HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.
BACKGROUND
The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies.


RESULTS
We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): 'HSP base Assignment using NGS data through Diploid Similarity' (HANDS). We show that HANDS correctly predicts subgenome-specific base-identity at >90% of assayed HSPs in the hexaploid bread wheat (Triticum aestivum) transcriptome, thus providing a substantial increase in accuracy versus previous methods for homeolog-specific base assignment.


CONCLUSIONS
We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics.
Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. nicholas.harberd@plants.ox.ac.uk.
Aziz
A
Mithani
Eric J
EJ
Belfield
Carly
C
Brown
Caifu
C
Jiang
Lindsey J
LJ
Leach
Nicholas P
NP
Harberd
D001483:Base Sequence; D001939:Bread; D032461:Chromosomes, Plant / Q000235:genetics; D004171:Diploidy; D018745:Genome, Plant / Q000235:genetics*; D011110:Polymorphism, Genetic; D011123:Polyploidy; D017422:Sequence Analysis, DNA / Q000379:methods*; D014908:Triticum / Q000235:genetics*