ArticleScientific reports2016
HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Review
- Subgenome evolution in allotetraploid plants.The Plant journal : for cell and molecular biology · 2021Article
- Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids.Briefings in bioinformatics · 2021Review
- Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics.Scientific reports · 2018Article
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
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Authors and funding
4 authors.
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Abstract
Characterization of homoeallelic base-identity in allopolyploids is difficult since homeologous subgenomes are closely related and becomes further challenging if diploid-progenitor data is missing. We present HANDS2, a next-generation sequencing-based tool that enables highly accurate (>90%) genome-wide discovery of homeolog-specific base-identity in allopolyploids even in the absence of a diploid-progenitor. We applied HANDS2 to the transcriptomes of various cruciferous plants belonging to genus Brassica. Our results suggest that the three C genomes in Brassica are more similar to each other than the three A genomes, and provide important insights into the relationships between various Brassica tetraploids and their diploid-progenitors at a single-base resolution.
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