HANDS: a tool for genome-wide discovery of subgenome- specific base-identity in polyploidsReport as inadecuate




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BMC Genomics

, 14:653

Plant genomics

Abstract

BackgroundThe 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.

ResultsWe 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.

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

KeywordsNext-generation sequencing RNA-seq Polyploidy Wheat Base-identity Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-653 contains supplementary material, which is available to authorized users.

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Author: Aziz Mithani - Eric J Belfield - Carly Brown - Caifu Jiang - Lindsey J Leach - Nicholas P Harberd

Source: https://link.springer.com/







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