Open Access Open Badges Methodology article

HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids

Aziz Mithani12, Eric J Belfield1, Carly Brown1, Caifu Jiang1, Lindsey J Leach13 and Nicholas P Harberd1*

Author Affiliations

1 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK

2 Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, D.H.A., Lahore 54792, Pakistan

3 School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK

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BMC Genomics 2013, 14:653  doi:10.1186/1471-2164-14-653

Published: 24 September 2013



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.


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.


We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics.

Next-generation sequencing; RNA-seq; Polyploidy; Wheat; Base-identity