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

BMC Genomics

Methodology Article

Caifu Jiang¹  Nicholas P Harberd¹  Carly Brown¹  Eric J Belfield¹  Aziz Mithani²  Lindsey J Leach³ 

[1] Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK;Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK;Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, D.H.A., 54792, Lahore, Pakistan;Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, Oxford, UK;School of Biosciences, University of Birmingham, B15 2TT, Edgbaston, Birmingham, UK;

关键词: Next-generation sequencing;    RNA-seq;    Polyploidy;    Wheat;    Base-identity;   

DOI  :  10.1186/1471-2164-14-653

 received in 2013-05-21, accepted in 2013-09-18,  发布年份 2013

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Mithani et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.