Dramatic improvement in genome assembly achieved using doubled-haploid genomes

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled...

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Autores principales: Zhang, Hong, Tan, Engkong, Suzuki, Yutaka, Hirose, Yusuke, Kinoshita, Shigeharu, Okano, Hideyuki, Kudoh, Jun, Shimizu, Atsushi, Saito, Kazuyoshi, Watabe, Shugo, Asakawa, Shuichi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2014
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381364/
https://www.ncbi.nlm.nih.gov/pubmed/25345569
http://dx.doi.org/10.1038/srep06780
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author Zhang, Hong
Tan, Engkong
Suzuki, Yutaka
Hirose, Yusuke
Kinoshita, Shigeharu
Okano, Hideyuki
Kudoh, Jun
Shimizu, Atsushi
Saito, Kazuyoshi
Watabe, Shugo
Asakawa, Shuichi
author_facet Zhang, Hong
Tan, Engkong
Suzuki, Yutaka
Hirose, Yusuke
Kinoshita, Shigeharu
Okano, Hideyuki
Kudoh, Jun
Shimizu, Atsushi
Saito, Kazuyoshi
Watabe, Shugo
Asakawa, Shuichi
author_sort Zhang, Hong
collection PubMed
description Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.
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spelling pubmed-53813642017-04-11 Dramatic improvement in genome assembly achieved using doubled-haploid genomes Zhang, Hong Tan, Engkong Suzuki, Yutaka Hirose, Yusuke Kinoshita, Shigeharu Okano, Hideyuki Kudoh, Jun Shimizu, Atsushi Saito, Kazuyoshi Watabe, Shugo Asakawa, Shuichi Sci Rep Article Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis. Nature Publishing Group 2014-10-27 /pmc/articles/PMC5381364/ /pubmed/25345569 http://dx.doi.org/10.1038/srep06780 Text en Copyright © 2014, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by/4.0/ 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 in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Zhang, Hong
Tan, Engkong
Suzuki, Yutaka
Hirose, Yusuke
Kinoshita, Shigeharu
Okano, Hideyuki
Kudoh, Jun
Shimizu, Atsushi
Saito, Kazuyoshi
Watabe, Shugo
Asakawa, Shuichi
Dramatic improvement in genome assembly achieved using doubled-haploid genomes
title Dramatic improvement in genome assembly achieved using doubled-haploid genomes
title_full Dramatic improvement in genome assembly achieved using doubled-haploid genomes
title_fullStr Dramatic improvement in genome assembly achieved using doubled-haploid genomes
title_full_unstemmed Dramatic improvement in genome assembly achieved using doubled-haploid genomes
title_short Dramatic improvement in genome assembly achieved using doubled-haploid genomes
title_sort dramatic improvement in genome assembly achieved using doubled-haploid genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5381364/
https://www.ncbi.nlm.nih.gov/pubmed/25345569
http://dx.doi.org/10.1038/srep06780
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