
Official URL
Rights statement
In Copyright
Additional information
IF = 29.0 (2024)