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: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2016
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| Acceso en línea: | https://hdl.handle.net/10568/165213 |
| _version_ | 1855530891380523008 |
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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_browse | Chen, Ling-Ling Copetti, Dario Danowitz, Ann Du, Bogu Goicoechea, Jose Luis Hurtado, Beatriz Elena Padilla Jiao, Wen-Biao Kudrna, Dave Lee, Seunghee Li, Weiming Luo, Meizhong Luo, Yijie Maldonado, Carlos Ernesto Mu, Ting Song, Jia-Ming Sun, Shuai Talag, Jayson Wang, Gongwei Wing, Rod A. Wu, Changyin Xie, Weibo Xing, Feng Xing, Yongzhong Xiong, Lizhong Yu, Sibin Yu, Yeisoo Zhang, Jianwei Zhang, Qifa Zhao, Yu Zhou, Dao-Xiu |
| 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 | Repository of Agricultural Research Outputs (CGSpace) |
| 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 | Journal Article |
| id | CGSpace165213 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1652132025-05-14T10:24:17Z 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 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. 2016-09-13 2024-12-19T12:54:49Z 2024-12-19T12:54:49Z Journal Article https://hdl.handle.net/10568/165213 en Open Access Springer 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. and Zhang, Qifa. 2016. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci Data, Volume 3, no. 1 |
| spellingShingle | 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 |
| url | https://hdl.handle.net/10568/165213 |
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