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Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data
Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Nature Publishing Group
2016
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020871/ https://www.ncbi.nlm.nih.gov/pubmed/27622467 http://dx.doi.org/10.1038/sdata.2016.76 |
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| author | Zhang, Jianwei Chen, Ling-Ling Sun, Shuai Kudrna, Dave Copetti, Dario Li, Weiming Mu, Ting Jiao, Wen-Biao Xing, Feng Lee, Seunghee Talag, Jayson Song, Jia-Ming Du, Bogu Xie, Weibo Luo, Meizhong Maldonado, Carlos Ernesto Goicoechea, Jose Luis Xiong, Lizhong Wu, Changyin Xing, Yongzhong Zhou, Dao-xiu Yu, Sibin Zhao, Yu Wang, Gongwei Yu, Yeisoo Luo, Yijie Hurtado, Beatriz Elena Padilla Danowitz, Ann Wing, Rod A. Zhang, Qifa |
| author_facet | Zhang, Jianwei Chen, Ling-Ling Sun, Shuai Kudrna, Dave Copetti, Dario Li, Weiming Mu, Ting Jiao, Wen-Biao Xing, Feng Lee, Seunghee Talag, Jayson Song, Jia-Ming Du, Bogu Xie, Weibo Luo, Meizhong Maldonado, Carlos Ernesto Goicoechea, Jose Luis Xiong, Lizhong Wu, Changyin Xing, Yongzhong Zhou, Dao-xiu Yu, Sibin Zhao, Yu Wang, Gongwei Yu, Yeisoo Luo, Yijie Hurtado, Beatriz Elena Padilla Danowitz, Ann Wing, Rod A. Zhang, Qifa |
| author_sort | Zhang, Jianwei |
| collection | PubMed |
| description | Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. With these data, we successfully assembled two platinum standard reference genomes that have been publicly released. Here we provide the full sets of raw data used to generate these two reference genome assemblies. These data sets can be used to test new programs for better genome assembly and annotation, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general. |
| format | Online Article Text |
| id | pubmed-5020871 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2016 |
| publisher | Nature Publishing Group |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-50208712016-09-23 Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data Zhang, Jianwei Chen, Ling-Ling Sun, Shuai Kudrna, Dave Copetti, Dario Li, Weiming Mu, Ting Jiao, Wen-Biao Xing, Feng Lee, Seunghee Talag, Jayson Song, Jia-Ming Du, Bogu Xie, Weibo Luo, Meizhong Maldonado, Carlos Ernesto Goicoechea, Jose Luis Xiong, Lizhong Wu, Changyin Xing, Yongzhong Zhou, Dao-xiu Yu, Sibin Zhao, Yu Wang, Gongwei Yu, Yeisoo Luo, Yijie Hurtado, Beatriz Elena Padilla Danowitz, Ann Wing, Rod A. Zhang, Qifa Sci Data Data Descriptor Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. With these data, we successfully assembled two platinum standard reference genomes that have been publicly released. Here we provide the full sets of raw data used to generate these two reference genome assemblies. These data sets can be used to test new programs for better genome assembly and annotation, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general. Nature Publishing Group 2016-09-13 /pmc/articles/PMC5020871/ /pubmed/27622467 http://dx.doi.org/10.1038/sdata.2016.76 Text en Copyright © 2016, The Author(s) 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 to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0 Metadata associated with this Data Descriptor is available at http://www.nature.com/sdata/ and is released under the CC0 waiver to maximize reuse. |
| spellingShingle | Data Descriptor Zhang, Jianwei Chen, Ling-Ling Sun, Shuai Kudrna, Dave Copetti, Dario Li, Weiming Mu, Ting Jiao, Wen-Biao Xing, Feng Lee, Seunghee Talag, Jayson Song, Jia-Ming Du, Bogu Xie, Weibo Luo, Meizhong Maldonado, Carlos Ernesto Goicoechea, Jose Luis Xiong, Lizhong Wu, Changyin Xing, Yongzhong Zhou, Dao-xiu Yu, Sibin Zhao, Yu Wang, Gongwei Yu, Yeisoo Luo, Yijie Hurtado, Beatriz Elena Padilla Danowitz, Ann Wing, Rod A. Zhang, Qifa Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data |
| title | Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data |
| title_full | Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data |
| title_fullStr | Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data |
| title_full_unstemmed | Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data |
| title_short | Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data |
| title_sort | building two indica rice reference genomes with pacbio long-read and illumina paired-end sequencing data |
| topic | Data Descriptor |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020871/ https://www.ncbi.nlm.nih.gov/pubmed/27622467 http://dx.doi.org/10.1038/sdata.2016.76 |
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