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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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Izdano u:Nature Genetics vol. 57, no. 9 (Sep 2025), p. 2289-2319
Glavni autor: Igolkina, Anna A.
Daljnji autori: 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
Izdano:
Nature Publishing Group
Teme:
Transcriptomes
Polymorphism
Gene polymorphism
Genomes
Gene mapping
Chromosomes
Mapping
Single-nucleotide polymorphism
Inbreeding
Satellites
Coordinates
Arabidopsis thaliana
Environmental
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Sažetak: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.
ISSN:1061-4036
1546-1718
Digitalni identifikator objekta:10.1038/s41588-025-02293-0
Izvor:Health & Medical Collection