Skip to main content
Figure 1 | BMC Genetics

Figure 1

From: Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms

Figure 1

Methods for read categorization. In all images, red lines represent the A-genome while blue lines represent the D-genome. Idealized forms of these methods are shown, ignoring structural differences, perfect conservation, and other sources of complication and error. With PolyCat, (a) homoeo-SNPs are first identified between the consensus sequences for already known A- and D-genome reads. Then all reads are mapped to a single reference sequence (A-genome in the example) and PolyCat categorizes them by source genome. With the full reference method (b), reads are mapped to a concatenation of the A- and D-genome reference sequences, so reads will naturally map to the part of the reference that represents its appropriate genome. With PolyDog (c), the same set of reads from an allotetraploid is mapped to both the A- and D-genome references. Then PolyDog examines each pair of mappings and categorizes that read to its genome of origin.

Back to article page