ArticleBMC genomics2013
HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids.Briefings in bioinformatics · 2021Review
- Current Strategies of Polyploid Plant Genome Sequence Assembly.Frontiers in plant science · 2018Review
- HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data.Scientific reports · 2016Article
- Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers.Molecular ecology · 2016Article
- Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms.BMC genetics · 2015Article
- Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.BMC genomics · 2014Article
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
6 authors.
Funding
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.
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Registered trials
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