Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipp...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Kawahara, Yoshihiro [verfasserIn] |
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E-Artikel |
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| Sprache: |
Englisch |
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2013 |
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© Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
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| Übergeordnetes Werk: |
Enthalten in: Rice - New York, NY : Springer New York, 2008, 6(2013), 1 vom: 06. Feb. |
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| Übergeordnetes Werk: |
volume:6 ; year:2013 ; number:1 ; day:06 ; month:02 |
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| DOI / URN: |
10.1186/1939-8433-6-4 |
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SPR02477846X |
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| 100 | 1 | |a Kawahara, Yoshihiro |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data |
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| 520 | |a Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. | ||
| 650 | 4 | |a Nipponbare |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Unified rice reference genome |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Pseudomolecules |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Minimum tiling path |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Optical mapping |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Genome re-sequencing |7 (dpeaa)DE-He213 | |
| 650 | 4 | |a Next-generation sequencing |7 (dpeaa)DE-He213 | |
| 700 | 1 | |a de la Bastide, Melissa |4 aut | |
| 700 | 1 | |a Hamilton, John P |4 aut | |
| 700 | 1 | |a Kanamori, Hiroyuki |4 aut | |
| 700 | 1 | |a McCombie, W Richard |4 aut | |
| 700 | 1 | |a Ouyang, Shu |4 aut | |
| 700 | 1 | |a Schwartz, David C |4 aut | |
| 700 | 1 | |a Tanaka, Tsuyoshi |4 aut | |
| 700 | 1 | |a Wu, Jianzhong |4 aut | |
| 700 | 1 | |a Zhou, Shiguo |4 aut | |
| 700 | 1 | |a Childs, Kevin L |4 aut | |
| 700 | 1 | |a Davidson, Rebecca M |4 aut | |
| 700 | 1 | |a Lin, Haining |4 aut | |
| 700 | 1 | |a Quesada-Ocampo, Lina |4 aut | |
| 700 | 1 | |a Vaillancourt, Brieanne |4 aut | |
| 700 | 1 | |a Sakai, Hiroaki |4 aut | |
| 700 | 1 | |a Lee, Sung Shin |4 aut | |
| 700 | 1 | |a Kim, Jungsok |4 aut | |
| 700 | 1 | |a Numa, Hisataka |4 aut | |
| 700 | 1 | |a Itoh, Takeshi |4 aut | |
| 700 | 1 | |a Buell, C Robin |4 aut | |
| 700 | 1 | |a Matsumoto, Takashi |4 aut | |
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10.1186/1939-8433-6-4 doi (DE-627)SPR02477846X (SPR)1939-8433-6-4-e DE-627 ger DE-627 rakwb eng Kawahara, Yoshihiro verfasserin aut Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. Nipponbare (dpeaa)DE-He213 Unified rice reference genome (dpeaa)DE-He213 Pseudomolecules (dpeaa)DE-He213 Minimum tiling path (dpeaa)DE-He213 Optical mapping (dpeaa)DE-He213 Genome re-sequencing (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 de la Bastide, Melissa aut Hamilton, John P aut Kanamori, Hiroyuki aut McCombie, W Richard aut Ouyang, Shu aut Schwartz, David C aut Tanaka, Tsuyoshi aut Wu, Jianzhong aut Zhou, Shiguo aut Childs, Kevin L aut Davidson, Rebecca M aut Lin, Haining aut Quesada-Ocampo, Lina aut Vaillancourt, Brieanne aut Sakai, Hiroaki aut Lee, Sung Shin aut Kim, Jungsok aut Numa, Hisataka aut Itoh, Takeshi aut Buell, C Robin aut Matsumoto, Takashi aut Enthalten in Rice New York, NY : Springer New York, 2008 6(2013), 1 vom: 06. Feb. (DE-627)582026636 (DE-600)2457103-9 1939-8433 nnns volume:6 year:2013 number:1 day:06 month:02 https://dx.doi.org/10.1186/1939-8433-6-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4367 GBV_ILN_4700 AR 6 2013 1 06 02 |
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10.1186/1939-8433-6-4 doi (DE-627)SPR02477846X (SPR)1939-8433-6-4-e DE-627 ger DE-627 rakwb eng Kawahara, Yoshihiro verfasserin aut Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. Nipponbare (dpeaa)DE-He213 Unified rice reference genome (dpeaa)DE-He213 Pseudomolecules (dpeaa)DE-He213 Minimum tiling path (dpeaa)DE-He213 Optical mapping (dpeaa)DE-He213 Genome re-sequencing (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 de la Bastide, Melissa aut Hamilton, John P aut Kanamori, Hiroyuki aut McCombie, W Richard aut Ouyang, Shu aut Schwartz, David C aut Tanaka, Tsuyoshi aut Wu, Jianzhong aut Zhou, Shiguo aut Childs, Kevin L aut Davidson, Rebecca M aut Lin, Haining aut Quesada-Ocampo, Lina aut Vaillancourt, Brieanne aut Sakai, Hiroaki aut Lee, Sung Shin aut Kim, Jungsok aut Numa, Hisataka aut Itoh, Takeshi aut Buell, C Robin aut Matsumoto, Takashi aut Enthalten in Rice New York, NY : Springer New York, 2008 6(2013), 1 vom: 06. Feb. (DE-627)582026636 (DE-600)2457103-9 1939-8433 nnns volume:6 year:2013 number:1 day:06 month:02 https://dx.doi.org/10.1186/1939-8433-6-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4367 GBV_ILN_4700 AR 6 2013 1 06 02 |
| allfields_unstemmed |
10.1186/1939-8433-6-4 doi (DE-627)SPR02477846X (SPR)1939-8433-6-4-e DE-627 ger DE-627 rakwb eng Kawahara, Yoshihiro verfasserin aut Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. Nipponbare (dpeaa)DE-He213 Unified rice reference genome (dpeaa)DE-He213 Pseudomolecules (dpeaa)DE-He213 Minimum tiling path (dpeaa)DE-He213 Optical mapping (dpeaa)DE-He213 Genome re-sequencing (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 de la Bastide, Melissa aut Hamilton, John P aut Kanamori, Hiroyuki aut McCombie, W Richard aut Ouyang, Shu aut Schwartz, David C aut Tanaka, Tsuyoshi aut Wu, Jianzhong aut Zhou, Shiguo aut Childs, Kevin L aut Davidson, Rebecca M aut Lin, Haining aut Quesada-Ocampo, Lina aut Vaillancourt, Brieanne aut Sakai, Hiroaki aut Lee, Sung Shin aut Kim, Jungsok aut Numa, Hisataka aut Itoh, Takeshi aut Buell, C Robin aut Matsumoto, Takashi aut Enthalten in Rice New York, NY : Springer New York, 2008 6(2013), 1 vom: 06. Feb. (DE-627)582026636 (DE-600)2457103-9 1939-8433 nnns volume:6 year:2013 number:1 day:06 month:02 https://dx.doi.org/10.1186/1939-8433-6-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4367 GBV_ILN_4700 AR 6 2013 1 06 02 |
| allfieldsGer |
10.1186/1939-8433-6-4 doi (DE-627)SPR02477846X (SPR)1939-8433-6-4-e DE-627 ger DE-627 rakwb eng Kawahara, Yoshihiro verfasserin aut Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. Nipponbare (dpeaa)DE-He213 Unified rice reference genome (dpeaa)DE-He213 Pseudomolecules (dpeaa)DE-He213 Minimum tiling path (dpeaa)DE-He213 Optical mapping (dpeaa)DE-He213 Genome re-sequencing (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 de la Bastide, Melissa aut Hamilton, John P aut Kanamori, Hiroyuki aut McCombie, W Richard aut Ouyang, Shu aut Schwartz, David C aut Tanaka, Tsuyoshi aut Wu, Jianzhong aut Zhou, Shiguo aut Childs, Kevin L aut Davidson, Rebecca M aut Lin, Haining aut Quesada-Ocampo, Lina aut Vaillancourt, Brieanne aut Sakai, Hiroaki aut Lee, Sung Shin aut Kim, Jungsok aut Numa, Hisataka aut Itoh, Takeshi aut Buell, C Robin aut Matsumoto, Takashi aut Enthalten in Rice New York, NY : Springer New York, 2008 6(2013), 1 vom: 06. Feb. (DE-627)582026636 (DE-600)2457103-9 1939-8433 nnns volume:6 year:2013 number:1 day:06 month:02 https://dx.doi.org/10.1186/1939-8433-6-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4367 GBV_ILN_4700 AR 6 2013 1 06 02 |
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10.1186/1939-8433-6-4 doi (DE-627)SPR02477846X (SPR)1939-8433-6-4-e DE-627 ger DE-627 rakwb eng Kawahara, Yoshihiro verfasserin aut Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. Nipponbare (dpeaa)DE-He213 Unified rice reference genome (dpeaa)DE-He213 Pseudomolecules (dpeaa)DE-He213 Minimum tiling path (dpeaa)DE-He213 Optical mapping (dpeaa)DE-He213 Genome re-sequencing (dpeaa)DE-He213 Next-generation sequencing (dpeaa)DE-He213 de la Bastide, Melissa aut Hamilton, John P aut Kanamori, Hiroyuki aut McCombie, W Richard aut Ouyang, Shu aut Schwartz, David C aut Tanaka, Tsuyoshi aut Wu, Jianzhong aut Zhou, Shiguo aut Childs, Kevin L aut Davidson, Rebecca M aut Lin, Haining aut Quesada-Ocampo, Lina aut Vaillancourt, Brieanne aut Sakai, Hiroaki aut Lee, Sung Shin aut Kim, Jungsok aut Numa, Hisataka aut Itoh, Takeshi aut Buell, C Robin aut Matsumoto, Takashi aut Enthalten in Rice New York, NY : Springer New York, 2008 6(2013), 1 vom: 06. Feb. (DE-627)582026636 (DE-600)2457103-9 1939-8433 nnns volume:6 year:2013 number:1 day:06 month:02 https://dx.doi.org/10.1186/1939-8433-6-4 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4367 GBV_ILN_4700 AR 6 2013 1 06 02 |
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Kawahara, Yoshihiro de la Bastide, Melissa Hamilton, John P Kanamori, Hiroyuki McCombie, W Richard Ouyang, Shu Schwartz, David C Tanaka, Tsuyoshi Wu, Jianzhong Zhou, Shiguo Childs, Kevin L Davidson, Rebecca M Lin, Haining Quesada-Ocampo, Lina Vaillancourt, Brieanne Sakai, Hiroaki Lee, Sung Shin Kim, Jungsok Numa, Hisataka Itoh, Takeshi Buell, C Robin Matsumoto, Takashi |
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Kawahara, Yoshihiro |
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10.1186/1939-8433-6-4 |
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improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data |
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Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data |
| abstract |
Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. © Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
| abstractGer |
Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. © Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
| abstract_unstemmed |
Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies. © Kawahara et al.; licensee Springer. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( |
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Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data |
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de la Bastide, Melissa Hamilton, John P Kanamori, Hiroyuki McCombie, W Richard Ouyang, Shu Schwartz, David C Tanaka, Tsuyoshi Wu, Jianzhong Zhou, Shiguo Childs, Kevin L Davidson, Rebecca M Lin, Haining Quesada-Ocampo, Lina Vaillancourt, Brieanne Sakai, Hiroaki Lee, Sung Shin Kim, Jungsok Numa, Hisataka Itoh, Takeshi Buell, C Robin Matsumoto, Takashi |
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de la Bastide, Melissa Hamilton, John P Kanamori, Hiroyuki McCombie, W Richard Ouyang, Shu Schwartz, David C Tanaka, Tsuyoshi Wu, Jianzhong Zhou, Shiguo Childs, Kevin L Davidson, Rebecca M Lin, Haining Quesada-Ocampo, Lina Vaillancourt, Brieanne Sakai, Hiroaki Lee, Sung Shin Kim, Jungsok Numa, Hisataka Itoh, Takeshi Buell, C Robin Matsumoto, Takashi |
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