Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Gabriel Keeble-Gagnère [verfasserIn] Philippe Rigault [verfasserIn] Josquin Tibbits [verfasserIn] Raj Pasam [verfasserIn] Matthew Hayden [verfasserIn] Kerrie Forrest [verfasserIn] Zeev Frenkel [verfasserIn] Abraham Korol [verfasserIn] B. Emma Huang [verfasserIn] Colin Cavanagh [verfasserIn] Jen Taylor [verfasserIn] Michael Abrouk [verfasserIn] Andrew Sharpe [verfasserIn] David Konkin [verfasserIn] Pierre Sourdille [verfasserIn] Benoît Darrier [verfasserIn] Frédéric Choulet [verfasserIn] Aurélien Bernard [verfasserIn] Simone Rochfort [verfasserIn] Adam Dimech [verfasserIn] Nathan Watson-Haigh [verfasserIn] Ute Baumann [verfasserIn] Paul Eckermann [verfasserIn] Delphine Fleury [verfasserIn] Angela Juhasz [verfasserIn] Sébastien Boisvert [verfasserIn] Marc-Alexandre Nolin [verfasserIn] Jaroslav Doležel [verfasserIn] Hana Šimková [verfasserIn] Helena Toegelová [verfasserIn] Jan Šafář [verfasserIn] Ming-Cheng Luo [verfasserIn] Francisco Câmara [verfasserIn] Matthias Pfeifer [verfasserIn] Don Isdale [verfasserIn] Johan Nyström-Persson [verfasserIn] IWGSC [verfasserIn] Dal-Hoe Koo [verfasserIn] Matthew Tinning [verfasserIn] Dangqun Cui [verfasserIn] Zhengang Ru [verfasserIn] Rudi Appels [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2018 |
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| Übergeordnetes Werk: |
In: Genome Biology - BMC, 2014, 19(2018), 1, Seite 18 |
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| Übergeordnetes Werk: |
volume:19 ; year:2018 ; number:1 ; pages:18 |
| Links: |
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| DOI / URN: |
10.1186/s13059-018-1475-4 |
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| Katalog-ID: |
DOAJ033030898 |
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| 520 | |a Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. | ||
| 650 | 4 | |a Wheat sequence finishing | |
| 650 | 4 | |a Megabase-scale integration | |
| 650 | 4 | |a Optical/physical maps Grain quality | |
| 650 | 4 | |a Yield | |
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10.1186/s13059-018-1475-4 doi (DE-627)DOAJ033030898 (DE-599)DOAJ0c850329a2e2415bae69d4ee3f8e54df DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Gabriel Keeble-Gagnère verfasserin aut Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. Wheat sequence finishing Megabase-scale integration Optical/physical maps Grain quality Yield Biology (General) Genetics Philippe Rigault verfasserin aut Josquin Tibbits verfasserin aut Raj Pasam verfasserin aut Matthew Hayden verfasserin aut Kerrie Forrest verfasserin aut Zeev Frenkel verfasserin aut Abraham Korol verfasserin aut B. Emma Huang verfasserin aut Colin Cavanagh verfasserin aut Jen Taylor verfasserin aut Michael Abrouk verfasserin aut Andrew Sharpe verfasserin aut David Konkin verfasserin aut Pierre Sourdille verfasserin aut Benoît Darrier verfasserin aut Frédéric Choulet verfasserin aut Aurélien Bernard verfasserin aut Simone Rochfort verfasserin aut Adam Dimech verfasserin aut Nathan Watson-Haigh verfasserin aut Ute Baumann verfasserin aut Paul Eckermann verfasserin aut Delphine Fleury verfasserin aut Angela Juhasz verfasserin aut Sébastien Boisvert verfasserin aut Marc-Alexandre Nolin verfasserin aut Jaroslav Doležel verfasserin aut Hana Šimková verfasserin aut Helena Toegelová verfasserin aut Jan Šafář verfasserin aut Ming-Cheng Luo verfasserin aut Francisco Câmara verfasserin aut Matthias Pfeifer verfasserin aut Don Isdale verfasserin aut Johan Nyström-Persson verfasserin aut IWGSC verfasserin aut Dal-Hoe Koo verfasserin aut Matthew Tinning verfasserin aut Dangqun Cui verfasserin aut Zhengang Ru verfasserin aut Rudi Appels verfasserin aut In Genome Biology BMC, 2014 19(2018), 1, Seite 18 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:19 year:2018 number:1 pages:18 https://doi.org/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/article/0c850329a2e2415bae69d4ee3f8e54df kostenfrei http://link.springer.com/article/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 19 2018 1 18 |
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10.1186/s13059-018-1475-4 doi (DE-627)DOAJ033030898 (DE-599)DOAJ0c850329a2e2415bae69d4ee3f8e54df DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Gabriel Keeble-Gagnère verfasserin aut Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. Wheat sequence finishing Megabase-scale integration Optical/physical maps Grain quality Yield Biology (General) Genetics Philippe Rigault verfasserin aut Josquin Tibbits verfasserin aut Raj Pasam verfasserin aut Matthew Hayden verfasserin aut Kerrie Forrest verfasserin aut Zeev Frenkel verfasserin aut Abraham Korol verfasserin aut B. Emma Huang verfasserin aut Colin Cavanagh verfasserin aut Jen Taylor verfasserin aut Michael Abrouk verfasserin aut Andrew Sharpe verfasserin aut David Konkin verfasserin aut Pierre Sourdille verfasserin aut Benoît Darrier verfasserin aut Frédéric Choulet verfasserin aut Aurélien Bernard verfasserin aut Simone Rochfort verfasserin aut Adam Dimech verfasserin aut Nathan Watson-Haigh verfasserin aut Ute Baumann verfasserin aut Paul Eckermann verfasserin aut Delphine Fleury verfasserin aut Angela Juhasz verfasserin aut Sébastien Boisvert verfasserin aut Marc-Alexandre Nolin verfasserin aut Jaroslav Doležel verfasserin aut Hana Šimková verfasserin aut Helena Toegelová verfasserin aut Jan Šafář verfasserin aut Ming-Cheng Luo verfasserin aut Francisco Câmara verfasserin aut Matthias Pfeifer verfasserin aut Don Isdale verfasserin aut Johan Nyström-Persson verfasserin aut IWGSC verfasserin aut Dal-Hoe Koo verfasserin aut Matthew Tinning verfasserin aut Dangqun Cui verfasserin aut Zhengang Ru verfasserin aut Rudi Appels verfasserin aut In Genome Biology BMC, 2014 19(2018), 1, Seite 18 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:19 year:2018 number:1 pages:18 https://doi.org/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/article/0c850329a2e2415bae69d4ee3f8e54df kostenfrei http://link.springer.com/article/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 19 2018 1 18 |
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10.1186/s13059-018-1475-4 doi (DE-627)DOAJ033030898 (DE-599)DOAJ0c850329a2e2415bae69d4ee3f8e54df DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Gabriel Keeble-Gagnère verfasserin aut Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. Wheat sequence finishing Megabase-scale integration Optical/physical maps Grain quality Yield Biology (General) Genetics Philippe Rigault verfasserin aut Josquin Tibbits verfasserin aut Raj Pasam verfasserin aut Matthew Hayden verfasserin aut Kerrie Forrest verfasserin aut Zeev Frenkel verfasserin aut Abraham Korol verfasserin aut B. Emma Huang verfasserin aut Colin Cavanagh verfasserin aut Jen Taylor verfasserin aut Michael Abrouk verfasserin aut Andrew Sharpe verfasserin aut David Konkin verfasserin aut Pierre Sourdille verfasserin aut Benoît Darrier verfasserin aut Frédéric Choulet verfasserin aut Aurélien Bernard verfasserin aut Simone Rochfort verfasserin aut Adam Dimech verfasserin aut Nathan Watson-Haigh verfasserin aut Ute Baumann verfasserin aut Paul Eckermann verfasserin aut Delphine Fleury verfasserin aut Angela Juhasz verfasserin aut Sébastien Boisvert verfasserin aut Marc-Alexandre Nolin verfasserin aut Jaroslav Doležel verfasserin aut Hana Šimková verfasserin aut Helena Toegelová verfasserin aut Jan Šafář verfasserin aut Ming-Cheng Luo verfasserin aut Francisco Câmara verfasserin aut Matthias Pfeifer verfasserin aut Don Isdale verfasserin aut Johan Nyström-Persson verfasserin aut IWGSC verfasserin aut Dal-Hoe Koo verfasserin aut Matthew Tinning verfasserin aut Dangqun Cui verfasserin aut Zhengang Ru verfasserin aut Rudi Appels verfasserin aut In Genome Biology BMC, 2014 19(2018), 1, Seite 18 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:19 year:2018 number:1 pages:18 https://doi.org/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/article/0c850329a2e2415bae69d4ee3f8e54df kostenfrei http://link.springer.com/article/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 19 2018 1 18 |
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10.1186/s13059-018-1475-4 doi (DE-627)DOAJ033030898 (DE-599)DOAJ0c850329a2e2415bae69d4ee3f8e54df DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Gabriel Keeble-Gagnère verfasserin aut Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. Wheat sequence finishing Megabase-scale integration Optical/physical maps Grain quality Yield Biology (General) Genetics Philippe Rigault verfasserin aut Josquin Tibbits verfasserin aut Raj Pasam verfasserin aut Matthew Hayden verfasserin aut Kerrie Forrest verfasserin aut Zeev Frenkel verfasserin aut Abraham Korol verfasserin aut B. Emma Huang verfasserin aut Colin Cavanagh verfasserin aut Jen Taylor verfasserin aut Michael Abrouk verfasserin aut Andrew Sharpe verfasserin aut David Konkin verfasserin aut Pierre Sourdille verfasserin aut Benoît Darrier verfasserin aut Frédéric Choulet verfasserin aut Aurélien Bernard verfasserin aut Simone Rochfort verfasserin aut Adam Dimech verfasserin aut Nathan Watson-Haigh verfasserin aut Ute Baumann verfasserin aut Paul Eckermann verfasserin aut Delphine Fleury verfasserin aut Angela Juhasz verfasserin aut Sébastien Boisvert verfasserin aut Marc-Alexandre Nolin verfasserin aut Jaroslav Doležel verfasserin aut Hana Šimková verfasserin aut Helena Toegelová verfasserin aut Jan Šafář verfasserin aut Ming-Cheng Luo verfasserin aut Francisco Câmara verfasserin aut Matthias Pfeifer verfasserin aut Don Isdale verfasserin aut Johan Nyström-Persson verfasserin aut IWGSC verfasserin aut Dal-Hoe Koo verfasserin aut Matthew Tinning verfasserin aut Dangqun Cui verfasserin aut Zhengang Ru verfasserin aut Rudi Appels verfasserin aut In Genome Biology BMC, 2014 19(2018), 1, Seite 18 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:19 year:2018 number:1 pages:18 https://doi.org/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/article/0c850329a2e2415bae69d4ee3f8e54df kostenfrei http://link.springer.com/article/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 19 2018 1 18 |
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10.1186/s13059-018-1475-4 doi (DE-627)DOAJ033030898 (DE-599)DOAJ0c850329a2e2415bae69d4ee3f8e54df DE-627 ger DE-627 rakwb eng QH301-705.5 QH426-470 Gabriel Keeble-Gagnère verfasserin aut Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome 2018 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. Wheat sequence finishing Megabase-scale integration Optical/physical maps Grain quality Yield Biology (General) Genetics Philippe Rigault verfasserin aut Josquin Tibbits verfasserin aut Raj Pasam verfasserin aut Matthew Hayden verfasserin aut Kerrie Forrest verfasserin aut Zeev Frenkel verfasserin aut Abraham Korol verfasserin aut B. Emma Huang verfasserin aut Colin Cavanagh verfasserin aut Jen Taylor verfasserin aut Michael Abrouk verfasserin aut Andrew Sharpe verfasserin aut David Konkin verfasserin aut Pierre Sourdille verfasserin aut Benoît Darrier verfasserin aut Frédéric Choulet verfasserin aut Aurélien Bernard verfasserin aut Simone Rochfort verfasserin aut Adam Dimech verfasserin aut Nathan Watson-Haigh verfasserin aut Ute Baumann verfasserin aut Paul Eckermann verfasserin aut Delphine Fleury verfasserin aut Angela Juhasz verfasserin aut Sébastien Boisvert verfasserin aut Marc-Alexandre Nolin verfasserin aut Jaroslav Doležel verfasserin aut Hana Šimková verfasserin aut Helena Toegelová verfasserin aut Jan Šafář verfasserin aut Ming-Cheng Luo verfasserin aut Francisco Câmara verfasserin aut Matthias Pfeifer verfasserin aut Don Isdale verfasserin aut Johan Nyström-Persson verfasserin aut IWGSC verfasserin aut Dal-Hoe Koo verfasserin aut Matthew Tinning verfasserin aut Dangqun Cui verfasserin aut Zhengang Ru verfasserin aut Rudi Appels verfasserin aut In Genome Biology BMC, 2014 19(2018), 1, Seite 18 (DE-627)326173617 (DE-600)2040529-7 1474760X nnns volume:19 year:2018 number:1 pages:18 https://doi.org/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/article/0c850329a2e2415bae69d4ee3f8e54df kostenfrei http://link.springer.com/article/10.1186/s13059-018-1475-4 kostenfrei https://doaj.org/toc/1474-760X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 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_4338 GBV_ILN_4367 GBV_ILN_4700 AR 19 2018 1 18 |
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Gabriel Keeble-Gagnère @@aut@@ Philippe Rigault @@aut@@ Josquin Tibbits @@aut@@ Raj Pasam @@aut@@ Matthew Hayden @@aut@@ Kerrie Forrest @@aut@@ Zeev Frenkel @@aut@@ Abraham Korol @@aut@@ B. Emma Huang @@aut@@ Colin Cavanagh @@aut@@ Jen Taylor @@aut@@ Michael Abrouk @@aut@@ Andrew Sharpe @@aut@@ David Konkin @@aut@@ Pierre Sourdille @@aut@@ Benoît Darrier @@aut@@ Frédéric Choulet @@aut@@ Aurélien Bernard @@aut@@ Simone Rochfort @@aut@@ Adam Dimech @@aut@@ Nathan Watson-Haigh @@aut@@ Ute Baumann @@aut@@ Paul Eckermann @@aut@@ Delphine Fleury @@aut@@ Angela Juhasz @@aut@@ Sébastien Boisvert @@aut@@ Marc-Alexandre Nolin @@aut@@ Jaroslav Doležel @@aut@@ Hana Šimková @@aut@@ Helena Toegelová @@aut@@ Jan Šafář @@aut@@ Ming-Cheng Luo @@aut@@ Francisco Câmara @@aut@@ Matthias Pfeifer @@aut@@ Don Isdale @@aut@@ Johan Nyström-Persson @@aut@@ IWGSC @@aut@@ Dal-Hoe Koo @@aut@@ Matthew Tinning @@aut@@ Dangqun Cui @@aut@@ Zhengang Ru @@aut@@ Rudi Appels @@aut@@ |
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Gabriel Keeble-Gagnère Philippe Rigault Josquin Tibbits Raj Pasam Matthew Hayden Kerrie Forrest Zeev Frenkel Abraham Korol B. Emma Huang Colin Cavanagh Jen Taylor Michael Abrouk Andrew Sharpe David Konkin Pierre Sourdille Benoît Darrier Frédéric Choulet Aurélien Bernard Simone Rochfort Adam Dimech Nathan Watson-Haigh Ute Baumann Paul Eckermann Delphine Fleury Angela Juhasz Sébastien Boisvert Marc-Alexandre Nolin Jaroslav Doležel Hana Šimková Helena Toegelová Jan Šafář Ming-Cheng Luo Francisco Câmara Matthias Pfeifer Don Isdale Johan Nyström-Persson IWGSC Dal-Hoe Koo Matthew Tinning Dangqun Cui Zhengang Ru Rudi Appels |
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optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome |
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Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome |
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Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. |
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Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. |
| abstract_unstemmed |
Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere. |
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Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome |
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Philippe Rigault Josquin Tibbits Raj Pasam Matthew Hayden Kerrie Forrest Zeev Frenkel Abraham Korol B. Emma Huang Colin Cavanagh Jen Taylor Michael Abrouk Andrew Sharpe David Konkin Pierre Sourdille Benoît Darrier Frédéric Choulet Aurélien Bernard Simone Rochfort Adam Dimech Nathan Watson-Haigh Ute Baumann Paul Eckermann Delphine Fleury Angela Juhasz Sébastien Boisvert Marc-Alexandre Nolin Jaroslav Doležel Hana Šimková Helena Toegelová Jan Šafář Ming-Cheng Luo Francisco Câmara Matthias Pfeifer Don Isdale Johan Nyström-Persson IWGSC Dal-Hoe Koo Matthew Tinning Dangqun Cui Zhengang Ru Rudi Appels |
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Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. 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