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

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

Abstract 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...

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Bibliographic Details
Main Authors: Tim Koorevaar, Johan H. Willemsen, Dominic Hildebrand, Richard G.F. Visser, Paul Arens, Chris Maliepaard
Format: Article
Language:English
Published: BMC 2024-11-01
Series:BMC Genomics
Subjects:
Allopolyploid
Strawberry
Fragaria x ananassa
Linkage disequilibrium
Average allele balance
Whole genome sequencing
Online Access:https://doi.org/10.1186/s12864-024-10987-8
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https://doi.org/10.1186/s12864-024-10987-8

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