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

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.

SUBMITTER: Khan A

PROVIDER: S-EPMC4932600 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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

Khan Amina A Belfield Eric J EJ Harberd Nicholas P NP Mithani Aziz A

Scientific reports 20160705

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 genu ...[more]

PMID: 27378447

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