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

Handle URI:
http://hdl.handle.net/10754/596788
Title:
HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.
Authors:
Mithani, Aziz; Belfield, Eric J; Brown, Carly; Jiang, Caifu; Leach, Lindsey J; Harberd, Nicholas P
Abstract:
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.
Citation:
Mithani A, Belfield EJ, Brown C, Jiang C, Leach LJ, et al. (2013) HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids. BMC Genomics 14: 653. Available: http://dx.doi.org/10.1186/1471-2164-14-653.
Publisher:
Springer Nature
Journal:
BMC Genomics
KAUST Grant Number:
KUK-I1-002-03
Issue Date:
24-Sep-2013
DOI:
10.1186/1471-2164-14-653
PubMed ID:
24063258
PubMed Central ID:
PMC3849207
Type:
Article
ISSN:
1471-2164
Sponsors:
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.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorMithani, Azizen
dc.contributor.authorBelfield, Eric Jen
dc.contributor.authorBrown, Carlyen
dc.contributor.authorJiang, Caifuen
dc.contributor.authorLeach, Lindsey Jen
dc.contributor.authorHarberd, Nicholas Pen
dc.date.accessioned2016-02-21T08:50:41Zen
dc.date.available2016-02-21T08:50:41Zen
dc.date.issued2013-09-24en
dc.identifier.citationMithani A, Belfield EJ, Brown C, Jiang C, Leach LJ, et al. (2013) HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids. BMC Genomics 14: 653. Available: http://dx.doi.org/10.1186/1471-2164-14-653.en
dc.identifier.issn1471-2164en
dc.identifier.pmid24063258en
dc.identifier.doi10.1186/1471-2164-14-653en
dc.identifier.urihttp://hdl.handle.net/10754/596788en
dc.description.abstractThe 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.en
dc.description.sponsorshipThis 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.en
dc.publisherSpringer Natureen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subject.meshDiploidyen
dc.subject.meshPolyploidyen
dc.subject.meshPolymorphism, Geneticen
dc.titleHANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.en
dc.typeArticleen
dc.identifier.journalBMC Genomicsen
dc.identifier.pmcidPMC3849207en
dc.contributor.institutionDepartment of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK. nicholas.harberd@plants.ox.ac.uk.en
kaust.grant.numberKUK-I1-002-03en

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