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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.
Details
; Ashkenazy, Haim 2
; Kornienko, Aleksandra E. 1 ; Fitz, Joffrey 2
; Collenberg, Max 2 ; Kubica, Christian 2
; Mollá Morales, Almudena 1
; Jaegle, Benjamin 1 ; Wrightsman, Travis 2 ; Voloshin, Vitaly 3
; Bezlepsky, Alexander D. 4 ; Llaca, Victor 5
; Nizhynska, Viktoria 1 ; Reichardt, Ilka 1
; Bezrukov, Ilja 2 ; Lanz, Christa 2 ; Bemm, Felix 2 ; Flood, Pádraic J. 6
; Nemomissa, Sileshi 7 ; Hancock, Angela 6
; Guo, Ya-Long 8
; Kersey, Paul 3 ; Weigel, Detlef 9
; Nordborg, Magnus 1
1 Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria (ROR: https://ror.org/03anc3s24) (GRID: grid.4299.6) (ISNI: 0000 0001 2169 3852)
2 Max Planck Institute for Biology Tübingen, Tübingen, Germany (ROR: https://ror.org/0243gzr89) (GRID: grid.419580.1) (ISNI: 0000 0001 0942 1125)
3 Royal Botanic Gardens Kew, London, UK (ROR: https://ror.org/00ynnr806) (GRID: grid.4903.e) (ISNI: 0000 0001 2097 4353)
4 All-Russian Research Institute of Agricultural Microbiology, Saint Petersburg, Russia (ROR: https://ror.org/01f02ww36) (GRID: grid.466463.5) (ISNI: 0000 0004 0445 582X)
5 Corteva Agriscience, Johnston, IA, USA (ROR: https://ror.org/02pm1jf23) (GRID: grid.508744.a) (ISNI: 0000 0004 7642 3544)
6 Max Planck Institute for Plant Breeding Research, Cologne, Germany (ROR: https://ror.org/044g3zk14) (GRID: grid.419498.9) (ISNI: 0000 0001 0660 6765)
7 Addis Ababa University, Addis Ababa, Ethiopia (ROR: https://ror.org/038b8e254) (GRID: grid.7123.7) (ISNI: 0000 0001 1250 5688)
8 Institute of Botany, Chinese Academy of Sciences, Beijing, China (ROR: https://ror.org/034t30j35) (GRID: grid.9227.e) (ISNI: 0000000119573309)
9 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)