Journal article
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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 802.1KB, Terms of use)
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- Publisher copy:
- 10.1038/srep29234
Authors
- Publisher:
- Nature Publishing Group
- Journal:
- Scientific Reports More from this journal
- Volume:
- 6
- Article number:
- 29234
- Publication date:
- 2016-07-05
- Acceptance date:
- 2016-06-14
- DOI:
- EISSN:
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2045-2322
- ISSN:
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2045-2322
- Pubs id:
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pubs:629164
- UUID:
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uuid:94ca5eda-65ea-40f4-9dfe-d7dec015f6c2
- Local pid:
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pubs:629164
- Source identifiers:
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629164
- Deposit date:
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2016-06-21
Terms of use
- Copyright holder:
- © Khan et al 2018
- Copyright date:
- 2016
- Notes:
- This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
- Licence:
- CC Attribution (CC BY)
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