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Article

How to handle high subgenome sequence similarity in allopolyploid Fragaria x ananassa: linkage disequilibrium based variant filtering.

BMC genomics - 28 Nov 2024

Koorevaar Tim, Willemsen Johan H, Hildebrand Dominic, Visser Richard G F, Arens Paul, Maliepaard Chris

Abstract excerpt

BACKGROUND: The allo-octoploid Fragaria x ananassa follows disomic inheritance, yet the high sequence similarity among its subgenomes can lead to misalignment of short sequencing reads (150 bp). This misalignment results in an increased number of erroneous variants during variant calling. To accurately associate traits with the appropriate subgenome, it is essential to filter out these erroneous variants. By...

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PMID: 39609731
DOI: 10.1186/s12864-024-10987-8
PMCID: PMC11606298

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