HANDS2: Accurate assignment of homoeallelic base-identity in allopolyploids despite missing data

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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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Khan, A., Belfield, E. J., Harberd, N. P., & Mithani, A. (2016). HANDS2: Accurate assignment of homoeallelic base-identity in allopolyploids despite missing data. Scientific Reports, 6. https://doi.org/10.1038/srep29234

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