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.
Bibliographical noteKAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): KUK-I1-002-03
Acknowledgements: This publication is based on work supported by Award No. KUK-I1-002-03, made by King Abdullah University of Science and Technology (KAUST). We thank Steve Reader, John Innes Centre, Norwich, UK, for supply of wheat lines, and David Buck, the Head of Genomic Services, and his team at the Wellcome Trust Centre for Human Genetics, Oxford, UK with advice and help regarding Illumina sequencing.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.