奥地利科学院Magnus Nordborg研究组宣布他们研制了27个拟南芥基因组的比较及其对遗传多态性的无偏定性。该项研究成果发表在2025年8月19日出版的《自然—遗传学》上。

本文通过分析拟南芥的27个基因组来阐明这些问题。基因组大小的变化主要是由于串联重复区域难以组装。

然而，虽然基因组的其余部分长度变化不大，但它充满了结构变异，主要是由于转座子插入。正因为如此，泛基因组坐标系统随着样本量的增加而迅速增长，最终比任何单个基因组的大小都要大70%，即使在n=27时也是如此。最后，该课题组人员展示了短读数据是如何通过读映射产生偏差的。SNP调用受参考基因组选择的影响，转录组和甲基组分析结果都受到参考基因组而不是被测个体基因组的定位读数的影响。

据介绍，理解全基因组多态性数据具有挑战性，但对于克服SNP数据的偏差至关重要。

附：英文原文

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

Author: Igolkina, Anna A., Vorbrugg, Sebastian, Rabanal, Fernando A., Liu, Hai-Jun, Ashkenazy, Haim, Kornienko, Aleksandra E., Fitz, Joffrey, Collenberg, Max, Kubica, Christian, Moll Morales, Almudena, Jaegle, Benjamin, Wrightsman, Travis, Voloshin, Vitaly, Bezlepsky, Alexander D., Llaca, Victor, Nizhynska, Viktoria, Reichardt, Ilka, Bezrukov, Ilja, Lanz, Christa, Bemm, Felix, Flood, Pdraic J., Nemomissa, Sileshi, Hancock, Angela, Guo, Ya-Long, Kersey, Paul, Weigel, Detlef, Nordborg, Magnus

Issue&Volume: 2025-08-19

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 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.

DOI: 10.1038/s41588-025-02293-0

Source: https://www.nature.com/articles/s41588-025-02293-0